Starting phenix.real_space_refine on Fri Feb 16 17:58:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zko_11256/02_2024/6zko_11256_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 42 5.49 5 S 468 5.16 5 C 43947 2.51 5 N 11226 2.21 5 O 12164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "9 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "d ARG 325": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 149": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67877 Number of models: 1 Model: "" Number of chains: 69 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3457 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2748 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 21, 'TRANS': 318} Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 276 Unusual residues: {'3PE': 3, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "M" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 172 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "V" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 216 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 26 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 75 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 104.437 52.718 239.902 1.00 15.45 S ATOM 4116 SG CYS 2 103 102.381 47.275 258.839 1.00 95.26 S ATOM 4150 SG CYS 2 108 100.249 44.766 260.828 1.00 65.66 S ATOM 4430 SG CYS 2 144 103.876 43.967 255.154 1.00 80.48 S ATOM 4453 SG CYS 2 148 102.051 40.855 256.639 1.00 86.42 S ATOM 5793 SG CYS 3 114 106.127 71.509 225.754 1.00100.59 S ATOM 5732 SG CYS 3 105 100.704 74.542 227.980 1.00109.70 S ATOM 5753 SG CYS 3 108 106.771 76.535 229.703 1.00133.79 S ATOM 6125 SG CYS 3 156 113.704 64.077 230.501 1.00 79.98 S ATOM 6102 SG CYS 3 153 111.191 66.900 235.776 1.00 59.94 S ATOM 6149 SG CYS 3 159 117.455 68.143 234.260 1.00 90.76 S ATOM 6479 SG CYS 3 203 113.237 70.451 230.477 1.00 67.19 S ATOM 5238 SG CYS 3 41 113.067 57.296 227.878 1.00103.73 S ATOM 5324 SG CYS 3 52 109.343 58.435 227.481 1.00 44.99 S ATOM 5349 SG CYS 3 55 109.644 53.602 223.605 1.00 86.60 S ATOM 5450 SG CYS 3 69 113.392 53.792 224.999 1.00 37.31 S ATOM 15674 SG CYS 6 54 83.551 94.632 203.075 1.00 63.53 S ATOM 17600 SG CYS 9 116 91.308 95.515 215.429 1.00 43.55 S ATOM 17647 SG CYS 9 122 91.872 91.058 220.028 1.00 8.72 S ATOM 17374 SG CYS 9 87 95.886 90.996 214.763 1.00 58.30 S ATOM 17676 SG CYS 9 126 94.148 87.638 227.231 1.00130.20 S ATOM 17347 SG CYS 9 83 97.767 89.517 222.232 1.00103.00 S ATOM 17305 SG CYS 9 77 99.704 91.295 228.015 1.00 43.69 S ATOM 17324 SG CYS 9 80 99.375 84.702 226.548 1.00148.07 S ATOM 41371 SG CYS b 59 96.103 82.747 242.815 1.00 84.34 S ATOM 41549 SG CYS b 84 98.915 82.984 240.414 1.00 85.62 S ATOM 41571 SG CYS b 87 97.327 85.689 241.183 1.00 41.91 S Time building chain proxies: 30.02, per 1000 atoms: 0.44 Number of scatterers: 67877 At special positions: 0 Unit cell: (175.96, 195.88, 290.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 468 16.00 P 42 15.00 O 12164 8.00 N 11226 7.00 C 43947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.03 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.02 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.38 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 500 " pdb="FE1 SF4 1 500 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 500 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 500 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 500 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " Number of angles added : 3 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 326 helices and 29 sheets defined 49.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.41 Creating SS restraints... Processing helix chain '1' and resid 33 through 36 No H-bonds generated for 'chain '1' and resid 33 through 36' Processing helix chain '1' and resid 46 through 63 removed outlier: 3.928A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.861A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 82 removed outlier: 3.565A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 107 through 113 Processing helix chain '1' and resid 115 through 129 removed outlier: 3.518A pdb=" N MET 1 129 " --> pdb=" O GLY 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 143 through 159 removed outlier: 3.667A pdb=" N ALA 1 159 " --> pdb=" O GLU 1 155 " (cutoff:3.500A) Processing helix chain '1' and resid 184 through 187 Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 243 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 319 through 324 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.545A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 4.253A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.804A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.112A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 4.068A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 4.032A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 32 Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 159 through 165 Processing helix chain '3' and resid 198 through 202 removed outlier: 3.903A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 296 through 309 removed outlier: 3.981A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER 3 309 " --> pdb=" O GLY 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 336 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 373 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 3.924A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 3 433 " --> pdb=" O GLN 3 430 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 4.121A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 480 removed outlier: 3.574A pdb=" N THR 3 479 " --> pdb=" O GLN 3 475 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER 3 480 " --> pdb=" O LYS 3 476 " (cutoff:3.500A) Processing helix chain '3' and resid 497 through 504 removed outlier: 4.572A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 631 removed outlier: 3.718A pdb=" N VAL 3 631 " --> pdb=" O PRO 3 628 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 628 through 631' Processing helix chain '3' and resid 642 through 650 Processing helix chain '3' and resid 682 through 691 Processing helix chain '4' and resid 8 through 14 removed outlier: 4.211A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 4.517A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 104 Proline residue: 4 101 - end of helix removed outlier: 4.191A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 159 Processing helix chain '4' and resid 165 through 184 removed outlier: 4.278A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 4.023A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 238 removed outlier: 3.535A pdb=" N ARG 4 238 " --> pdb=" O ILE 4 234 " (cutoff:3.500A) Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 263 removed outlier: 4.454A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 315 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 352 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.586A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.751A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 3.934A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 4.471A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG 5 65 " --> pdb=" O THR 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 137 removed outlier: 3.913A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 43 Processing helix chain '6' and resid 54 through 62 removed outlier: 3.567A pdb=" N GLU 6 58 " --> pdb=" O CYS 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 118 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 85 No H-bonds generated for 'chain '9' and resid 82 through 85' Processing helix chain '9' and resid 122 through 125 No H-bonds generated for 'chain '9' and resid 122 through 125' Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 172 removed outlier: 5.653A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.121A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 removed outlier: 4.149A pdb=" N LEU A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.549A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 3 through 10 Processing helix chain 'H' and resid 12 through 32 removed outlier: 4.297A pdb=" N VAL H 17 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 removed outlier: 3.688A pdb=" N LEU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.061A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 142 removed outlier: 3.911A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 152 Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 164 through 167 No H-bonds generated for 'chain 'H' and resid 164 through 167' Processing helix chain 'H' and resid 179 through 192 removed outlier: 4.052A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 221 through 242 removed outlier: 4.087A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 289 removed outlier: 3.578A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.936A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU J 9 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 4.002A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU J 45 " --> pdb=" O CYS J 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 73 removed outlier: 4.086A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 removed outlier: 3.743A pdb=" N THR J 92 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS J 109 " --> pdb=" O TYR J 105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP J 110 " --> pdb=" O TYR J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 146 removed outlier: 3.679A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.914A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 51 Processing helix chain 'K' and resid 54 through 84 removed outlier: 4.053A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 5.482A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET K 80 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR K 84 " --> pdb=" O VAL K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 24 removed outlier: 3.700A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 56 removed outlier: 4.153A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 110 Proline residue: L 91 - end of helix removed outlier: 3.899A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS L 109 " --> pdb=" O MET L 105 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER L 110 " --> pdb=" O TRP L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.919A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 232 through 237 removed outlier: 4.357A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.417A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.759A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 350 removed outlier: 4.641A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 390 removed outlier: 3.663A pdb=" N TYR L 390 " --> pdb=" O THR L 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 387 through 390' Processing helix chain 'L' and resid 392 through 400 Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.699A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.855A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.506A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 532 removed outlier: 4.104A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix No H-bonds generated for 'chain 'L' and resid 526 through 532' Processing helix chain 'L' and resid 536 through 547 removed outlier: 3.652A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.172A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 25 through 41 removed outlier: 4.387A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.808A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 110 removed outlier: 3.504A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 5.106A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 168 removed outlier: 3.860A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.808A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.929A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.466A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.940A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.308A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 393 through 415 removed outlier: 3.703A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU M 411 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix removed outlier: 3.971A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.066A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 168 Processing helix chain 'N' and resid 175 through 193 removed outlier: 4.181A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.233A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.677A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 269 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 4.103A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 4.064A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.802A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 79 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 107 through 129 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.588A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 4.017A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 116 Processing helix chain 'X' and resid 8 through 21 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 57 through 74 removed outlier: 3.781A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Y' and resid 123 through 125 No H-bonds generated for 'chain 'Y' and resid 123 through 125' Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 removed outlier: 4.260A pdb=" N LYS Z 57 " --> pdb=" O ARG Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 116 removed outlier: 4.532A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 172 Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.840A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 25 No H-bonds generated for 'chain 'b' and resid 23 through 25' Processing helix chain 'b' and resid 40 through 43 No H-bonds generated for 'chain 'b' and resid 40 through 43' Processing helix chain 'c' and resid 27 through 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.377A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 118 through 122 Processing helix chain 'd' and resid 30 through 39 Processing helix chain 'd' and resid 54 through 62 removed outlier: 4.906A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 183 Processing helix chain 'd' and resid 195 through 197 No H-bonds generated for 'chain 'd' and resid 195 through 197' Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 265 through 270 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 300 through 303 removed outlier: 3.627A pdb=" N LEU d 303 " --> pdb=" O LEU d 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 300 through 303' Processing helix chain 'd' and resid 314 through 321 removed outlier: 5.647A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 39 removed outlier: 3.574A pdb=" N ILE e 36 " --> pdb=" O VAL e 32 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS e 38 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.666A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 4.351A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 4.240A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 103 Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 56 Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.873A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 30 Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.825A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 83 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 38 through 45 Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 80 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 3.912A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 211 through 217 removed outlier: 5.393A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.340A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 33 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 36 through 46 removed outlier: 3.757A pdb=" N LYS m 39 " --> pdb=" O PRO m 36 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 28 through 36 Processing helix chain 'n' and resid 45 through 48 No H-bonds generated for 'chain 'n' and resid 45 through 48' Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.615A pdb=" N ARG o 19 " --> pdb=" O ASP o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 4.119A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.725A pdb=" N ALA p 31 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 Processing helix chain 'p' and resid 83 through 92 removed outlier: 4.008A pdb=" N LEU p 91 " --> pdb=" O LEU p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 91 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 93 through 96 No H-bonds generated for 'chain 'q' and resid 93 through 96' Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 135 Processing helix chain 'q' and resid 138 through 141 No H-bonds generated for 'chain 'q' and resid 138 through 141' Processing helix chain 'r' and resid 5 through 25 Processing helix chain 'r' and resid 68 through 73 Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 48 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 95 No H-bonds generated for 'chain 't' and resid 93 through 95' Processing helix chain 't' and resid 100 through 104 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 140 removed outlier: 4.408A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 71 through 78 Processing helix chain 'w' and resid 83 through 100 removed outlier: 3.784A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA w 89 " --> pdb=" O GLN w 86 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 44 Processing helix chain 'y' and resid 16 through 30 Processing helix chain 'z' and resid 2 through 27 removed outlier: 3.882A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 4.850A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 54 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 6.475A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 266 through 271 Processing sheet with id= C, first strand: chain '2' and resid 137 through 142 removed outlier: 6.576A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 282 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.575A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.501A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 572 through 574 Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.908A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 85 through 89 removed outlier: 7.071A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 65 through 67 Processing sheet with id= R, first strand: chain '9' and resid 92 through 98 removed outlier: 5.703A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.616A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.481A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL d 91 " --> pdb=" O ILE d 130 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE d 132 " --> pdb=" O VAL d 91 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASN d 93 " --> pdb=" O ILE d 132 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N HIS d 134 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.914A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.267A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.842A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC 2701 hydrogen bonds defined for protein. 7605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.54 Time building geometry restraints manager: 26.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 28590 1.43 - 1.66: 40129 1.66 - 1.89: 761 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69560 Sorted by residual: bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.335 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.25e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.451 1.339 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.00e-02 1.00e+04 2.99e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.342 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 69555 not shown) Histogram of bond angle deviations from ideal: 63.11 - 78.36: 72 78.36 - 93.61: 8 93.61 - 108.86: 5584 108.86 - 124.10: 86336 124.10 - 139.35: 2035 Bond angle restraints: 94035 Sorted by residual: angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.65 13.68 1.14e+00 7.69e-01 1.44e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 90.96 13.37 1.14e+00 7.69e-01 1.38e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 130.54 -22.80 1.95e+00 2.62e-01 1.36e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.44 13.89 1.20e+00 6.94e-01 1.34e+02 angle pdb="FE1 FES 2 300 " pdb=" S2 FES 2 300 " pdb="FE2 FES 2 300 " ideal model delta sigma weight residual 75.66 88.43 -12.77 1.14e+00 7.69e-01 1.25e+02 ... (remaining 94030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 41514 34.87 - 69.74: 686 69.74 - 104.61: 52 104.61 - 139.48: 4 139.48 - 174.35: 3 Dihedral angle restraints: 42259 sinusoidal: 18284 harmonic: 23975 Sorted by residual: dihedral pdb=" CA ILE J 115 " pdb=" C ILE J 115 " pdb=" N VAL J 116 " pdb=" CA VAL J 116 " ideal model delta harmonic sigma weight residual -180.00 -111.90 -68.10 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -128.46 -51.54 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -138.84 -41.16 0 5.00e+00 4.00e-02 6.78e+01 ... (remaining 42256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.227: 10153 4.227 - 8.453: 5 8.453 - 12.680: 0 12.680 - 16.906: 0 16.906 - 21.133: 24 Chirality restraints: 10182 Sorted by residual: chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S3 SF4 3 802 " pdb=" S4 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.13 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10179 not shown) Planarity restraints: 11744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " -0.034 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR 6 125 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 115 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE J 115 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE J 115 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL J 116 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR z 23 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C THR z 23 " -0.054 2.00e-02 2.50e+03 pdb=" O THR z 23 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA z 24 " 0.018 2.00e-02 2.50e+03 ... (remaining 11741 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 17262 2.80 - 3.38: 72258 3.38 - 3.97: 136130 3.97 - 4.55: 189444 4.55 - 5.14: 282422 Nonbonded interactions: 697516 Sorted by model distance: nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP L 111 " pdb=" OH TYR t 96 " model vdw 2.235 2.440 nonbonded pdb=" O TYR W 28 " pdb=" OG SER w 67 " model vdw 2.253 2.440 nonbonded pdb=" O GLU d 285 " pdb=" OG1 THR d 289 " model vdw 2.258 2.440 ... (remaining 697511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'X' and resid 5 through 86) selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 6.890 Check model and map are aligned: 0.770 Set scattering table: 0.490 Process input model: 176.840 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 69560 Z= 0.396 Angle : 0.950 22.802 94035 Z= 0.512 Chirality : 1.024 21.133 10182 Planarity : 0.008 0.071 11744 Dihedral : 12.398 174.348 26779 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.07), residues: 8122 helix: -2.19 (0.06), residues: 4185 sheet: -2.18 (0.22), residues: 399 loop : -2.20 (0.09), residues: 3538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP 1 371 HIS 0.017 0.002 HIS Z 55 PHE 0.041 0.003 PHE H 224 TYR 0.056 0.002 TYR 6 125 ARG 0.012 0.001 ARG Y 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2719 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2713 time to evaluate : 7.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 145 GLU cc_start: 0.8271 (mp0) cc_final: 0.7565 (mp0) REVERT: 1 294 LEU cc_start: 0.7612 (tp) cc_final: 0.7287 (tt) REVERT: 1 347 ILE cc_start: 0.9094 (mm) cc_final: 0.8875 (mm) REVERT: 1 398 GLN cc_start: 0.8706 (mt0) cc_final: 0.8505 (mt0) REVERT: 2 34 ILE cc_start: 0.9290 (mt) cc_final: 0.9052 (mm) REVERT: 2 38 TYR cc_start: 0.8952 (m-80) cc_final: 0.8740 (m-10) REVERT: 2 43 LYS cc_start: 0.8752 (tttt) cc_final: 0.8389 (ttmm) REVERT: 2 82 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8607 (mt-10) REVERT: 2 93 LYS cc_start: 0.8913 (mttm) cc_final: 0.8339 (tttm) REVERT: 2 112 ASN cc_start: 0.7820 (t0) cc_final: 0.7374 (t0) REVERT: 3 31 GLU cc_start: 0.8854 (tt0) cc_final: 0.8265 (tm-30) REVERT: 3 100 ASN cc_start: 0.8977 (m-40) cc_final: 0.8683 (m-40) REVERT: 3 225 THR cc_start: 0.9685 (m) cc_final: 0.9369 (p) REVERT: 3 261 GLU cc_start: 0.8527 (pt0) cc_final: 0.8186 (pt0) REVERT: 3 342 THR cc_start: 0.7928 (m) cc_final: 0.7710 (t) REVERT: 3 385 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7429 (ttt180) REVERT: 3 475 GLN cc_start: 0.6324 (mm110) cc_final: 0.5915 (tp40) REVERT: 3 476 LYS cc_start: 0.8531 (tttm) cc_final: 0.8157 (mmtm) REVERT: 3 568 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7798 (mt-10) REVERT: 3 678 SER cc_start: 0.9153 (m) cc_final: 0.8369 (p) REVERT: 4 20 TYR cc_start: 0.7580 (m-80) cc_final: 0.7225 (m-10) REVERT: 4 108 TYR cc_start: 0.8240 (p90) cc_final: 0.8039 (p90) REVERT: 4 326 ASP cc_start: 0.8424 (t0) cc_final: 0.8140 (t0) REVERT: 4 331 SER cc_start: 0.9350 (m) cc_final: 0.9011 (p) REVERT: 4 343 GLU cc_start: 0.8911 (mp0) cc_final: 0.8640 (mp0) REVERT: 6 42 ARG cc_start: 0.8810 (ptt-90) cc_final: 0.8404 (ttp-110) REVERT: 6 62 MET cc_start: 0.8442 (tmm) cc_final: 0.8026 (tmm) REVERT: 6 145 TYR cc_start: 0.9402 (m-80) cc_final: 0.9094 (m-80) REVERT: 6 156 LEU cc_start: 0.9439 (tp) cc_final: 0.8330 (tp) REVERT: 9 17 VAL cc_start: 0.9411 (t) cc_final: 0.9177 (p) REVERT: A 1 MET cc_start: 0.6561 (tpp) cc_final: 0.5430 (ptp) REVERT: A 77 TRP cc_start: 0.8736 (m-10) cc_final: 0.8439 (m100) REVERT: A 87 MET cc_start: 0.8256 (tmt) cc_final: 0.7832 (tmt) REVERT: A 90 MET cc_start: 0.7924 (mmp) cc_final: 0.7641 (mmp) REVERT: H 1 MET cc_start: 0.8090 (ttp) cc_final: 0.7049 (mmt) REVERT: H 57 ILE cc_start: 0.9264 (pt) cc_final: 0.9062 (pt) REVERT: H 59 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8082 (tm-30) REVERT: H 108 MET cc_start: 0.8682 (mmt) cc_final: 0.8304 (mmt) REVERT: H 227 GLU cc_start: 0.8526 (tt0) cc_final: 0.8158 (tp30) REVERT: H 228 TYR cc_start: 0.8127 (m-10) cc_final: 0.7886 (m-10) REVERT: H 279 ARG cc_start: 0.8443 (ttp-170) cc_final: 0.8134 (ttp80) REVERT: H 284 GLN cc_start: 0.8927 (mt0) cc_final: 0.8623 (mt0) REVERT: J 2 MET cc_start: 0.8255 (tpt) cc_final: 0.8051 (mtt) REVERT: J 44 VAL cc_start: 0.9286 (p) cc_final: 0.8928 (p) REVERT: J 95 THR cc_start: 0.7804 (m) cc_final: 0.7602 (m) REVERT: J 143 ILE cc_start: 0.9204 (mt) cc_final: 0.8971 (mt) REVERT: J 169 MET cc_start: 0.8100 (mtp) cc_final: 0.7869 (tpt) REVERT: J 170 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7569 (mm-30) REVERT: K 91 GLN cc_start: 0.8390 (pm20) cc_final: 0.7910 (mp10) REVERT: L 3 LEU cc_start: 0.8196 (tp) cc_final: 0.7726 (tt) REVERT: L 49 ILE cc_start: 0.8624 (mp) cc_final: 0.8391 (mt) REVERT: L 128 MET cc_start: 0.7939 (tpt) cc_final: 0.7695 (tmm) REVERT: L 142 ILE cc_start: 0.8950 (mt) cc_final: 0.8750 (pt) REVERT: L 202 PHE cc_start: 0.7615 (m-10) cc_final: 0.7325 (m-10) REVERT: L 251 THR cc_start: 0.8136 (m) cc_final: 0.7864 (p) REVERT: L 290 MET cc_start: 0.5873 (ttp) cc_final: 0.4975 (ppp) REVERT: L 293 LEU cc_start: 0.8049 (mt) cc_final: 0.7631 (mt) REVERT: L 341 MET cc_start: 0.8688 (mtp) cc_final: 0.8425 (mtp) REVERT: L 354 GLN cc_start: 0.6106 (mt0) cc_final: 0.5897 (tt0) REVERT: L 429 PHE cc_start: 0.8258 (m-80) cc_final: 0.7913 (m-80) REVERT: L 475 MET cc_start: 0.7591 (mmm) cc_final: 0.6691 (mmt) REVERT: L 540 MET cc_start: 0.5851 (mtm) cc_final: 0.4228 (ppp) REVERT: L 596 LEU cc_start: 0.8196 (mm) cc_final: 0.7995 (mm) REVERT: M 12 MET cc_start: 0.8689 (mmt) cc_final: 0.8398 (tmm) REVERT: M 22 MET cc_start: 0.8504 (mmp) cc_final: 0.7573 (ttt) REVERT: M 92 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8134 (mtmm) REVERT: M 210 TYR cc_start: 0.8469 (t80) cc_final: 0.7982 (t80) REVERT: M 229 MET cc_start: 0.8994 (mtp) cc_final: 0.8741 (mtt) REVERT: M 259 TYR cc_start: 0.8406 (m-80) cc_final: 0.8194 (m-10) REVERT: M 271 MET cc_start: 0.7941 (mmp) cc_final: 0.7688 (mmm) REVERT: M 288 TYR cc_start: 0.8793 (m-80) cc_final: 0.8550 (m-80) REVERT: M 304 GLN cc_start: 0.8963 (pt0) cc_final: 0.8710 (pt0) REVERT: M 415 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7468 (mm-40) REVERT: M 436 LEU cc_start: 0.8530 (tp) cc_final: 0.8305 (tt) REVERT: N 1 MET cc_start: 0.7255 (ttm) cc_final: 0.7040 (ttm) REVERT: N 35 MET cc_start: 0.8952 (ttm) cc_final: 0.8703 (mtp) REVERT: N 36 ASN cc_start: 0.8254 (t0) cc_final: 0.7938 (t0) REVERT: N 58 LYS cc_start: 0.7790 (mttt) cc_final: 0.7475 (mtpt) REVERT: N 77 ASN cc_start: 0.8550 (t0) cc_final: 0.8189 (t0) REVERT: N 276 ILE cc_start: 0.8610 (mm) cc_final: 0.8381 (mp) REVERT: V 4 LEU cc_start: 0.7543 (mm) cc_final: 0.7190 (mt) REVERT: V 7 GLN cc_start: 0.7249 (pt0) cc_final: 0.6191 (tm-30) REVERT: V 38 TYR cc_start: 0.8135 (m-80) cc_final: 0.7900 (m-80) REVERT: W 19 LYS cc_start: 0.8028 (mtpm) cc_final: 0.7810 (mtmp) REVERT: W 21 PHE cc_start: 0.8867 (t80) cc_final: 0.8635 (t80) REVERT: W 109 GLU cc_start: 0.8819 (tp30) cc_final: 0.8509 (tp30) REVERT: W 119 ASP cc_start: 0.8544 (p0) cc_final: 0.8212 (p0) REVERT: X 20 LYS cc_start: 0.7301 (mtmt) cc_final: 0.7079 (mttm) REVERT: X 71 MET cc_start: 0.7334 (mmt) cc_final: 0.7069 (mmt) REVERT: Y 18 LYS cc_start: 0.7835 (mmmm) cc_final: 0.7246 (mtmm) REVERT: Y 43 MET cc_start: 0.7544 (mmm) cc_final: 0.7297 (mmt) REVERT: Y 51 ASP cc_start: 0.7698 (t0) cc_final: 0.7278 (t70) REVERT: Y 54 ARG cc_start: 0.7777 (mmp80) cc_final: 0.7237 (tpp-160) REVERT: Y 61 LEU cc_start: 0.7728 (mt) cc_final: 0.7521 (mm) REVERT: Y 107 ASP cc_start: 0.7699 (m-30) cc_final: 0.7463 (t70) REVERT: Y 112 ASP cc_start: 0.7800 (m-30) cc_final: 0.7570 (m-30) REVERT: Z 6 LYS cc_start: 0.6912 (mmtm) cc_final: 0.5986 (mtmm) REVERT: Z 8 VAL cc_start: 0.7443 (p) cc_final: 0.6621 (p) REVERT: Z 81 VAL cc_start: 0.8035 (m) cc_final: 0.7669 (t) REVERT: Z 123 ASN cc_start: 0.7749 (m-40) cc_final: 0.7304 (t0) REVERT: Z 138 TYR cc_start: 0.8643 (t80) cc_final: 0.8406 (t80) REVERT: Z 167 LYS cc_start: 0.7664 (tttm) cc_final: 0.7429 (tmtt) REVERT: c 97 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8161 (tm-30) REVERT: c 114 LYS cc_start: 0.7367 (mmtm) cc_final: 0.6500 (mmmt) REVERT: d 36 ASN cc_start: 0.8584 (t160) cc_final: 0.8200 (t0) REVERT: d 54 TYR cc_start: 0.8767 (t80) cc_final: 0.8116 (t80) REVERT: d 57 MET cc_start: 0.9264 (mmp) cc_final: 0.8518 (mpp) REVERT: d 154 LYS cc_start: 0.8573 (tttm) cc_final: 0.8203 (ttpt) REVERT: d 162 GLU cc_start: 0.6749 (mp0) cc_final: 0.6473 (tm-30) REVERT: d 180 ASN cc_start: 0.8424 (m-40) cc_final: 0.8142 (m-40) REVERT: d 281 ARG cc_start: 0.8407 (ptp90) cc_final: 0.7980 (ptt90) REVERT: e 25 ARG cc_start: 0.7633 (mmt-90) cc_final: 0.7418 (ptp-170) REVERT: e 39 ARG cc_start: 0.7576 (mtt180) cc_final: 0.6623 (mmt-90) REVERT: e 58 SER cc_start: 0.8903 (t) cc_final: 0.8221 (p) REVERT: e 59 ASP cc_start: 0.7382 (m-30) cc_final: 0.6867 (t70) REVERT: e 61 GLN cc_start: 0.7208 (mt0) cc_final: 0.6842 (mm110) REVERT: e 72 GLN cc_start: 0.8365 (mm110) cc_final: 0.8107 (mt0) REVERT: f 43 TYR cc_start: 0.8395 (t80) cc_final: 0.8027 (t80) REVERT: f 53 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8596 (tm-30) REVERT: f 54 LYS cc_start: 0.8392 (mttp) cc_final: 0.7905 (mttt) REVERT: f 57 ILE cc_start: 0.8547 (mt) cc_final: 0.8103 (mt) REVERT: h 39 LYS cc_start: 0.9063 (tptm) cc_final: 0.7828 (pttt) REVERT: i 12 GLN cc_start: 0.8727 (pt0) cc_final: 0.8354 (tp40) REVERT: i 37 THR cc_start: 0.8929 (m) cc_final: 0.8714 (p) REVERT: i 53 LYS cc_start: 0.7684 (mmtm) cc_final: 0.6906 (pttm) REVERT: i 58 ARG cc_start: 0.9144 (mmm-85) cc_final: 0.8926 (mmm-85) REVERT: i 92 CYS cc_start: 0.8771 (m) cc_final: 0.8301 (t) REVERT: i 134 ILE cc_start: 0.9369 (mm) cc_final: 0.9162 (mt) REVERT: j 18 VAL cc_start: 0.8517 (t) cc_final: 0.8298 (p) REVERT: k 13 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7195 (mmtt) REVERT: k 37 LYS cc_start: 0.6898 (pttp) cc_final: 0.6215 (mmtt) REVERT: k 97 GLN cc_start: 0.8088 (tp40) cc_final: 0.7874 (tp40) REVERT: k 143 PHE cc_start: 0.7190 (m-10) cc_final: 0.6759 (m-10) REVERT: k 198 TYR cc_start: 0.7649 (t80) cc_final: 0.7024 (t80) REVERT: k 244 ASP cc_start: 0.6948 (p0) cc_final: 0.6511 (m-30) REVERT: k 253 ASP cc_start: 0.7082 (m-30) cc_final: 0.6862 (m-30) REVERT: l 52 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7957 (tm-30) REVERT: l 53 LYS cc_start: 0.8467 (pttm) cc_final: 0.7981 (tptt) REVERT: m 9 LYS cc_start: 0.7224 (ttpp) cc_final: 0.6789 (mptt) REVERT: m 39 LYS cc_start: 0.8309 (ttpm) cc_final: 0.8077 (ptpp) REVERT: m 46 ARG cc_start: 0.8089 (ptp-110) cc_final: 0.7796 (mtm180) REVERT: m 70 GLN cc_start: 0.8309 (mt0) cc_final: 0.6732 (pp30) REVERT: o 8 ARG cc_start: 0.7681 (mpt-90) cc_final: 0.6335 (mtm110) REVERT: o 45 ASP cc_start: 0.8465 (t70) cc_final: 0.8149 (t0) REVERT: o 94 ILE cc_start: 0.8682 (mt) cc_final: 0.8462 (pt) REVERT: o 95 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8261 (mptt) REVERT: p 41 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7704 (ttm-80) REVERT: p 50 TYR cc_start: 0.7864 (t80) cc_final: 0.7506 (t80) REVERT: p 79 PHE cc_start: 0.7142 (t80) cc_final: 0.6701 (t80) REVERT: p 100 TRP cc_start: 0.8475 (m100) cc_final: 0.8055 (m100) REVERT: p 107 ASP cc_start: 0.6887 (t70) cc_final: 0.6685 (t70) REVERT: q 9 MET cc_start: 0.8490 (mmm) cc_final: 0.8284 (mmm) REVERT: q 26 ARG cc_start: 0.7540 (tmt170) cc_final: 0.6963 (mtt90) REVERT: q 27 ARG cc_start: 0.6815 (ptm160) cc_final: 0.5760 (ttm-80) REVERT: q 59 LEU cc_start: 0.7935 (mt) cc_final: 0.7442 (tt) REVERT: q 130 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7801 (mm-30) REVERT: q 142 TYR cc_start: 0.7266 (t80) cc_final: 0.7025 (t80) REVERT: r 4 THR cc_start: 0.7241 (p) cc_final: 0.6993 (t) REVERT: r 24 ASP cc_start: 0.6671 (m-30) cc_final: 0.6457 (m-30) REVERT: r 82 HIS cc_start: 0.8153 (t70) cc_final: 0.7724 (t70) REVERT: r 109 ILE cc_start: 0.7813 (mm) cc_final: 0.7580 (mp) REVERT: s 28 TYR cc_start: 0.7036 (t80) cc_final: 0.6697 (t80) REVERT: s 37 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7172 (tm-30) REVERT: s 71 ASP cc_start: 0.7340 (m-30) cc_final: 0.7109 (p0) REVERT: s 114 ARG cc_start: 0.6604 (tpp80) cc_final: 0.6166 (ttp-170) REVERT: s 117 ARG cc_start: 0.2876 (ttp-170) cc_final: 0.0723 (ttt-90) REVERT: t 18 LEU cc_start: 0.8431 (tp) cc_final: 0.8218 (tp) REVERT: t 94 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6175 (tm-30) REVERT: t 102 CYS cc_start: 0.8497 (m) cc_final: 0.8021 (t) REVERT: t 138 GLN cc_start: 0.6561 (tt0) cc_final: 0.6005 (tm-30) REVERT: t 158 LYS cc_start: 0.6531 (mttp) cc_final: 0.6131 (ptmt) REVERT: t 161 ASP cc_start: 0.4375 (m-30) cc_final: 0.3645 (t70) REVERT: t 174 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7964 (mtm110) REVERT: u 7 ILE cc_start: 0.8141 (mm) cc_final: 0.7426 (mp) REVERT: u 12 ARG cc_start: 0.7416 (mtt-85) cc_final: 0.6603 (ttt180) REVERT: u 14 PHE cc_start: 0.6360 (t80) cc_final: 0.5347 (p90) REVERT: u 20 SER cc_start: 0.7779 (t) cc_final: 0.7572 (p) REVERT: u 45 ASP cc_start: 0.8174 (m-30) cc_final: 0.7904 (m-30) REVERT: u 51 PHE cc_start: 0.7578 (m-80) cc_final: 0.7172 (m-10) REVERT: v 8 MET cc_start: 0.6510 (mmm) cc_final: 0.6126 (mmm) REVERT: v 120 GLU cc_start: 0.8439 (tp30) cc_final: 0.7801 (mt-10) REVERT: v 132 GLN cc_start: 0.6607 (mt0) cc_final: 0.6128 (mt0) REVERT: v 138 LEU cc_start: 0.8391 (mt) cc_final: 0.7536 (mt) REVERT: v 140 LEU cc_start: 0.8270 (mt) cc_final: 0.7697 (mt) REVERT: v 157 GLU cc_start: 0.4793 (mm-30) cc_final: 0.3844 (mm-30) REVERT: w 49 LYS cc_start: 0.8298 (ptpt) cc_final: 0.8066 (pttt) REVERT: w 122 GLU cc_start: 0.7164 (pm20) cc_final: 0.6132 (mm-30) REVERT: y 22 PHE cc_start: 0.7864 (t80) cc_final: 0.7644 (t80) REVERT: y 25 TYR cc_start: 0.7966 (t80) cc_final: 0.7081 (m-10) REVERT: y 28 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7088 (mtm180) REVERT: z 4 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8412 (mt-10) REVERT: z 18 ILE cc_start: 0.8796 (mt) cc_final: 0.8564 (mm) REVERT: z 63 SER cc_start: 0.8760 (m) cc_final: 0.8510 (p) outliers start: 6 outliers final: 1 residues processed: 2716 average time/residue: 0.7028 time to fit residues: 3136.9356 Evaluate side-chains 1671 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1670 time to evaluate : 5.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 30.0000 chunk 607 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 410 optimal weight: 10.0000 chunk 324 optimal weight: 30.0000 chunk 628 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 382 optimal weight: 8.9990 chunk 467 optimal weight: 30.0000 chunk 728 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN 1 148 ASN 1 150 GLN 1 250 ASN 1 257 ASN ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 313 ASN 4 34 ASN 4 135 GLN 4 252 ASN 5 71 GLN 6 106 GLN 6 121 ASN 9 65 HIS H 32 GLN H 230 ASN H 287 HIS K 52 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 ASN L 348 HIS ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 546 GLN M 82 HIS M 184 GLN M 304 GLN M 333 ASN M 390 ASN N 186 HIS N 289 ASN V 7 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 GLN Y 63 ASN Y 142 HIS Y 150 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 GLN d 87 HIS d 131 HIS d 296 HIS d 306 GLN ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 HIS f 49 GLN g 125 HIS ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 50 ASN i 12 GLN i 31 ASN i 112 ASN k 190 HIS l 26 HIS l 44 HIS ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 59 HIS o 61 GLN o 117 HIS ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN s 53 GLN s 75 ASN t 25 HIS t 50 HIS t 138 GLN v 55 GLN v 87 ASN v 137 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 36 ASN y 39 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.276 69560 Z= 0.573 Angle : 1.601 51.080 94035 Z= 1.026 Chirality : 0.306 6.539 10182 Planarity : 0.005 0.058 11744 Dihedral : 12.864 165.387 10517 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.11 % Favored : 95.88 % Rotamer: Outliers : 2.88 % Allowed : 11.32 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.09), residues: 8122 helix: -0.69 (0.07), residues: 4226 sheet: -1.64 (0.24), residues: 381 loop : -1.71 (0.10), residues: 3515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 272 HIS 0.011 0.001 HIS k 151 PHE 0.030 0.002 PHE u 14 TYR 0.034 0.002 TYR 6 125 ARG 0.008 0.001 ARG p 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1994 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1787 time to evaluate : 6.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 107 ASP cc_start: 0.8193 (m-30) cc_final: 0.7945 (m-30) REVERT: 1 145 GLU cc_start: 0.8176 (mp0) cc_final: 0.7669 (mp0) REVERT: 1 317 MET cc_start: 0.9073 (mmm) cc_final: 0.8640 (tpp) REVERT: 2 82 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8651 (mt-10) REVERT: 2 93 LYS cc_start: 0.8936 (mttm) cc_final: 0.8445 (tttm) REVERT: 3 31 GLU cc_start: 0.8922 (tt0) cc_final: 0.8269 (tm-30) REVERT: 3 58 GLU cc_start: 0.8410 (tt0) cc_final: 0.7892 (tp30) REVERT: 3 121 MET cc_start: 0.9111 (mmm) cc_final: 0.8282 (mmm) REVERT: 3 174 THR cc_start: 0.9329 (p) cc_final: 0.9106 (p) REVERT: 3 225 THR cc_start: 0.9656 (m) cc_final: 0.9450 (p) REVERT: 3 237 ASN cc_start: 0.7695 (m-40) cc_final: 0.7357 (m-40) REVERT: 3 475 GLN cc_start: 0.6457 (mm110) cc_final: 0.6065 (tp40) REVERT: 3 476 LYS cc_start: 0.8518 (tttm) cc_final: 0.8231 (mttm) REVERT: 3 568 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7660 (mt-10) REVERT: 4 20 TYR cc_start: 0.7402 (m-80) cc_final: 0.6976 (m-10) REVERT: 4 72 MET cc_start: 0.8980 (mmm) cc_final: 0.8279 (mmm) REVERT: 4 83 LEU cc_start: 0.8913 (tt) cc_final: 0.8430 (tp) REVERT: 4 326 ASP cc_start: 0.8415 (t0) cc_final: 0.7967 (t0) REVERT: 4 331 SER cc_start: 0.9435 (m) cc_final: 0.9069 (p) REVERT: 4 343 GLU cc_start: 0.8922 (mp0) cc_final: 0.8544 (mp0) REVERT: 5 200 ASN cc_start: 0.9223 (m110) cc_final: 0.8751 (m-40) REVERT: 6 25 ARG cc_start: 0.6336 (ttt180) cc_final: 0.4567 (tpt170) REVERT: 6 42 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8550 (ttp-110) REVERT: 6 145 TYR cc_start: 0.9305 (m-80) cc_final: 0.9034 (m-80) REVERT: 9 14 MET cc_start: 0.7893 (tpt) cc_final: 0.7685 (tpt) REVERT: 9 129 ASP cc_start: 0.8887 (m-30) cc_final: 0.8639 (m-30) REVERT: A 1 MET cc_start: 0.6632 (tpp) cc_final: 0.5572 (ptp) REVERT: A 10 ASN cc_start: 0.8248 (m-40) cc_final: 0.7862 (m-40) REVERT: A 87 MET cc_start: 0.8206 (tmt) cc_final: 0.7958 (tmt) REVERT: A 90 MET cc_start: 0.8141 (mmp) cc_final: 0.7888 (mmp) REVERT: H 1 MET cc_start: 0.7066 (ttp) cc_final: 0.6168 (mmt) REVERT: H 30 TYR cc_start: 0.8925 (m-80) cc_final: 0.8442 (m-80) REVERT: H 204 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7719 (mm-30) REVERT: H 258 ASN cc_start: 0.7740 (t0) cc_final: 0.7511 (t0) REVERT: H 279 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.8143 (ttp80) REVERT: J 2 MET cc_start: 0.8417 (tpt) cc_final: 0.8005 (mtt) REVERT: J 103 MET cc_start: 0.7557 (mmt) cc_final: 0.7276 (mmt) REVERT: J 143 ILE cc_start: 0.9227 (mt) cc_final: 0.8935 (mt) REVERT: J 170 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7669 (mm-30) REVERT: K 78 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8128 (tm) REVERT: K 91 GLN cc_start: 0.8269 (pm20) cc_final: 0.7636 (mp10) REVERT: L 3 LEU cc_start: 0.8418 (tp) cc_final: 0.7914 (tt) REVERT: L 75 LYS cc_start: 0.7618 (tttm) cc_final: 0.7397 (tttm) REVERT: L 79 SER cc_start: 0.7881 (m) cc_final: 0.7617 (p) REVERT: L 128 MET cc_start: 0.7991 (tpt) cc_final: 0.7674 (tmm) REVERT: L 203 MET cc_start: 0.8069 (tpp) cc_final: 0.7827 (mtp) REVERT: L 251 THR cc_start: 0.8150 (m) cc_final: 0.7761 (p) REVERT: L 290 MET cc_start: 0.5771 (ttp) cc_final: 0.5488 (ppp) REVERT: L 341 MET cc_start: 0.8729 (mtp) cc_final: 0.8384 (mtp) REVERT: L 354 GLN cc_start: 0.6214 (mt0) cc_final: 0.5892 (tt0) REVERT: L 445 GLU cc_start: 0.7592 (pp20) cc_final: 0.7185 (pt0) REVERT: L 457 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8106 (mp) REVERT: L 524 ASN cc_start: 0.8322 (t0) cc_final: 0.8070 (t0) REVERT: L 540 MET cc_start: 0.5828 (mtm) cc_final: 0.4912 (ppp) REVERT: L 544 MET cc_start: 0.5338 (mtt) cc_final: 0.5095 (ppp) REVERT: L 589 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.7907 (mt) REVERT: M 22 MET cc_start: 0.8603 (mmp) cc_final: 0.7637 (mtt) REVERT: M 70 MET cc_start: 0.8667 (mtp) cc_final: 0.8379 (mtm) REVERT: M 92 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8116 (mtmm) REVERT: M 195 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8768 (tpp) REVERT: M 210 TYR cc_start: 0.8604 (t80) cc_final: 0.7921 (t80) REVERT: M 263 MET cc_start: 0.8182 (mmt) cc_final: 0.7840 (mmt) REVERT: M 271 MET cc_start: 0.7787 (mmp) cc_final: 0.7484 (mmm) REVERT: M 374 ASN cc_start: 0.8807 (m-40) cc_final: 0.8388 (m-40) REVERT: M 400 MET cc_start: 0.8124 (ttm) cc_final: 0.7920 (ttm) REVERT: M 415 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7529 (mm-40) REVERT: N 35 MET cc_start: 0.8918 (ttm) cc_final: 0.8570 (mtp) REVERT: N 36 ASN cc_start: 0.8394 (t0) cc_final: 0.7945 (t0) REVERT: N 58 LYS cc_start: 0.7906 (mttt) cc_final: 0.7624 (mtpt) REVERT: N 77 ASN cc_start: 0.8651 (t0) cc_final: 0.8257 (t0) REVERT: N 213 SER cc_start: 0.9327 (m) cc_final: 0.8837 (t) REVERT: N 235 ASN cc_start: 0.7966 (t160) cc_final: 0.7722 (t0) REVERT: N 329 MET cc_start: 0.8233 (mtm) cc_final: 0.8006 (mtm) REVERT: V 4 LEU cc_start: 0.7599 (mm) cc_final: 0.7347 (mt) REVERT: V 7 GLN cc_start: 0.7085 (pt0) cc_final: 0.6081 (tm-30) REVERT: V 90 LEU cc_start: 0.8303 (mt) cc_final: 0.8004 (mt) REVERT: V 91 ILE cc_start: 0.7818 (mt) cc_final: 0.7421 (tp) REVERT: X 49 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7514 (tm-30) REVERT: X 71 MET cc_start: 0.7374 (mmt) cc_final: 0.7171 (mmt) REVERT: Y 18 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7548 (mtmm) REVERT: Y 51 ASP cc_start: 0.7763 (t0) cc_final: 0.7310 (t70) REVERT: Y 61 LEU cc_start: 0.7783 (mt) cc_final: 0.7539 (mm) REVERT: Y 112 ASP cc_start: 0.7726 (m-30) cc_final: 0.7472 (m-30) REVERT: Z 81 VAL cc_start: 0.8155 (m) cc_final: 0.7882 (t) REVERT: Z 123 ASN cc_start: 0.7679 (m-40) cc_final: 0.7132 (t0) REVERT: a 45 ASP cc_start: 0.8322 (t0) cc_final: 0.8032 (t0) REVERT: b 76 ASP cc_start: 0.8332 (m-30) cc_final: 0.8085 (m-30) REVERT: c 97 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8184 (tm-30) REVERT: c 114 LYS cc_start: 0.7608 (mmtm) cc_final: 0.6641 (mmmt) REVERT: d 54 TYR cc_start: 0.8819 (t80) cc_final: 0.8435 (t80) REVERT: d 57 MET cc_start: 0.9321 (mmp) cc_final: 0.9103 (tpp) REVERT: d 154 LYS cc_start: 0.8604 (tttm) cc_final: 0.8168 (ttmt) REVERT: d 162 GLU cc_start: 0.6883 (mp0) cc_final: 0.6371 (tm-30) REVERT: d 270 PHE cc_start: 0.5314 (m-80) cc_final: 0.4795 (t80) REVERT: d 281 ARG cc_start: 0.8526 (ptp90) cc_final: 0.7985 (ptt90) REVERT: e 39 ARG cc_start: 0.7864 (mtt180) cc_final: 0.6385 (mmt-90) REVERT: e 58 SER cc_start: 0.8952 (t) cc_final: 0.8481 (p) REVERT: e 59 ASP cc_start: 0.7576 (m-30) cc_final: 0.7125 (t70) REVERT: e 61 GLN cc_start: 0.7448 (mt0) cc_final: 0.6996 (mm110) REVERT: f 43 TYR cc_start: 0.8359 (t80) cc_final: 0.7915 (t80) REVERT: f 53 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8570 (tm-30) REVERT: f 57 ILE cc_start: 0.8551 (mt) cc_final: 0.8076 (mt) REVERT: h 5 ARG cc_start: 0.7706 (tpt90) cc_final: 0.7272 (ptt180) REVERT: h 39 LYS cc_start: 0.9047 (tptm) cc_final: 0.7730 (pttt) REVERT: i 12 GLN cc_start: 0.8748 (pt0) cc_final: 0.8372 (tp40) REVERT: i 26 VAL cc_start: 0.9146 (p) cc_final: 0.8939 (t) REVERT: i 37 THR cc_start: 0.8987 (m) cc_final: 0.8739 (p) REVERT: i 53 LYS cc_start: 0.7670 (mmtm) cc_final: 0.7026 (pttm) REVERT: j 51 ILE cc_start: 0.8680 (mm) cc_final: 0.8452 (mm) REVERT: j 54 MET cc_start: 0.7574 (mtt) cc_final: 0.6685 (tmm) REVERT: k 90 ASP cc_start: 0.6175 (p0) cc_final: 0.5282 (t70) REVERT: k 113 GLU cc_start: 0.7978 (pp20) cc_final: 0.7622 (pp20) REVERT: k 143 PHE cc_start: 0.7156 (m-10) cc_final: 0.6641 (m-10) REVERT: k 201 ASP cc_start: 0.6681 (m-30) cc_final: 0.6436 (m-30) REVERT: k 253 ASP cc_start: 0.7149 (m-30) cc_final: 0.6710 (m-30) REVERT: l 52 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7993 (tm-30) REVERT: l 53 LYS cc_start: 0.8436 (pttm) cc_final: 0.8007 (tptt) REVERT: m 9 LYS cc_start: 0.7293 (ttpp) cc_final: 0.6746 (mptt) REVERT: m 39 LYS cc_start: 0.8201 (ttpm) cc_final: 0.7962 (ptpp) REVERT: m 70 GLN cc_start: 0.8369 (mt0) cc_final: 0.6949 (pp30) REVERT: n 53 MET cc_start: 0.8264 (ttp) cc_final: 0.8049 (ttp) REVERT: o 8 ARG cc_start: 0.7667 (mpt-90) cc_final: 0.6307 (mtm110) REVERT: o 45 ASP cc_start: 0.8561 (t70) cc_final: 0.8241 (t0) REVERT: o 95 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8205 (mptt) REVERT: p 35 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7681 (mtt90) REVERT: p 60 GLU cc_start: 0.7976 (tt0) cc_final: 0.7712 (tp30) REVERT: p 79 PHE cc_start: 0.7066 (t80) cc_final: 0.6563 (t80) REVERT: q 26 ARG cc_start: 0.7754 (tmt170) cc_final: 0.7146 (mtt90) REVERT: q 27 ARG cc_start: 0.6939 (ptm160) cc_final: 0.5847 (ttm-80) REVERT: q 59 LEU cc_start: 0.7866 (mt) cc_final: 0.7386 (tt) REVERT: q 130 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7724 (mm-30) REVERT: q 131 GLU cc_start: 0.8169 (tt0) cc_final: 0.7756 (pm20) REVERT: r 26 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8042 (mm-30) REVERT: r 75 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5785 (mt) REVERT: r 82 HIS cc_start: 0.7990 (t70) cc_final: 0.7705 (t70) REVERT: r 109 ILE cc_start: 0.7928 (mm) cc_final: 0.7708 (mp) REVERT: s 28 TYR cc_start: 0.6987 (t80) cc_final: 0.6665 (t80) REVERT: s 37 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7274 (tm-30) REVERT: s 57 TYR cc_start: 0.6648 (m-80) cc_final: 0.6043 (m-10) REVERT: s 71 ASP cc_start: 0.7457 (m-30) cc_final: 0.7221 (p0) REVERT: s 95 VAL cc_start: 0.8174 (p) cc_final: 0.7822 (m) REVERT: s 114 ARG cc_start: 0.6629 (tpp80) cc_final: 0.6310 (ttp-170) REVERT: s 117 ARG cc_start: 0.2932 (ttp-170) cc_final: 0.0790 (ttt-90) REVERT: t 50 HIS cc_start: 0.7059 (t-90) cc_final: 0.6476 (t-170) REVERT: t 94 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6386 (tm-30) REVERT: t 102 CYS cc_start: 0.8733 (m) cc_final: 0.8359 (t) REVERT: t 150 THR cc_start: 0.7733 (m) cc_final: 0.7509 (p) REVERT: t 174 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7877 (mtm110) REVERT: u 7 ILE cc_start: 0.7804 (mm) cc_final: 0.7573 (mp) REVERT: u 12 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7126 (ttt90) REVERT: u 14 PHE cc_start: 0.6239 (t80) cc_final: 0.5293 (p90) REVERT: v 105 LEU cc_start: 0.6704 (tp) cc_final: 0.6420 (tp) REVERT: v 157 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5201 (mm-30) REVERT: w 36 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7360 (t0) REVERT: w 122 GLU cc_start: 0.7119 (pm20) cc_final: 0.6093 (mm-30) REVERT: y 25 TYR cc_start: 0.7987 (t80) cc_final: 0.7078 (m-10) REVERT: y 28 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.6919 (mtm180) REVERT: y 53 GLU cc_start: 0.6949 (pm20) cc_final: 0.6704 (pm20) REVERT: z 17 PHE cc_start: 0.7967 (t80) cc_final: 0.7724 (t80) REVERT: z 63 SER cc_start: 0.8759 (m) cc_final: 0.8478 (p) outliers start: 207 outliers final: 132 residues processed: 1898 average time/residue: 0.6465 time to fit residues: 2082.7313 Evaluate side-chains 1689 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1551 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 257 ASN Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 4 residue 34 ASN Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 169 SER Chi-restraints excluded: chain 6 residue 83 SER Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 6 MET Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 269 ASN Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 417 SER Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 250 SER Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 37 MET Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain d residue 3 HIS Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 13 LEU Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain g residue 119 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain j residue 50 ILE Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain k residue 289 SER Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 68 THR Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 8 LYS Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 103 ILE Chi-restraints excluded: chain s residue 53 GLN Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 50 HIS Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 606 optimal weight: 9.9990 chunk 495 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 729 optimal weight: 40.0000 chunk 788 optimal weight: 20.0000 chunk 649 optimal weight: 10.0000 chunk 723 optimal weight: 0.0270 chunk 248 optimal weight: 6.9990 chunk 585 optimal weight: 0.0060 overall best weight: 5.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 402 HIS ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN 5 21 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 444 ASN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN N 222 ASN ** Z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 GLN Z 139 GLN ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN d 216 ASN d 306 GLN ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 190 HIS l 26 HIS ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS s 43 GLN v 55 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN z 31 ASN ** z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 69560 Z= 0.563 Angle : 1.585 50.716 94035 Z= 1.019 Chirality : 0.309 6.411 10182 Planarity : 0.005 0.055 11744 Dihedral : 12.242 163.224 10516 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.40 % Favored : 95.59 % Rotamer: Outliers : 3.63 % Allowed : 13.17 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8122 helix: -0.09 (0.08), residues: 4218 sheet: -1.36 (0.25), residues: 388 loop : -1.41 (0.10), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 272 HIS 0.012 0.001 HIS N 112 PHE 0.034 0.002 PHE M 122 TYR 0.039 0.002 TYR 6 125 ARG 0.006 0.000 ARG 4 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1907 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1646 time to evaluate : 6.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 145 GLU cc_start: 0.8212 (mp0) cc_final: 0.7631 (mp0) REVERT: 1 317 MET cc_start: 0.9063 (mmm) cc_final: 0.8635 (tpp) REVERT: 2 93 LYS cc_start: 0.8961 (mttm) cc_final: 0.8402 (tttm) REVERT: 2 112 ASN cc_start: 0.8008 (t0) cc_final: 0.7313 (t0) REVERT: 3 31 GLU cc_start: 0.8915 (tt0) cc_final: 0.8282 (tm-30) REVERT: 3 121 MET cc_start: 0.9120 (mmm) cc_final: 0.8437 (mmm) REVERT: 3 237 ASN cc_start: 0.7818 (m-40) cc_final: 0.7464 (t0) REVERT: 3 452 VAL cc_start: 0.9440 (t) cc_final: 0.9205 (m) REVERT: 3 475 GLN cc_start: 0.6449 (mm110) cc_final: 0.6175 (tp40) REVERT: 3 476 LYS cc_start: 0.8528 (tttm) cc_final: 0.8215 (mmtp) REVERT: 3 515 ARG cc_start: 0.7676 (mtt-85) cc_final: 0.7218 (ptm160) REVERT: 3 568 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7656 (mt-10) REVERT: 4 20 TYR cc_start: 0.7575 (m-80) cc_final: 0.7241 (m-10) REVERT: 4 72 MET cc_start: 0.8505 (mmm) cc_final: 0.8266 (mmm) REVERT: 4 261 ARG cc_start: 0.9373 (mtm-85) cc_final: 0.9172 (mtm-85) REVERT: 4 326 ASP cc_start: 0.8354 (t0) cc_final: 0.7949 (t0) REVERT: 4 331 SER cc_start: 0.9443 (m) cc_final: 0.9107 (p) REVERT: 4 343 GLU cc_start: 0.8900 (mp0) cc_final: 0.8546 (mp0) REVERT: 5 200 ASN cc_start: 0.9255 (m110) cc_final: 0.8787 (m-40) REVERT: 6 42 ARG cc_start: 0.8793 (ptt-90) cc_final: 0.8578 (ttp-110) REVERT: 6 62 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7620 (ttp) REVERT: 6 145 TYR cc_start: 0.9326 (m-80) cc_final: 0.9051 (m-80) REVERT: 6 156 LEU cc_start: 0.9487 (tp) cc_final: 0.9222 (tp) REVERT: 9 14 MET cc_start: 0.7908 (tpt) cc_final: 0.7701 (tpt) REVERT: A 1 MET cc_start: 0.6688 (tpp) cc_final: 0.5606 (ptt) REVERT: A 10 ASN cc_start: 0.8224 (m-40) cc_final: 0.7860 (m-40) REVERT: A 87 MET cc_start: 0.8260 (tmt) cc_final: 0.7949 (tmt) REVERT: A 90 MET cc_start: 0.8199 (mmp) cc_final: 0.7969 (mmp) REVERT: H 1 MET cc_start: 0.6907 (ttp) cc_final: 0.5819 (mmt) REVERT: H 30 TYR cc_start: 0.8914 (m-80) cc_final: 0.8423 (m-80) REVERT: H 227 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8330 (tm-30) REVERT: H 258 ASN cc_start: 0.7750 (t0) cc_final: 0.7445 (t0) REVERT: H 279 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8254 (ttp80) REVERT: J 2 MET cc_start: 0.8429 (tpt) cc_final: 0.8004 (mtt) REVERT: J 103 MET cc_start: 0.7644 (mmt) cc_final: 0.7410 (mmt) REVERT: J 111 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6439 (ttpt) REVERT: J 143 ILE cc_start: 0.9221 (mt) cc_final: 0.8946 (mt) REVERT: J 170 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7689 (mm-30) REVERT: K 9 MET cc_start: 0.8197 (mpp) cc_final: 0.7814 (mtm) REVERT: K 91 GLN cc_start: 0.8055 (pm20) cc_final: 0.7666 (mp10) REVERT: L 3 LEU cc_start: 0.8479 (tp) cc_final: 0.8016 (tt) REVERT: L 75 LYS cc_start: 0.7664 (tttm) cc_final: 0.7418 (tttm) REVERT: L 79 SER cc_start: 0.7888 (m) cc_final: 0.7674 (p) REVERT: L 128 MET cc_start: 0.8058 (tpt) cc_final: 0.7630 (tmm) REVERT: L 203 MET cc_start: 0.8119 (tpp) cc_final: 0.7830 (mtp) REVERT: L 251 THR cc_start: 0.8176 (m) cc_final: 0.7793 (p) REVERT: L 269 ASN cc_start: 0.8072 (t0) cc_final: 0.7648 (t0) REVERT: L 270 ASN cc_start: 0.8724 (t0) cc_final: 0.8485 (t0) REVERT: L 314 MET cc_start: 0.8153 (tpp) cc_final: 0.7487 (tpp) REVERT: L 341 MET cc_start: 0.8657 (mtp) cc_final: 0.8353 (mtp) REVERT: L 354 GLN cc_start: 0.6280 (mt0) cc_final: 0.5840 (tt0) REVERT: L 444 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7645 (p0) REVERT: L 445 GLU cc_start: 0.7641 (pp20) cc_final: 0.7259 (pt0) REVERT: L 565 THR cc_start: 0.8362 (p) cc_final: 0.8050 (t) REVERT: L 589 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7951 (mt) REVERT: M 12 MET cc_start: 0.8557 (mmp) cc_final: 0.8163 (tmm) REVERT: M 22 MET cc_start: 0.8607 (mmp) cc_final: 0.7719 (mtt) REVERT: M 195 MET cc_start: 0.9050 (tpt) cc_final: 0.8822 (tpp) REVERT: M 210 TYR cc_start: 0.8616 (t80) cc_final: 0.7931 (t80) REVERT: M 243 MET cc_start: 0.9244 (mtp) cc_final: 0.8928 (mtp) REVERT: M 263 MET cc_start: 0.8254 (mmt) cc_final: 0.7809 (mmt) REVERT: M 271 MET cc_start: 0.7840 (mmp) cc_final: 0.7524 (mmm) REVERT: M 346 ARG cc_start: 0.8282 (mtm110) cc_final: 0.6959 (mtp-110) REVERT: M 374 ASN cc_start: 0.8691 (m-40) cc_final: 0.8240 (m-40) REVERT: M 383 MET cc_start: 0.8188 (mmp) cc_final: 0.7778 (mmp) REVERT: M 415 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7587 (mm-40) REVERT: N 36 ASN cc_start: 0.8412 (t0) cc_final: 0.8085 (t0) REVERT: N 43 ILE cc_start: 0.8361 (mm) cc_final: 0.8127 (mm) REVERT: N 58 LYS cc_start: 0.7861 (mttt) cc_final: 0.7619 (mtpt) REVERT: N 77 ASN cc_start: 0.8708 (t0) cc_final: 0.8348 (t0) REVERT: N 91 ASN cc_start: 0.8316 (t0) cc_final: 0.8115 (t0) REVERT: N 213 SER cc_start: 0.9297 (m) cc_final: 0.8881 (t) REVERT: N 235 ASN cc_start: 0.7927 (t160) cc_final: 0.7678 (t0) REVERT: N 277 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8511 (mt) REVERT: N 329 MET cc_start: 0.8284 (mtm) cc_final: 0.8082 (mtm) REVERT: V 4 LEU cc_start: 0.7643 (mm) cc_final: 0.7360 (mt) REVERT: V 7 GLN cc_start: 0.7006 (pt0) cc_final: 0.6096 (tm-30) REVERT: V 60 PHE cc_start: 0.7635 (t80) cc_final: 0.7419 (t80) REVERT: V 90 LEU cc_start: 0.8279 (mt) cc_final: 0.8003 (mt) REVERT: V 91 ILE cc_start: 0.7861 (mt) cc_final: 0.7446 (tp) REVERT: V 117 MET cc_start: 0.7820 (mtp) cc_final: 0.7412 (mtp) REVERT: W 88 GLU cc_start: 0.8214 (mp0) cc_final: 0.7793 (mm-30) REVERT: W 115 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7679 (ttm-80) REVERT: W 119 ASP cc_start: 0.8377 (p0) cc_final: 0.7457 (t0) REVERT: X 49 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7634 (tm-30) REVERT: Y 18 LYS cc_start: 0.8263 (mmmm) cc_final: 0.7491 (mtmm) REVERT: Y 51 ASP cc_start: 0.7790 (t0) cc_final: 0.7353 (t70) REVERT: Y 112 ASP cc_start: 0.7701 (m-30) cc_final: 0.7441 (m-30) REVERT: Z 81 VAL cc_start: 0.8184 (m) cc_final: 0.7947 (t) REVERT: Z 123 ASN cc_start: 0.7610 (m-40) cc_final: 0.7138 (t0) REVERT: a 45 ASP cc_start: 0.8366 (t0) cc_final: 0.8076 (t0) REVERT: c 97 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8174 (tm-30) REVERT: c 114 LYS cc_start: 0.7641 (mmtm) cc_final: 0.6709 (mmmt) REVERT: d 54 TYR cc_start: 0.8826 (t80) cc_final: 0.8401 (t80) REVERT: d 57 MET cc_start: 0.9309 (mmp) cc_final: 0.9086 (tpp) REVERT: d 162 GLU cc_start: 0.6935 (mp0) cc_final: 0.6396 (tm-30) REVERT: d 270 PHE cc_start: 0.5211 (OUTLIER) cc_final: 0.4822 (t80) REVERT: d 271 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.3684 (mm-30) REVERT: d 281 ARG cc_start: 0.8637 (ptp90) cc_final: 0.7943 (ptt90) REVERT: e 39 ARG cc_start: 0.7988 (mtt180) cc_final: 0.6287 (mmt-90) REVERT: e 58 SER cc_start: 0.9080 (t) cc_final: 0.8489 (p) REVERT: e 59 ASP cc_start: 0.7552 (m-30) cc_final: 0.7142 (t70) REVERT: e 61 GLN cc_start: 0.7452 (mt0) cc_final: 0.6946 (mm110) REVERT: f 43 TYR cc_start: 0.8335 (t80) cc_final: 0.7857 (t80) REVERT: f 53 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8574 (tm-30) REVERT: f 57 ILE cc_start: 0.8556 (mt) cc_final: 0.8063 (mt) REVERT: f 86 GLU cc_start: 0.8722 (tp30) cc_final: 0.8151 (tt0) REVERT: g 39 TYR cc_start: 0.8216 (t80) cc_final: 0.7952 (t80) REVERT: h 39 LYS cc_start: 0.9035 (tptm) cc_final: 0.7600 (pttt) REVERT: i 12 GLN cc_start: 0.8687 (pt0) cc_final: 0.8252 (tp40) REVERT: i 34 ARG cc_start: 0.8252 (ptt-90) cc_final: 0.8024 (ptt-90) REVERT: i 37 THR cc_start: 0.9012 (m) cc_final: 0.8732 (p) REVERT: i 53 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7048 (pttm) REVERT: j 54 MET cc_start: 0.7458 (mtt) cc_final: 0.6746 (tmm) REVERT: j 71 MET cc_start: 0.6727 (mmm) cc_final: 0.6116 (ptt) REVERT: k 90 ASP cc_start: 0.6172 (p0) cc_final: 0.5097 (t0) REVERT: k 113 GLU cc_start: 0.8034 (pp20) cc_final: 0.7765 (pp20) REVERT: k 201 ASP cc_start: 0.6619 (m-30) cc_final: 0.6371 (m-30) REVERT: l 52 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7883 (tm-30) REVERT: l 53 LYS cc_start: 0.8483 (pttm) cc_final: 0.8026 (tptt) REVERT: m 9 LYS cc_start: 0.7266 (ttpp) cc_final: 0.6659 (mptt) REVERT: m 15 GLU cc_start: 0.8735 (mp0) cc_final: 0.8190 (mp0) REVERT: m 39 LYS cc_start: 0.8181 (ttpm) cc_final: 0.7954 (ptpp) REVERT: m 70 GLN cc_start: 0.8415 (mt0) cc_final: 0.7046 (pp30) REVERT: o 8 ARG cc_start: 0.7713 (mpt-90) cc_final: 0.6266 (mtm110) REVERT: o 45 ASP cc_start: 0.8578 (t70) cc_final: 0.8242 (t0) REVERT: o 95 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8240 (mptt) REVERT: p 34 GLU cc_start: 0.7888 (tt0) cc_final: 0.7516 (tt0) REVERT: p 50 TYR cc_start: 0.7745 (t80) cc_final: 0.7430 (t80) REVERT: p 60 GLU cc_start: 0.7971 (tt0) cc_final: 0.7719 (tp30) REVERT: p 79 PHE cc_start: 0.6850 (t80) cc_final: 0.6538 (t80) REVERT: p 92 PHE cc_start: 0.7946 (m-80) cc_final: 0.7664 (m-80) REVERT: q 26 ARG cc_start: 0.7857 (tmt170) cc_final: 0.7196 (mtt90) REVERT: q 27 ARG cc_start: 0.6971 (ptm160) cc_final: 0.5749 (ttm-80) REVERT: q 59 LEU cc_start: 0.7776 (mt) cc_final: 0.7378 (tt) REVERT: q 103 TRP cc_start: 0.6925 (t-100) cc_final: 0.6520 (t60) REVERT: q 130 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7767 (mm-30) REVERT: r 109 ILE cc_start: 0.7906 (mm) cc_final: 0.7664 (mp) REVERT: s 21 MET cc_start: 0.7562 (ptt) cc_final: 0.7263 (ptt) REVERT: s 28 TYR cc_start: 0.6982 (t80) cc_final: 0.6610 (t80) REVERT: s 71 ASP cc_start: 0.7385 (m-30) cc_final: 0.7163 (p0) REVERT: s 114 ARG cc_start: 0.6548 (tpp80) cc_final: 0.6174 (ttp-170) REVERT: s 117 ARG cc_start: 0.2877 (ttp-170) cc_final: 0.1406 (ttt-90) REVERT: t 50 HIS cc_start: 0.6937 (t-90) cc_final: 0.6436 (t-170) REVERT: t 174 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7854 (mtm110) REVERT: u 12 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7124 (ttt90) REVERT: u 14 PHE cc_start: 0.6208 (t80) cc_final: 0.5347 (p90) REVERT: v 42 MET cc_start: 0.8132 (mmm) cc_final: 0.7634 (mmm) REVERT: v 102 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6917 (p) REVERT: v 105 LEU cc_start: 0.6551 (tp) cc_final: 0.6263 (tp) REVERT: v 157 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5334 (mm-30) REVERT: w 36 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7360 (t0) REVERT: w 122 GLU cc_start: 0.7192 (pm20) cc_final: 0.6152 (mm-30) REVERT: y 25 TYR cc_start: 0.7971 (t80) cc_final: 0.7042 (m-10) REVERT: z 17 PHE cc_start: 0.7982 (t80) cc_final: 0.7627 (t80) REVERT: z 21 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7794 (ptt) REVERT: z 25 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7262 (ptt90) REVERT: z 63 SER cc_start: 0.8638 (m) cc_final: 0.8427 (p) REVERT: z 68 ASN cc_start: 0.6878 (t0) cc_final: 0.6560 (m110) outliers start: 261 outliers final: 178 residues processed: 1782 average time/residue: 0.6602 time to fit residues: 2013.8041 Evaluate side-chains 1707 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1520 time to evaluate : 6.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 473 ILE Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 3 residue 678 SER Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 201 SER Chi-restraints excluded: chain 6 residue 62 MET Chi-restraints excluded: chain 6 residue 83 SER Chi-restraints excluded: chain 9 residue 36 MET Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 6 MET Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 417 SER Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 444 ASN Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain V residue 129 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 37 MET Chi-restraints excluded: chain Y residue 35 CYS Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain g residue 119 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 50 ILE Chi-restraints excluded: chain j residue 62 ILE Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 38 ILE Chi-restraints excluded: chain p residue 47 GLN Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 89 ASN Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 50 HIS Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 121 THR Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 97 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 34 LEU Chi-restraints excluded: chain y residue 45 LYS Chi-restraints excluded: chain z residue 21 MET Chi-restraints excluded: chain z residue 34 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 0.3980 chunk 548 optimal weight: 6.9990 chunk 378 optimal weight: 0.4980 chunk 80 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 489 optimal weight: 8.9990 chunk 732 optimal weight: 5.9990 chunk 775 optimal weight: 6.9990 chunk 382 optimal weight: 9.9990 chunk 693 optimal weight: 30.0000 chunk 208 optimal weight: 9.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 214 GLN ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN 4 135 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN N 222 ASN N 316 GLN V 6 HIS ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN d 216 ASN g 25 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 33 ASN k 190 HIS ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN u 58 GLN v 55 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN z 68 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69560 Z= 0.550 Angle : 1.576 50.698 94035 Z= 1.015 Chirality : 0.309 6.389 10182 Planarity : 0.004 0.057 11744 Dihedral : 11.871 163.052 10516 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.25 % Favored : 95.74 % Rotamer: Outliers : 3.52 % Allowed : 14.87 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.09), residues: 8122 helix: 0.24 (0.08), residues: 4215 sheet: -1.22 (0.25), residues: 396 loop : -1.22 (0.10), residues: 3511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP z 2 HIS 0.011 0.001 HIS N 112 PHE 0.047 0.002 PHE W 21 TYR 0.033 0.002 TYR 6 125 ARG 0.009 0.000 ARG 4 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1873 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1620 time to evaluate : 6.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 145 GLU cc_start: 0.8189 (mp0) cc_final: 0.7597 (mp0) REVERT: 1 281 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: 1 317 MET cc_start: 0.9047 (mmm) cc_final: 0.8690 (tpp) REVERT: 2 93 LYS cc_start: 0.8955 (mttm) cc_final: 0.8377 (tttm) REVERT: 2 112 ASN cc_start: 0.8002 (t0) cc_final: 0.7325 (t0) REVERT: 3 31 GLU cc_start: 0.8911 (tt0) cc_final: 0.8251 (tm-30) REVERT: 3 121 MET cc_start: 0.9051 (mmm) cc_final: 0.8401 (mmm) REVERT: 3 237 ASN cc_start: 0.7857 (m-40) cc_final: 0.7474 (t0) REVERT: 3 475 GLN cc_start: 0.6389 (mm110) cc_final: 0.6098 (tp40) REVERT: 3 476 LYS cc_start: 0.8442 (tttm) cc_final: 0.8155 (mmtp) REVERT: 3 515 ARG cc_start: 0.7656 (mtt-85) cc_final: 0.7188 (ptm160) REVERT: 3 568 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7674 (mt-10) REVERT: 4 20 TYR cc_start: 0.7647 (m-80) cc_final: 0.7348 (m-10) REVERT: 4 175 GLU cc_start: 0.8825 (tp30) cc_final: 0.8391 (mt-10) REVERT: 4 232 ASN cc_start: 0.9022 (t0) cc_final: 0.8474 (t0) REVERT: 4 326 ASP cc_start: 0.8348 (t0) cc_final: 0.8035 (t0) REVERT: 4 331 SER cc_start: 0.9427 (m) cc_final: 0.9100 (p) REVERT: 4 343 GLU cc_start: 0.8879 (mp0) cc_final: 0.8531 (mp0) REVERT: 5 200 ASN cc_start: 0.9270 (m110) cc_final: 0.8888 (m-40) REVERT: 6 111 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8791 (ptt90) REVERT: 6 145 TYR cc_start: 0.9328 (m-80) cc_final: 0.9073 (m-80) REVERT: A 1 MET cc_start: 0.6767 (tpp) cc_final: 0.5644 (ptt) REVERT: A 10 ASN cc_start: 0.8180 (m-40) cc_final: 0.7817 (m-40) REVERT: A 87 MET cc_start: 0.8273 (tmt) cc_final: 0.7970 (tmt) REVERT: H 1 MET cc_start: 0.6797 (ttp) cc_final: 0.5787 (mmt) REVERT: H 30 TYR cc_start: 0.8882 (m-80) cc_final: 0.8407 (m-80) REVERT: H 227 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8452 (tm-30) REVERT: H 258 ASN cc_start: 0.7741 (t0) cc_final: 0.7431 (t0) REVERT: H 279 ARG cc_start: 0.8653 (ttp-170) cc_final: 0.8247 (ttp80) REVERT: J 2 MET cc_start: 0.8438 (tpt) cc_final: 0.8006 (mtt) REVERT: J 139 GLU cc_start: 0.8104 (pm20) cc_final: 0.7872 (pm20) REVERT: J 143 ILE cc_start: 0.9212 (mt) cc_final: 0.8944 (mt) REVERT: J 170 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7651 (mm-30) REVERT: K 91 GLN cc_start: 0.7925 (pm20) cc_final: 0.7633 (mp10) REVERT: L 3 LEU cc_start: 0.8496 (tp) cc_final: 0.8127 (tt) REVERT: L 53 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.7012 (ttm) REVERT: L 128 MET cc_start: 0.8118 (tpt) cc_final: 0.7641 (tmm) REVERT: L 203 MET cc_start: 0.8105 (tpp) cc_final: 0.7848 (mtp) REVERT: L 251 THR cc_start: 0.8194 (m) cc_final: 0.7859 (p) REVERT: L 269 ASN cc_start: 0.8030 (t0) cc_final: 0.7723 (t0) REVERT: L 339 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8150 (tt) REVERT: L 354 GLN cc_start: 0.6251 (mt0) cc_final: 0.5790 (tt0) REVERT: L 445 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: L 589 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.7970 (mt) REVERT: M 12 MET cc_start: 0.8510 (mmp) cc_final: 0.8125 (tmm) REVERT: M 22 MET cc_start: 0.8595 (mmp) cc_final: 0.7670 (mtt) REVERT: M 141 GLU cc_start: 0.8129 (pm20) cc_final: 0.7829 (pt0) REVERT: M 147 LEU cc_start: 0.8357 (mt) cc_final: 0.8054 (mp) REVERT: M 195 MET cc_start: 0.8996 (tpt) cc_final: 0.8762 (tpp) REVERT: M 210 TYR cc_start: 0.8603 (t80) cc_final: 0.7845 (t80) REVERT: M 243 MET cc_start: 0.9240 (mtp) cc_final: 0.8987 (mtp) REVERT: M 263 MET cc_start: 0.8279 (mmt) cc_final: 0.7857 (mmt) REVERT: M 271 MET cc_start: 0.7893 (mmp) cc_final: 0.7593 (mmm) REVERT: M 279 GLN cc_start: 0.8836 (tp40) cc_final: 0.8519 (tp40) REVERT: M 346 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7042 (mtp-110) REVERT: M 374 ASN cc_start: 0.8580 (m-40) cc_final: 0.8161 (m-40) REVERT: M 415 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7555 (mm-40) REVERT: M 441 MET cc_start: 0.8494 (tpt) cc_final: 0.7991 (tpt) REVERT: N 35 MET cc_start: 0.8822 (ttm) cc_final: 0.8481 (mtp) REVERT: N 36 ASN cc_start: 0.8327 (t0) cc_final: 0.7902 (t0) REVERT: N 43 ILE cc_start: 0.8346 (mm) cc_final: 0.8130 (mm) REVERT: N 77 ASN cc_start: 0.8732 (t0) cc_final: 0.8369 (t0) REVERT: N 135 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8288 (mttp) REVERT: N 213 SER cc_start: 0.9268 (m) cc_final: 0.8858 (t) REVERT: N 235 ASN cc_start: 0.7873 (t160) cc_final: 0.7604 (t0) REVERT: N 251 MET cc_start: 0.8242 (ttp) cc_final: 0.7715 (ttp) REVERT: N 268 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: N 313 MET cc_start: 0.7770 (mmt) cc_final: 0.7488 (mmm) REVERT: V 60 PHE cc_start: 0.7644 (t80) cc_final: 0.7411 (t80) REVERT: V 91 ILE cc_start: 0.7864 (mt) cc_final: 0.7479 (tp) REVERT: V 117 MET cc_start: 0.7795 (mtp) cc_final: 0.7375 (mtp) REVERT: W 119 ASP cc_start: 0.8383 (p0) cc_final: 0.7481 (t0) REVERT: X 49 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7696 (tm-30) REVERT: X 51 ILE cc_start: 0.8712 (tt) cc_final: 0.8480 (mm) REVERT: Y 18 LYS cc_start: 0.8258 (mmmm) cc_final: 0.7514 (mtmm) REVERT: Y 51 ASP cc_start: 0.7796 (t0) cc_final: 0.7428 (t70) REVERT: Y 112 ASP cc_start: 0.7630 (m-30) cc_final: 0.7393 (m-30) REVERT: Z 81 VAL cc_start: 0.8209 (m) cc_final: 0.7984 (t) REVERT: Z 123 ASN cc_start: 0.7593 (m-40) cc_final: 0.7092 (t0) REVERT: a 45 ASP cc_start: 0.8358 (t0) cc_final: 0.8091 (t0) REVERT: c 90 GLU cc_start: 0.8455 (pm20) cc_final: 0.7895 (mm-30) REVERT: c 97 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8119 (tm-30) REVERT: c 114 LYS cc_start: 0.7683 (mmtm) cc_final: 0.6761 (mmmt) REVERT: d 162 GLU cc_start: 0.6902 (mp0) cc_final: 0.6388 (tm-30) REVERT: d 270 PHE cc_start: 0.5280 (OUTLIER) cc_final: 0.4832 (t80) REVERT: d 271 GLU cc_start: 0.5577 (OUTLIER) cc_final: 0.3702 (mm-30) REVERT: d 281 ARG cc_start: 0.8647 (ptp90) cc_final: 0.7900 (ptt90) REVERT: e 39 ARG cc_start: 0.7990 (mtt180) cc_final: 0.6249 (mmt-90) REVERT: e 58 SER cc_start: 0.9054 (t) cc_final: 0.8493 (p) REVERT: e 59 ASP cc_start: 0.7535 (m-30) cc_final: 0.7131 (t70) REVERT: e 61 GLN cc_start: 0.7474 (mt0) cc_final: 0.6974 (mm110) REVERT: f 43 TYR cc_start: 0.8333 (t80) cc_final: 0.7974 (t80) REVERT: f 53 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8544 (tm-30) REVERT: f 57 ILE cc_start: 0.8549 (mt) cc_final: 0.8060 (mt) REVERT: g 90 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8412 (tp30) REVERT: h 5 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7592 (ttp-170) REVERT: h 6 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8655 (tp) REVERT: h 39 LYS cc_start: 0.9078 (tptm) cc_final: 0.7691 (pttt) REVERT: i 12 GLN cc_start: 0.8691 (pt0) cc_final: 0.8245 (tp40) REVERT: i 37 THR cc_start: 0.9014 (m) cc_final: 0.8705 (p) REVERT: i 53 LYS cc_start: 0.7666 (mmtm) cc_final: 0.7073 (pttm) REVERT: j 54 MET cc_start: 0.7435 (mtt) cc_final: 0.6748 (tmm) REVERT: j 68 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6832 (tm-30) REVERT: j 71 MET cc_start: 0.6610 (mmm) cc_final: 0.6164 (ptt) REVERT: k 90 ASP cc_start: 0.6166 (p0) cc_final: 0.5116 (t70) REVERT: k 113 GLU cc_start: 0.7944 (pp20) cc_final: 0.7703 (pp20) REVERT: k 201 ASP cc_start: 0.6587 (m-30) cc_final: 0.6353 (m-30) REVERT: l 52 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8001 (tm-30) REVERT: l 53 LYS cc_start: 0.8517 (pttm) cc_final: 0.7995 (tptt) REVERT: m 9 LYS cc_start: 0.7290 (ttpp) cc_final: 0.6660 (mptt) REVERT: m 15 GLU cc_start: 0.8707 (mp0) cc_final: 0.8199 (mp0) REVERT: m 39 LYS cc_start: 0.8143 (ttpm) cc_final: 0.7935 (ptpp) REVERT: m 70 GLN cc_start: 0.8422 (mt0) cc_final: 0.7030 (pp30) REVERT: o 8 ARG cc_start: 0.7651 (mpt-90) cc_final: 0.6269 (mtm110) REVERT: o 45 ASP cc_start: 0.8612 (t70) cc_final: 0.8263 (t0) REVERT: o 95 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8243 (mptt) REVERT: p 34 GLU cc_start: 0.7861 (tt0) cc_final: 0.7544 (tt0) REVERT: p 50 TYR cc_start: 0.7670 (t80) cc_final: 0.7465 (t80) REVERT: p 60 GLU cc_start: 0.7976 (tt0) cc_final: 0.7737 (tp30) REVERT: p 79 PHE cc_start: 0.6640 (t80) cc_final: 0.6326 (t80) REVERT: p 92 PHE cc_start: 0.7943 (m-80) cc_final: 0.7676 (m-80) REVERT: p 102 TYR cc_start: 0.6872 (t80) cc_final: 0.6069 (t80) REVERT: q 26 ARG cc_start: 0.7833 (tmt170) cc_final: 0.7214 (mtt90) REVERT: q 27 ARG cc_start: 0.7028 (ptm160) cc_final: 0.5766 (ttm-80) REVERT: q 59 LEU cc_start: 0.7767 (mt) cc_final: 0.7360 (tt) REVERT: q 103 TRP cc_start: 0.6835 (t-100) cc_final: 0.6560 (t60) REVERT: q 130 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7774 (mm-30) REVERT: r 75 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6131 (mt) REVERT: r 109 ILE cc_start: 0.7830 (mm) cc_final: 0.7589 (mp) REVERT: s 21 MET cc_start: 0.7486 (ptt) cc_final: 0.7165 (ptt) REVERT: s 28 TYR cc_start: 0.6966 (t80) cc_final: 0.6600 (t80) REVERT: s 71 ASP cc_start: 0.7396 (m-30) cc_final: 0.7142 (p0) REVERT: s 117 ARG cc_start: 0.3158 (ttp-170) cc_final: 0.1094 (ttt-90) REVERT: t 50 HIS cc_start: 0.7021 (t-90) cc_final: 0.6489 (t-170) REVERT: t 139 LEU cc_start: 0.8415 (tp) cc_final: 0.8164 (mt) REVERT: t 174 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7762 (mtm110) REVERT: u 12 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7033 (ttt90) REVERT: u 14 PHE cc_start: 0.6231 (t80) cc_final: 0.5355 (p90) REVERT: v 32 GLU cc_start: 0.6741 (mp0) cc_final: 0.6459 (mp0) REVERT: v 42 MET cc_start: 0.8036 (mmm) cc_final: 0.7758 (mmm) REVERT: v 102 CYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6829 (p) REVERT: v 105 LEU cc_start: 0.6568 (tp) cc_final: 0.6276 (tp) REVERT: v 138 LEU cc_start: 0.8314 (mt) cc_final: 0.7812 (mt) REVERT: v 157 GLU cc_start: 0.5752 (mm-30) cc_final: 0.5327 (mm-30) REVERT: w 36 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7350 (t0) REVERT: w 86 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8294 (tp40) REVERT: w 122 GLU cc_start: 0.7172 (pm20) cc_final: 0.6131 (mm-30) REVERT: y 25 TYR cc_start: 0.7968 (t80) cc_final: 0.6997 (m-10) REVERT: z 17 PHE cc_start: 0.7988 (t80) cc_final: 0.7651 (t80) REVERT: z 21 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7811 (ptt) REVERT: z 25 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7275 (ptt90) REVERT: z 63 SER cc_start: 0.8603 (m) cc_final: 0.8395 (p) REVERT: z 68 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6571 (m110) outliers start: 253 outliers final: 175 residues processed: 1756 average time/residue: 0.6423 time to fit residues: 1936.6460 Evaluate side-chains 1693 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1502 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 2 residue 169 ILE Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 221 GLU Chi-restraints excluded: chain 3 residue 261 GLU Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 473 ILE Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 623 LEU Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 3 residue 678 SER Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 185 SER Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 16 ASP Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 201 SER Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 135 LYS Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain V residue 129 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 37 MET Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 98 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain g residue 119 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 50 ILE Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 267 LEU Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 47 GLN Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 89 ASN Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 20 SER Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 34 LEU Chi-restraints excluded: chain y residue 45 LYS Chi-restraints excluded: chain z residue 21 MET Chi-restraints excluded: chain z residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 20.0000 chunk 440 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 577 optimal weight: 0.9990 chunk 319 optimal weight: 7.9990 chunk 661 optimal weight: 20.0000 chunk 535 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 395 optimal weight: 20.0000 chunk 695 optimal weight: 30.0000 chunk 195 optimal weight: 7.9990 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN 1 257 ASN 2 214 GLN ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 HIS V 6 HIS V 78 GLN W 135 HIS Y 30 HIS d 321 HIS g 25 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 97 HIS o 117 HIS p 47 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN v 55 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.237 69560 Z= 0.613 Angle : 1.615 50.779 94035 Z= 1.030 Chirality : 0.309 6.390 10182 Planarity : 0.005 0.055 11744 Dihedral : 11.902 160.677 10516 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.58 % Favored : 94.41 % Rotamer: Outliers : 4.58 % Allowed : 15.45 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.09), residues: 8122 helix: 0.23 (0.08), residues: 4216 sheet: -1.11 (0.26), residues: 393 loop : -1.22 (0.11), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP z 2 HIS 0.009 0.001 HIS 4 190 PHE 0.046 0.002 PHE W 21 TYR 0.036 0.002 TYR 9 118 ARG 0.010 0.001 ARG 4 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1878 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1549 time to evaluate : 6.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 141 GLU cc_start: 0.7400 (mp0) cc_final: 0.6594 (mp0) REVERT: 1 145 GLU cc_start: 0.8274 (mp0) cc_final: 0.7524 (mp0) REVERT: 1 281 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: 1 317 MET cc_start: 0.9078 (mmm) cc_final: 0.8776 (tpp) REVERT: 1 432 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6824 (ptt180) REVERT: 2 93 LYS cc_start: 0.9030 (mttm) cc_final: 0.8431 (tttm) REVERT: 2 112 ASN cc_start: 0.8164 (t0) cc_final: 0.7461 (t0) REVERT: 3 31 GLU cc_start: 0.8981 (tt0) cc_final: 0.8333 (tm-30) REVERT: 3 121 MET cc_start: 0.9066 (mmm) cc_final: 0.8467 (mmm) REVERT: 3 475 GLN cc_start: 0.6619 (mm110) cc_final: 0.6411 (tp40) REVERT: 3 476 LYS cc_start: 0.8576 (tttm) cc_final: 0.8322 (mttm) REVERT: 3 515 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7206 (ptm160) REVERT: 3 568 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7722 (mt-10) REVERT: 4 20 TYR cc_start: 0.7800 (m-80) cc_final: 0.7578 (m-10) REVERT: 4 175 GLU cc_start: 0.8869 (tp30) cc_final: 0.8401 (mt-10) REVERT: 4 326 ASP cc_start: 0.8321 (t0) cc_final: 0.8039 (t0) REVERT: 4 343 GLU cc_start: 0.8912 (mp0) cc_final: 0.8636 (mp0) REVERT: 5 200 ASN cc_start: 0.9346 (m110) cc_final: 0.8971 (m-40) REVERT: 6 42 ARG cc_start: 0.8905 (ptt-90) cc_final: 0.8482 (ptt-90) REVERT: 6 111 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8746 (ptt90) REVERT: 6 137 ASP cc_start: 0.8835 (p0) cc_final: 0.8290 (t0) REVERT: 6 145 TYR cc_start: 0.9332 (m-80) cc_final: 0.8991 (m-80) REVERT: 6 156 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9331 (tp) REVERT: A 1 MET cc_start: 0.6910 (tpp) cc_final: 0.5674 (ptt) REVERT: A 10 ASN cc_start: 0.8265 (m-40) cc_final: 0.7885 (m-40) REVERT: H 1 MET cc_start: 0.6615 (ttp) cc_final: 0.5740 (mmt) REVERT: H 30 TYR cc_start: 0.8877 (m-80) cc_final: 0.8410 (m-80) REVERT: H 227 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8501 (tm-30) REVERT: H 258 ASN cc_start: 0.8063 (t0) cc_final: 0.7661 (t0) REVERT: H 284 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8627 (mt0) REVERT: J 2 MET cc_start: 0.8447 (tpt) cc_final: 0.8004 (mtt) REVERT: J 87 LYS cc_start: 0.8010 (ptpt) cc_final: 0.6492 (tmtt) REVERT: J 111 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6560 (ttpt) REVERT: J 139 GLU cc_start: 0.8132 (pm20) cc_final: 0.7927 (pm20) REVERT: J 143 ILE cc_start: 0.9195 (mt) cc_final: 0.8894 (mt) REVERT: J 169 MET cc_start: 0.8943 (tpt) cc_final: 0.8715 (tpt) REVERT: K 9 MET cc_start: 0.8281 (mpp) cc_final: 0.8076 (mtt) REVERT: K 91 GLN cc_start: 0.7975 (pm20) cc_final: 0.7744 (mp10) REVERT: L 3 LEU cc_start: 0.8630 (tp) cc_final: 0.8405 (tt) REVERT: L 79 SER cc_start: 0.7230 (p) cc_final: 0.6746 (m) REVERT: L 82 MET cc_start: 0.8311 (mmt) cc_final: 0.7758 (mmt) REVERT: L 128 MET cc_start: 0.8236 (tpt) cc_final: 0.7705 (tmm) REVERT: L 251 THR cc_start: 0.8201 (m) cc_final: 0.7784 (p) REVERT: L 270 ASN cc_start: 0.8761 (t0) cc_final: 0.8506 (t0) REVERT: L 354 GLN cc_start: 0.6519 (mt0) cc_final: 0.5910 (tt0) REVERT: L 445 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: L 589 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8039 (mt) REVERT: M 12 MET cc_start: 0.8525 (mmp) cc_final: 0.8155 (tmm) REVERT: M 22 MET cc_start: 0.8698 (mmp) cc_final: 0.7862 (mtt) REVERT: M 92 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8056 (mtmt) REVERT: M 141 GLU cc_start: 0.8263 (pm20) cc_final: 0.7994 (pt0) REVERT: M 147 LEU cc_start: 0.8462 (mt) cc_final: 0.8198 (mp) REVERT: M 195 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8790 (tpp) REVERT: M 243 MET cc_start: 0.9327 (mtp) cc_final: 0.9032 (mtp) REVERT: M 263 MET cc_start: 0.8384 (mmt) cc_final: 0.8065 (mmt) REVERT: M 271 MET cc_start: 0.7949 (mmp) cc_final: 0.7691 (mmm) REVERT: M 325 MET cc_start: 0.8940 (tpp) cc_final: 0.8737 (tpp) REVERT: M 374 ASN cc_start: 0.8717 (m-40) cc_final: 0.8245 (m-40) REVERT: M 441 MET cc_start: 0.8712 (tpt) cc_final: 0.8309 (tpp) REVERT: N 36 ASN cc_start: 0.8438 (t0) cc_final: 0.8038 (t0) REVERT: N 77 ASN cc_start: 0.8707 (t0) cc_final: 0.8443 (t0) REVERT: N 213 SER cc_start: 0.9329 (m) cc_final: 0.8931 (t) REVERT: N 251 MET cc_start: 0.8280 (ttp) cc_final: 0.7760 (ttp) REVERT: N 268 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: N 308 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.7027 (m) REVERT: V 7 GLN cc_start: 0.6915 (pt0) cc_final: 0.5866 (tm-30) REVERT: V 38 TYR cc_start: 0.7737 (m-80) cc_final: 0.7460 (m-80) REVERT: W 119 ASP cc_start: 0.8452 (p0) cc_final: 0.7642 (t0) REVERT: X 49 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7777 (mm-30) REVERT: X 51 ILE cc_start: 0.8734 (tt) cc_final: 0.8511 (mm) REVERT: Y 18 LYS cc_start: 0.8356 (mmmm) cc_final: 0.7577 (mtmm) REVERT: Y 51 ASP cc_start: 0.7884 (t0) cc_final: 0.7592 (t70) REVERT: Y 103 GLN cc_start: 0.7496 (tt0) cc_final: 0.7287 (pp30) REVERT: Y 112 ASP cc_start: 0.7607 (m-30) cc_final: 0.7358 (m-30) REVERT: Z 42 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.6990 (tmt170) REVERT: Z 81 VAL cc_start: 0.8223 (m) cc_final: 0.8023 (t) REVERT: Z 123 ASN cc_start: 0.7574 (m-40) cc_final: 0.7134 (t0) REVERT: Z 129 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8075 (tm-30) REVERT: a 45 ASP cc_start: 0.8410 (t0) cc_final: 0.8087 (t0) REVERT: c 51 ASN cc_start: 0.8860 (t160) cc_final: 0.8620 (t0) REVERT: c 90 GLU cc_start: 0.8412 (pm20) cc_final: 0.7915 (mm-30) REVERT: c 97 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8180 (tm-30) REVERT: c 114 LYS cc_start: 0.7829 (mmtm) cc_final: 0.6942 (mmmt) REVERT: d 162 GLU cc_start: 0.7248 (mp0) cc_final: 0.6511 (tm-30) REVERT: d 270 PHE cc_start: 0.5434 (OUTLIER) cc_final: 0.4933 (t80) REVERT: d 271 GLU cc_start: 0.5483 (OUTLIER) cc_final: 0.3577 (mm-30) REVERT: d 281 ARG cc_start: 0.8741 (ptp90) cc_final: 0.7870 (ptt90) REVERT: d 327 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7378 (mm) REVERT: e 39 ARG cc_start: 0.8068 (mtt180) cc_final: 0.6204 (mmt-90) REVERT: e 58 SER cc_start: 0.9134 (t) cc_final: 0.8522 (p) REVERT: e 59 ASP cc_start: 0.7546 (m-30) cc_final: 0.7163 (t70) REVERT: e 61 GLN cc_start: 0.7539 (mt0) cc_final: 0.6893 (mm110) REVERT: f 43 TYR cc_start: 0.8386 (t80) cc_final: 0.7918 (t80) REVERT: f 53 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8523 (tm-30) REVERT: f 57 ILE cc_start: 0.8588 (mt) cc_final: 0.8103 (mt) REVERT: h 6 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8704 (tp) REVERT: h 8 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: h 39 LYS cc_start: 0.9105 (tptm) cc_final: 0.7814 (pttt) REVERT: i 12 GLN cc_start: 0.8711 (pt0) cc_final: 0.8173 (tp40) REVERT: i 37 THR cc_start: 0.9041 (m) cc_final: 0.8696 (p) REVERT: i 53 LYS cc_start: 0.7734 (mmtm) cc_final: 0.7170 (pttm) REVERT: i 124 TYR cc_start: 0.8713 (t80) cc_final: 0.8445 (t80) REVERT: j 54 MET cc_start: 0.7512 (mtt) cc_final: 0.6793 (tmm) REVERT: j 71 MET cc_start: 0.6916 (mmm) cc_final: 0.6411 (ptt) REVERT: k 37 LYS cc_start: 0.7220 (pttp) cc_final: 0.6702 (mmtt) REVERT: k 113 GLU cc_start: 0.8104 (pp20) cc_final: 0.7894 (pp20) REVERT: k 201 ASP cc_start: 0.6668 (m-30) cc_final: 0.6415 (m-30) REVERT: k 253 ASP cc_start: 0.7080 (m-30) cc_final: 0.6832 (t0) REVERT: l 5 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.8974 (p) REVERT: l 42 CYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6984 (t) REVERT: l 52 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8010 (tm-30) REVERT: l 53 LYS cc_start: 0.8589 (pttm) cc_final: 0.8091 (tptt) REVERT: m 9 LYS cc_start: 0.7190 (ttpp) cc_final: 0.6593 (mptt) REVERT: m 15 GLU cc_start: 0.8753 (mp0) cc_final: 0.8237 (mp0) REVERT: m 39 LYS cc_start: 0.8287 (ttpm) cc_final: 0.8012 (ptpp) REVERT: m 70 GLN cc_start: 0.8502 (mt0) cc_final: 0.7198 (pp30) REVERT: o 8 ARG cc_start: 0.7725 (mpt-90) cc_final: 0.6159 (mtm110) REVERT: o 11 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7738 (tp) REVERT: o 45 ASP cc_start: 0.8646 (t70) cc_final: 0.8318 (t0) REVERT: o 95 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8400 (mptt) REVERT: o 103 GLU cc_start: 0.6068 (mm-30) cc_final: 0.5663 (tm-30) REVERT: p 60 GLU cc_start: 0.8054 (tt0) cc_final: 0.7756 (tp30) REVERT: p 71 ARG cc_start: 0.6746 (mmm-85) cc_final: 0.6445 (mmm-85) REVERT: p 79 PHE cc_start: 0.6594 (t80) cc_final: 0.6279 (t80) REVERT: p 92 PHE cc_start: 0.7890 (m-80) cc_final: 0.7620 (m-80) REVERT: p 102 TYR cc_start: 0.6944 (t80) cc_final: 0.6040 (t80) REVERT: q 9 MET cc_start: 0.8288 (mmm) cc_final: 0.8045 (mmt) REVERT: q 26 ARG cc_start: 0.7847 (tmt170) cc_final: 0.7281 (mtt90) REVERT: q 27 ARG cc_start: 0.7201 (ptm160) cc_final: 0.5706 (ttm-80) REVERT: q 59 LEU cc_start: 0.7833 (mt) cc_final: 0.7385 (tt) REVERT: q 130 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7802 (mm-30) REVERT: r 75 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6113 (mt) REVERT: r 109 ILE cc_start: 0.7894 (mm) cc_final: 0.7663 (mp) REVERT: s 21 MET cc_start: 0.7521 (ptt) cc_final: 0.7273 (ptt) REVERT: s 28 TYR cc_start: 0.6999 (t80) cc_final: 0.6622 (t80) REVERT: s 71 ASP cc_start: 0.7409 (m-30) cc_final: 0.7114 (p0) REVERT: s 117 ARG cc_start: 0.2884 (ttp-170) cc_final: 0.1092 (ttt-90) REVERT: t 50 HIS cc_start: 0.7084 (t-90) cc_final: 0.6597 (t-170) REVERT: t 139 LEU cc_start: 0.8368 (tp) cc_final: 0.8021 (mt) REVERT: t 174 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7950 (mtm110) REVERT: u 14 PHE cc_start: 0.6210 (t80) cc_final: 0.5385 (p90) REVERT: u 45 ASP cc_start: 0.8254 (m-30) cc_final: 0.8023 (m-30) REVERT: v 32 GLU cc_start: 0.6873 (mp0) cc_final: 0.6527 (mp0) REVERT: v 42 MET cc_start: 0.7960 (mmm) cc_final: 0.7573 (mmm) REVERT: v 91 THR cc_start: 0.7158 (p) cc_final: 0.6926 (t) REVERT: v 105 LEU cc_start: 0.6840 (tp) cc_final: 0.6594 (tp) REVERT: v 157 GLU cc_start: 0.5788 (mm-30) cc_final: 0.5394 (mm-30) REVERT: w 86 GLN cc_start: 0.8607 (tm-30) cc_final: 0.7990 (mm-40) REVERT: w 122 GLU cc_start: 0.7172 (pm20) cc_final: 0.6122 (mm-30) REVERT: y 25 TYR cc_start: 0.8072 (t80) cc_final: 0.6997 (m-10) REVERT: y 28 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.6956 (mtm180) REVERT: z 17 PHE cc_start: 0.8072 (t80) cc_final: 0.7828 (t80) REVERT: z 21 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7815 (ptt) REVERT: z 25 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7329 (ptt90) REVERT: z 63 SER cc_start: 0.8649 (m) cc_final: 0.8376 (p) REVERT: z 69 ILE cc_start: 0.7756 (pt) cc_final: 0.7536 (mt) outliers start: 329 outliers final: 231 residues processed: 1739 average time/residue: 0.6773 time to fit residues: 2035.2912 Evaluate side-chains 1726 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1475 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 248 GLU Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 9 HIS Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 2 residue 169 ILE Chi-restraints excluded: chain 3 residue 20 VAL Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 221 GLU Chi-restraints excluded: chain 3 residue 241 SER Chi-restraints excluded: chain 3 residue 261 GLU Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 466 ILE Chi-restraints excluded: chain 3 residue 473 ILE Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 623 LEU Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 3 residue 678 SER Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 185 SER Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 83 ILE Chi-restraints excluded: chain 5 residue 201 SER Chi-restraints excluded: chain 6 residue 83 SER Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 6 residue 156 LEU Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 6 MET Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 417 SER Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 122 PHE Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 37 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 98 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain d residue 327 LEU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 13 LEU Chi-restraints excluded: chain f residue 48 GLU Chi-restraints excluded: chain g residue 46 VAL Chi-restraints excluded: chain g residue 119 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 26 VAL Chi-restraints excluded: chain i residue 31 ASN Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 47 GLN Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain j residue 50 ILE Chi-restraints excluded: chain j residue 62 ILE Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 218 CYS Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain k residue 279 LEU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 42 CYS Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 117 HIS Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 47 GLN Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain q residue 136 THR Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 53 GLN Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 143 THR Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 20 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 52 ASP Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 97 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 34 LEU Chi-restraints excluded: chain y residue 45 LYS Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 8.9990 chunk 698 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 455 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 775 optimal weight: 6.9990 chunk 644 optimal weight: 30.0000 chunk 359 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 407 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN 4 149 ASN ** 4 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 ASN N 222 ASN V 6 HIS V 78 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 GLN g 25 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN o 61 GLN p 47 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 66 HIS ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.240 69560 Z= 0.553 Angle : 1.583 50.670 94035 Z= 1.017 Chirality : 0.309 6.387 10182 Planarity : 0.004 0.060 11744 Dihedral : 11.530 159.487 10516 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 3.98 % Allowed : 17.01 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 8122 helix: 0.45 (0.08), residues: 4194 sheet: -0.95 (0.26), residues: 398 loop : -1.04 (0.11), residues: 3530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP z 2 HIS 0.022 0.001 HIS o 117 PHE 0.031 0.002 PHE M 122 TYR 0.033 0.002 TYR 9 118 ARG 0.008 0.000 ARG g 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1846 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1560 time to evaluate : 6.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 149 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8955 (mp) REVERT: 1 281 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: 1 317 MET cc_start: 0.9054 (mmm) cc_final: 0.8770 (tpp) REVERT: 1 432 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6756 (ptt180) REVERT: 2 93 LYS cc_start: 0.9031 (mttm) cc_final: 0.8440 (tttm) REVERT: 2 112 ASN cc_start: 0.8144 (t0) cc_final: 0.7425 (t0) REVERT: 3 31 GLU cc_start: 0.8931 (tt0) cc_final: 0.8312 (tm-30) REVERT: 3 121 MET cc_start: 0.9014 (mmm) cc_final: 0.8398 (mmm) REVERT: 3 475 GLN cc_start: 0.6619 (mm110) cc_final: 0.6355 (tp40) REVERT: 3 476 LYS cc_start: 0.8499 (tttm) cc_final: 0.8246 (mttm) REVERT: 3 515 ARG cc_start: 0.7656 (mtt-85) cc_final: 0.7144 (ptm160) REVERT: 3 568 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7711 (mt-10) REVERT: 4 20 TYR cc_start: 0.7773 (m-80) cc_final: 0.7556 (m-10) REVERT: 4 175 GLU cc_start: 0.8837 (tp30) cc_final: 0.8442 (mt-10) REVERT: 4 326 ASP cc_start: 0.8339 (t0) cc_final: 0.8067 (t0) REVERT: 4 343 GLU cc_start: 0.8875 (mp0) cc_final: 0.8513 (mp0) REVERT: 5 200 ASN cc_start: 0.9296 (m110) cc_final: 0.9056 (m-40) REVERT: 6 62 MET cc_start: 0.7839 (ttp) cc_final: 0.7569 (ttp) REVERT: 6 111 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8753 (ptt90) REVERT: 6 137 ASP cc_start: 0.8811 (p0) cc_final: 0.8291 (t0) REVERT: 6 145 TYR cc_start: 0.9331 (m-80) cc_final: 0.9063 (m-80) REVERT: 6 156 LEU cc_start: 0.9513 (tp) cc_final: 0.9162 (tp) REVERT: 9 172 ASP cc_start: 0.8985 (m-30) cc_final: 0.8715 (m-30) REVERT: A 1 MET cc_start: 0.6896 (tpp) cc_final: 0.5602 (ptt) REVERT: A 87 MET cc_start: 0.8251 (tmt) cc_final: 0.7972 (tmt) REVERT: H 1 MET cc_start: 0.6546 (ttp) cc_final: 0.5651 (mmt) REVERT: H 30 TYR cc_start: 0.8812 (m-80) cc_final: 0.8440 (m-80) REVERT: H 227 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 258 ASN cc_start: 0.7941 (t0) cc_final: 0.7533 (t0) REVERT: H 286 MET cc_start: 0.9135 (tpp) cc_final: 0.8848 (mmm) REVERT: J 2 MET cc_start: 0.8424 (tpt) cc_final: 0.7956 (mtt) REVERT: J 139 GLU cc_start: 0.8137 (pm20) cc_final: 0.7936 (pm20) REVERT: J 143 ILE cc_start: 0.9184 (mt) cc_final: 0.8904 (mt) REVERT: K 91 GLN cc_start: 0.7920 (pm20) cc_final: 0.7689 (mp10) REVERT: L 3 LEU cc_start: 0.8646 (tp) cc_final: 0.8378 (tt) REVERT: L 79 SER cc_start: 0.7342 (p) cc_final: 0.6767 (m) REVERT: L 82 MET cc_start: 0.8341 (mmt) cc_final: 0.7776 (mmt) REVERT: L 128 MET cc_start: 0.8159 (tpt) cc_final: 0.7746 (tmm) REVERT: L 251 THR cc_start: 0.8031 (m) cc_final: 0.7642 (p) REVERT: L 270 ASN cc_start: 0.8762 (t0) cc_final: 0.8381 (t0) REVERT: L 354 GLN cc_start: 0.6567 (mt0) cc_final: 0.5732 (tt0) REVERT: L 445 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: L 589 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8036 (mt) REVERT: M 10 MET cc_start: 0.8133 (ttm) cc_final: 0.7773 (ttm) REVERT: M 12 MET cc_start: 0.8457 (mmp) cc_final: 0.8110 (tmm) REVERT: M 22 MET cc_start: 0.8660 (mmp) cc_final: 0.7761 (mtt) REVERT: M 141 GLU cc_start: 0.8262 (pm20) cc_final: 0.7928 (pt0) REVERT: M 147 LEU cc_start: 0.8447 (mt) cc_final: 0.8177 (mp) REVERT: M 222 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7617 (mm-30) REVERT: M 243 MET cc_start: 0.9317 (mtp) cc_final: 0.8970 (mtp) REVERT: M 263 MET cc_start: 0.8389 (mmt) cc_final: 0.8109 (mmt) REVERT: M 271 MET cc_start: 0.7843 (mmp) cc_final: 0.7635 (mmm) REVERT: M 374 ASN cc_start: 0.8582 (m-40) cc_final: 0.8174 (m-40) REVERT: M 432 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8430 (ttp80) REVERT: N 36 ASN cc_start: 0.8325 (t0) cc_final: 0.7792 (t0) REVERT: N 77 ASN cc_start: 0.8720 (t0) cc_final: 0.8388 (t0) REVERT: N 213 SER cc_start: 0.9330 (m) cc_final: 0.8926 (t) REVERT: N 251 MET cc_start: 0.8303 (ttp) cc_final: 0.7783 (ttp) REVERT: N 268 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: N 329 MET cc_start: 0.8297 (mtm) cc_final: 0.8089 (mtm) REVERT: V 38 TYR cc_start: 0.7517 (m-80) cc_final: 0.7265 (m-80) REVERT: V 117 MET cc_start: 0.7788 (mtp) cc_final: 0.7481 (mtp) REVERT: W 91 MET cc_start: 0.7908 (mmt) cc_final: 0.7585 (mmm) REVERT: W 119 ASP cc_start: 0.8416 (p0) cc_final: 0.7592 (t0) REVERT: X 49 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7798 (mm-30) REVERT: X 51 ILE cc_start: 0.8708 (tt) cc_final: 0.8460 (mm) REVERT: Y 9 LEU cc_start: 0.8059 (mt) cc_final: 0.7754 (mp) REVERT: Y 18 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7658 (mtmm) REVERT: Y 51 ASP cc_start: 0.7829 (t0) cc_final: 0.7546 (t70) REVERT: Y 112 ASP cc_start: 0.7567 (m-30) cc_final: 0.7328 (m-30) REVERT: Z 42 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.6963 (tmt170) REVERT: Z 81 VAL cc_start: 0.8187 (m) cc_final: 0.7958 (t) REVERT: Z 113 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8069 (tm-30) REVERT: Z 123 ASN cc_start: 0.7532 (m-40) cc_final: 0.7080 (t0) REVERT: Z 129 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8161 (tm-30) REVERT: a 45 ASP cc_start: 0.8405 (t0) cc_final: 0.8095 (t0) REVERT: c 51 ASN cc_start: 0.8818 (t160) cc_final: 0.8574 (t0) REVERT: c 90 GLU cc_start: 0.8401 (pm20) cc_final: 0.7890 (mm-30) REVERT: c 97 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8181 (tm-30) REVERT: c 114 LYS cc_start: 0.7837 (mmtm) cc_final: 0.6908 (mmmt) REVERT: d 162 GLU cc_start: 0.7096 (mp0) cc_final: 0.6425 (tm-30) REVERT: d 270 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.4872 (t80) REVERT: d 271 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.3423 (mm-30) REVERT: d 281 ARG cc_start: 0.8752 (ptp90) cc_final: 0.7873 (ptt90) REVERT: e 39 ARG cc_start: 0.8017 (mtt180) cc_final: 0.6216 (mmt-90) REVERT: e 58 SER cc_start: 0.9105 (t) cc_final: 0.8529 (p) REVERT: e 59 ASP cc_start: 0.7577 (m-30) cc_final: 0.7232 (t70) REVERT: e 61 GLN cc_start: 0.7542 (mt0) cc_final: 0.6987 (mm110) REVERT: f 43 TYR cc_start: 0.8327 (t80) cc_final: 0.7975 (t80) REVERT: f 53 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8518 (tm-30) REVERT: f 57 ILE cc_start: 0.8601 (mt) cc_final: 0.8106 (mt) REVERT: h 6 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8674 (tp) REVERT: h 8 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: h 39 LYS cc_start: 0.9100 (tptm) cc_final: 0.7804 (pttt) REVERT: i 12 GLN cc_start: 0.8701 (pt0) cc_final: 0.8152 (tp40) REVERT: i 37 THR cc_start: 0.9060 (m) cc_final: 0.8713 (p) REVERT: i 53 LYS cc_start: 0.7693 (mmtm) cc_final: 0.7117 (pttm) REVERT: j 54 MET cc_start: 0.7523 (mtt) cc_final: 0.6748 (tmm) REVERT: j 68 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6844 (tm-30) REVERT: k 37 LYS cc_start: 0.7190 (pttp) cc_final: 0.6601 (mmtt) REVERT: k 201 ASP cc_start: 0.6606 (m-30) cc_final: 0.6348 (m-30) REVERT: l 5 VAL cc_start: 0.9289 (m) cc_final: 0.8981 (p) REVERT: l 53 LYS cc_start: 0.8514 (pttm) cc_final: 0.8089 (tptt) REVERT: l 56 LYS cc_start: 0.8441 (ttmp) cc_final: 0.7937 (pttm) REVERT: l 63 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6916 (ttm-80) REVERT: m 9 LYS cc_start: 0.7160 (ttpp) cc_final: 0.6555 (mptt) REVERT: m 15 GLU cc_start: 0.8668 (mp0) cc_final: 0.8126 (mp0) REVERT: m 39 LYS cc_start: 0.8204 (ttpm) cc_final: 0.7950 (ptpp) REVERT: o 8 ARG cc_start: 0.7750 (mpt-90) cc_final: 0.6183 (mtm110) REVERT: o 11 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7766 (tp) REVERT: o 45 ASP cc_start: 0.8629 (t70) cc_final: 0.8331 (t0) REVERT: o 95 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8273 (mptt) REVERT: o 103 GLU cc_start: 0.6070 (mm-30) cc_final: 0.5642 (tm-30) REVERT: p 34 GLU cc_start: 0.7587 (tt0) cc_final: 0.7119 (tt0) REVERT: p 60 GLU cc_start: 0.8022 (tt0) cc_final: 0.7760 (tp30) REVERT: p 79 PHE cc_start: 0.6542 (t80) cc_final: 0.6257 (t80) REVERT: p 92 PHE cc_start: 0.7876 (m-80) cc_final: 0.7626 (m-80) REVERT: p 102 TYR cc_start: 0.6936 (t80) cc_final: 0.6015 (t80) REVERT: q 9 MET cc_start: 0.8307 (mmm) cc_final: 0.8029 (mmt) REVERT: q 26 ARG cc_start: 0.7801 (tmt170) cc_final: 0.7241 (mtt90) REVERT: q 59 LEU cc_start: 0.7812 (mt) cc_final: 0.7365 (tt) REVERT: q 130 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7801 (mm-30) REVERT: r 75 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6169 (mt) REVERT: r 109 ILE cc_start: 0.7834 (mm) cc_final: 0.7577 (mp) REVERT: s 21 MET cc_start: 0.7567 (ptt) cc_final: 0.7349 (ptt) REVERT: s 28 TYR cc_start: 0.6937 (t80) cc_final: 0.6564 (t80) REVERT: s 71 ASP cc_start: 0.7423 (m-30) cc_final: 0.7166 (p0) REVERT: s 117 ARG cc_start: 0.2738 (ttp-170) cc_final: 0.1031 (ttt-90) REVERT: t 20 LYS cc_start: 0.8458 (tmmt) cc_final: 0.7629 (ttmm) REVERT: t 50 HIS cc_start: 0.7112 (t-90) cc_final: 0.6612 (t-170) REVERT: t 139 LEU cc_start: 0.8283 (tp) cc_final: 0.8001 (mt) REVERT: t 174 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7889 (mtm110) REVERT: u 14 PHE cc_start: 0.6206 (t80) cc_final: 0.5424 (p90) REVERT: u 38 TRP cc_start: 0.7743 (t-100) cc_final: 0.7541 (t-100) REVERT: u 66 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.5452 (tp) REVERT: v 32 GLU cc_start: 0.6904 (mp0) cc_final: 0.6515 (mp0) REVERT: v 42 MET cc_start: 0.7896 (mmm) cc_final: 0.7504 (mmm) REVERT: v 91 THR cc_start: 0.7173 (p) cc_final: 0.6959 (t) REVERT: v 105 LEU cc_start: 0.6824 (tp) cc_final: 0.6589 (tp) REVERT: v 157 GLU cc_start: 0.5805 (mm-30) cc_final: 0.5416 (mm-30) REVERT: w 36 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7384 (t0) REVERT: w 47 TYR cc_start: 0.8628 (m-80) cc_final: 0.8308 (m-80) REVERT: w 86 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8231 (tp40) REVERT: w 122 GLU cc_start: 0.7160 (pm20) cc_final: 0.6120 (mm-30) REVERT: y 25 TYR cc_start: 0.8054 (t80) cc_final: 0.6969 (m-10) REVERT: z 17 PHE cc_start: 0.8029 (t80) cc_final: 0.7780 (t80) REVERT: z 21 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7840 (ptt) REVERT: z 25 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7378 (ptt90) REVERT: z 69 ILE cc_start: 0.7763 (pt) cc_final: 0.7419 (mt) outliers start: 286 outliers final: 208 residues processed: 1710 average time/residue: 0.6448 time to fit residues: 1893.6550 Evaluate side-chains 1704 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1480 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 122 CYS Chi-restraints excluded: chain 1 residue 149 LEU Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 2 residue 169 ILE Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 221 GLU Chi-restraints excluded: chain 3 residue 241 SER Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 357 ASP Chi-restraints excluded: chain 3 residue 473 ILE Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 623 LEU Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 3 residue 678 SER Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 185 SER Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 410 MET Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 83 ILE Chi-restraints excluded: chain 5 residue 201 SER Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 98 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 136 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 13 LEU Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain h residue 54 CYS Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 47 GLN Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain j residue 50 ILE Chi-restraints excluded: chain j residue 62 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain k residue 267 LEU Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 117 HIS Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 47 GLN Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 23 ILE Chi-restraints excluded: chain u residue 66 ILE Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 69 VAL Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 34 LEU Chi-restraints excluded: chain z residue 21 MET Chi-restraints excluded: chain z residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 566 optimal weight: 30.0000 chunk 439 optimal weight: 30.0000 chunk 653 optimal weight: 30.0000 chunk 433 optimal weight: 0.6980 chunk 772 optimal weight: 30.0000 chunk 483 optimal weight: 9.9990 chunk 471 optimal weight: 40.0000 chunk 356 optimal weight: 9.9990 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 55 HIS 4 135 GLN ** 4 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 87 GLN 5 95 ASN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN J 120 ASN L 116 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 ASN M 139 GLN M 304 GLN N 222 ASN V 6 HIS ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 94 GLN e 92 ASN f 49 GLN g 25 ASN g 94 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 258 ASN l 76 ASN p 47 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 55 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.237 69560 Z= 0.583 Angle : 1.602 50.717 94035 Z= 1.024 Chirality : 0.309 6.393 10182 Planarity : 0.005 0.058 11744 Dihedral : 11.451 159.328 10516 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.49 % Favored : 94.50 % Rotamer: Outliers : 4.38 % Allowed : 17.30 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.09), residues: 8122 helix: 0.43 (0.08), residues: 4189 sheet: -1.03 (0.26), residues: 405 loop : -1.05 (0.11), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP p 100 HIS 0.009 0.001 HIS N 112 PHE 0.031 0.002 PHE M 122 TYR 0.032 0.002 TYR 9 118 ARG 0.010 0.001 ARG p 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1829 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1514 time to evaluate : 6.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 145 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7408 (mm-30) REVERT: 1 149 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9000 (mp) REVERT: 1 228 VAL cc_start: 0.9485 (OUTLIER) cc_final: 0.9267 (p) REVERT: 1 281 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: 1 317 MET cc_start: 0.9072 (mmm) cc_final: 0.8804 (tpp) REVERT: 1 432 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6825 (ptt180) REVERT: 2 93 LYS cc_start: 0.9034 (mttm) cc_final: 0.8441 (tttm) REVERT: 2 112 ASN cc_start: 0.8189 (t0) cc_final: 0.7469 (t0) REVERT: 3 31 GLU cc_start: 0.8964 (tt0) cc_final: 0.8359 (tm-30) REVERT: 3 475 GLN cc_start: 0.6696 (mm110) cc_final: 0.6438 (tp40) REVERT: 3 476 LYS cc_start: 0.8490 (tttm) cc_final: 0.8222 (mttm) REVERT: 3 515 ARG cc_start: 0.7670 (mtt-85) cc_final: 0.7173 (ptm160) REVERT: 4 83 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8372 (tp) REVERT: 4 175 GLU cc_start: 0.8877 (tp30) cc_final: 0.8460 (mt-10) REVERT: 4 326 ASP cc_start: 0.8337 (t0) cc_final: 0.7917 (t70) REVERT: 4 343 GLU cc_start: 0.8866 (mp0) cc_final: 0.8485 (mp0) REVERT: 4 410 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: 5 200 ASN cc_start: 0.9303 (m110) cc_final: 0.9081 (m-40) REVERT: 6 42 ARG cc_start: 0.8831 (ptt-90) cc_final: 0.8469 (ttp-170) REVERT: 6 96 MET cc_start: 0.8480 (tpp) cc_final: 0.8079 (mmt) REVERT: 6 111 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8797 (ptt90) REVERT: 6 125 TYR cc_start: 0.9358 (t80) cc_final: 0.8891 (t80) REVERT: 6 156 LEU cc_start: 0.9525 (tp) cc_final: 0.9307 (tp) REVERT: A 1 MET cc_start: 0.6915 (tpp) cc_final: 0.5596 (ptt) REVERT: A 87 MET cc_start: 0.8257 (tmt) cc_final: 0.7987 (tmt) REVERT: H 1 MET cc_start: 0.6454 (ttp) cc_final: 0.5593 (mmt) REVERT: H 30 TYR cc_start: 0.8831 (m-80) cc_final: 0.8527 (m-80) REVERT: H 235 ASN cc_start: 0.8971 (t0) cc_final: 0.8708 (t0) REVERT: H 258 ASN cc_start: 0.8056 (t0) cc_final: 0.7639 (t0) REVERT: H 286 MET cc_start: 0.9101 (tpp) cc_final: 0.8785 (mmm) REVERT: J 2 MET cc_start: 0.8437 (tpt) cc_final: 0.7963 (mtt) REVERT: J 87 LYS cc_start: 0.8022 (ptpt) cc_final: 0.6639 (tmtt) REVERT: J 143 ILE cc_start: 0.9181 (mt) cc_final: 0.8890 (mt) REVERT: L 3 LEU cc_start: 0.8633 (tp) cc_final: 0.8247 (tt) REVERT: L 79 SER cc_start: 0.7533 (p) cc_final: 0.6909 (m) REVERT: L 128 MET cc_start: 0.8226 (tpt) cc_final: 0.7657 (tmm) REVERT: L 270 ASN cc_start: 0.8806 (t0) cc_final: 0.8517 (t0) REVERT: L 354 GLN cc_start: 0.6548 (mt0) cc_final: 0.5815 (tt0) REVERT: L 445 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: L 589 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.7986 (mt) REVERT: M 10 MET cc_start: 0.8125 (ttm) cc_final: 0.7775 (ttm) REVERT: M 12 MET cc_start: 0.8449 (mmp) cc_final: 0.8098 (tmm) REVERT: M 22 MET cc_start: 0.8703 (mmp) cc_final: 0.7869 (mtt) REVERT: M 70 MET cc_start: 0.8912 (mtm) cc_final: 0.8600 (mtm) REVERT: M 141 GLU cc_start: 0.8272 (pm20) cc_final: 0.8016 (pt0) REVERT: M 222 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7506 (mm-30) REVERT: M 243 MET cc_start: 0.9330 (mtp) cc_final: 0.8997 (mtp) REVERT: M 263 MET cc_start: 0.8408 (mmt) cc_final: 0.8113 (mmt) REVERT: M 271 MET cc_start: 0.7896 (mmp) cc_final: 0.7668 (mmm) REVERT: M 374 ASN cc_start: 0.8650 (m-40) cc_final: 0.8224 (m-40) REVERT: N 36 ASN cc_start: 0.8383 (t0) cc_final: 0.7983 (t0) REVERT: N 71 MET cc_start: 0.9107 (mmm) cc_final: 0.8898 (mmm) REVERT: N 77 ASN cc_start: 0.8737 (t0) cc_final: 0.8428 (t0) REVERT: N 213 SER cc_start: 0.9328 (m) cc_final: 0.8911 (t) REVERT: N 268 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: N 313 MET cc_start: 0.7680 (mmt) cc_final: 0.7348 (mmt) REVERT: N 329 MET cc_start: 0.8367 (mtm) cc_final: 0.8158 (mtm) REVERT: V 38 TYR cc_start: 0.7605 (m-80) cc_final: 0.7326 (m-80) REVERT: V 117 MET cc_start: 0.7864 (mtp) cc_final: 0.7527 (mtp) REVERT: W 28 TYR cc_start: 0.7882 (m-10) cc_final: 0.7597 (m-10) REVERT: W 119 ASP cc_start: 0.8409 (p0) cc_final: 0.7650 (t0) REVERT: X 49 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7839 (mm-30) REVERT: X 51 ILE cc_start: 0.8741 (tt) cc_final: 0.8512 (mm) REVERT: Y 9 LEU cc_start: 0.8057 (mt) cc_final: 0.7757 (mp) REVERT: Y 18 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7523 (mtmm) REVERT: Y 51 ASP cc_start: 0.7847 (t0) cc_final: 0.7513 (t70) REVERT: Y 112 ASP cc_start: 0.7553 (m-30) cc_final: 0.7338 (m-30) REVERT: Z 42 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.6939 (tmt170) REVERT: Z 81 VAL cc_start: 0.8224 (m) cc_final: 0.8009 (t) REVERT: Z 123 ASN cc_start: 0.7496 (m-40) cc_final: 0.7028 (t0) REVERT: Z 129 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8164 (tm-30) REVERT: a 45 ASP cc_start: 0.8457 (t0) cc_final: 0.8177 (t0) REVERT: c 51 ASN cc_start: 0.8880 (t160) cc_final: 0.8621 (t0) REVERT: c 52 THR cc_start: 0.9347 (p) cc_final: 0.9030 (t) REVERT: c 90 GLU cc_start: 0.8379 (pm20) cc_final: 0.7870 (mm-30) REVERT: c 97 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8203 (tm-30) REVERT: c 114 LYS cc_start: 0.7890 (mmtm) cc_final: 0.6964 (mmmt) REVERT: d 127 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8137 (mm-30) REVERT: d 162 GLU cc_start: 0.7137 (mp0) cc_final: 0.6459 (tm-30) REVERT: d 270 PHE cc_start: 0.5300 (OUTLIER) cc_final: 0.4727 (t80) REVERT: d 271 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.3481 (mm-30) REVERT: d 281 ARG cc_start: 0.8774 (ptp90) cc_final: 0.7866 (ptt90) REVERT: e 39 ARG cc_start: 0.8005 (mtt180) cc_final: 0.6194 (mmt-90) REVERT: e 58 SER cc_start: 0.9102 (t) cc_final: 0.8492 (p) REVERT: e 59 ASP cc_start: 0.7549 (m-30) cc_final: 0.7198 (t70) REVERT: e 61 GLN cc_start: 0.7598 (mt0) cc_final: 0.6890 (mm110) REVERT: f 43 TYR cc_start: 0.8392 (t80) cc_final: 0.7951 (t80) REVERT: f 53 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8509 (tm-30) REVERT: f 57 ILE cc_start: 0.8621 (mt) cc_final: 0.8118 (mt) REVERT: f 92 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8413 (mtmm) REVERT: g 90 GLU cc_start: 0.8637 (tp30) cc_final: 0.8434 (tm-30) REVERT: h 6 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8657 (tp) REVERT: h 8 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: h 39 LYS cc_start: 0.9152 (tptm) cc_final: 0.7853 (pttt) REVERT: i 12 GLN cc_start: 0.8689 (pt0) cc_final: 0.8154 (tp40) REVERT: i 37 THR cc_start: 0.9099 (m) cc_final: 0.8780 (p) REVERT: i 51 ASP cc_start: 0.8317 (t0) cc_final: 0.7976 (t0) REVERT: i 53 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7083 (ptpp) REVERT: j 54 MET cc_start: 0.7492 (mtt) cc_final: 0.6788 (tmm) REVERT: k 37 LYS cc_start: 0.7314 (pttp) cc_final: 0.6742 (mmtt) REVERT: k 201 ASP cc_start: 0.6673 (m-30) cc_final: 0.6421 (m-30) REVERT: k 238 ILE cc_start: 0.7501 (mt) cc_final: 0.7268 (tp) REVERT: l 5 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9060 (p) REVERT: l 52 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8003 (tm-30) REVERT: l 53 LYS cc_start: 0.8490 (pttm) cc_final: 0.7978 (tptt) REVERT: l 63 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6940 (ttm-80) REVERT: m 9 LYS cc_start: 0.7154 (ttpp) cc_final: 0.6525 (mptt) REVERT: m 15 GLU cc_start: 0.8659 (mp0) cc_final: 0.8194 (mp0) REVERT: m 39 LYS cc_start: 0.8309 (ttpm) cc_final: 0.8027 (ptpp) REVERT: o 8 ARG cc_start: 0.7746 (mpt-90) cc_final: 0.6263 (mtm110) REVERT: o 11 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7724 (tp) REVERT: o 45 ASP cc_start: 0.8658 (t70) cc_final: 0.8360 (t0) REVERT: o 95 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8293 (mptt) REVERT: o 103 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5705 (tm-30) REVERT: p 60 GLU cc_start: 0.8045 (tt0) cc_final: 0.7755 (tp30) REVERT: p 79 PHE cc_start: 0.6514 (t80) cc_final: 0.6212 (t80) REVERT: p 92 PHE cc_start: 0.7896 (m-80) cc_final: 0.7659 (m-80) REVERT: p 102 TYR cc_start: 0.6919 (t80) cc_final: 0.5966 (t80) REVERT: q 9 MET cc_start: 0.8306 (mmm) cc_final: 0.8061 (mmt) REVERT: q 26 ARG cc_start: 0.7855 (tmt170) cc_final: 0.7366 (mtt90) REVERT: q 59 LEU cc_start: 0.7859 (mt) cc_final: 0.7390 (tt) REVERT: q 130 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7821 (mm-30) REVERT: r 75 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6207 (mt) REVERT: r 109 ILE cc_start: 0.7844 (mm) cc_final: 0.7581 (mp) REVERT: s 28 TYR cc_start: 0.6947 (t80) cc_final: 0.6559 (t80) REVERT: s 34 LYS cc_start: 0.6395 (ptpt) cc_final: 0.5632 (tppt) REVERT: s 71 ASP cc_start: 0.7443 (m-30) cc_final: 0.7187 (p0) REVERT: s 117 ARG cc_start: 0.2774 (ttp-170) cc_final: 0.1065 (ttt-90) REVERT: t 50 HIS cc_start: 0.7124 (t-90) cc_final: 0.6634 (t-170) REVERT: t 102 CYS cc_start: 0.8800 (m) cc_final: 0.8575 (t) REVERT: t 139 LEU cc_start: 0.8339 (tp) cc_final: 0.8066 (mt) REVERT: t 174 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7872 (mtm110) REVERT: u 14 PHE cc_start: 0.6211 (t80) cc_final: 0.5428 (p90) REVERT: v 32 GLU cc_start: 0.6967 (mp0) cc_final: 0.6668 (mp0) REVERT: v 42 MET cc_start: 0.7849 (mmm) cc_final: 0.6971 (mpp) REVERT: v 91 THR cc_start: 0.7196 (p) cc_final: 0.6984 (t) REVERT: v 102 CYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6893 (p) REVERT: v 105 LEU cc_start: 0.6951 (tp) cc_final: 0.6744 (tp) REVERT: v 157 GLU cc_start: 0.5763 (mm-30) cc_final: 0.5363 (mm-30) REVERT: w 36 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7444 (t0) REVERT: w 86 GLN cc_start: 0.8654 (tm-30) cc_final: 0.7972 (mm-40) REVERT: w 122 GLU cc_start: 0.7191 (pm20) cc_final: 0.6119 (mm-30) REVERT: y 25 TYR cc_start: 0.8134 (t80) cc_final: 0.6993 (m-10) REVERT: z 4 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7494 (mm-30) REVERT: z 17 PHE cc_start: 0.8082 (t80) cc_final: 0.7853 (t80) REVERT: z 25 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7347 (ptt90) REVERT: z 69 ILE cc_start: 0.7830 (pt) cc_final: 0.7456 (mt) outliers start: 315 outliers final: 238 residues processed: 1685 average time/residue: 0.6440 time to fit residues: 1860.9555 Evaluate side-chains 1715 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1458 time to evaluate : 5.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 122 CYS Chi-restraints excluded: chain 1 residue 149 LEU Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 1 residue 266 CYS Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 373 ASN Chi-restraints excluded: chain 1 residue 379 PHE Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 2 residue 169 ILE Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 118 ASP Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 221 GLU Chi-restraints excluded: chain 3 residue 241 SER Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 357 ASP Chi-restraints excluded: chain 3 residue 473 ILE Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 617 ASP Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 623 LEU Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 3 residue 678 SER Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 185 SER Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 410 MET Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 16 ASP Chi-restraints excluded: chain 5 residue 83 ILE Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 6 MET Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain W residue 18 ASP Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 45 THR Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 98 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 136 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 13 LEU Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain h residue 54 CYS Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 47 GLN Chi-restraints excluded: chain j residue 49 GLU Chi-restraints excluded: chain j residue 50 ILE Chi-restraints excluded: chain j residue 62 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain k residue 279 LEU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 47 GLN Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 19 ASP Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 53 GLN Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 23 ILE Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain x residue 6 GLU Chi-restraints excluded: chain y residue 34 LEU Chi-restraints excluded: chain y residue 45 LYS Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 68 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 20.0000 chunk 308 optimal weight: 5.9990 chunk 461 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 491 optimal weight: 30.0000 chunk 526 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 607 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN ** 4 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN L 116 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN N 222 ASN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN g 25 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 88 HIS u 58 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.239 69560 Z= 0.558 Angle : 1.591 50.665 94035 Z= 1.020 Chirality : 0.308 6.392 10182 Planarity : 0.004 0.060 11744 Dihedral : 11.239 159.013 10516 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.69 % Favored : 95.30 % Rotamer: Outliers : 3.95 % Allowed : 18.07 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.09), residues: 8122 helix: 0.55 (0.08), residues: 4195 sheet: -0.93 (0.26), residues: 395 loop : -0.97 (0.11), residues: 3532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP p 100 HIS 0.008 0.001 HIS N 112 PHE 0.031 0.002 PHE M 122 TYR 0.033 0.002 TYR 6 145 ARG 0.009 0.000 ARG 4 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1810 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1526 time to evaluate : 6.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 107 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: 1 145 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: 1 149 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8954 (mp) REVERT: 1 228 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9240 (p) REVERT: 1 281 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: 1 317 MET cc_start: 0.9067 (mmm) cc_final: 0.8812 (tpp) REVERT: 1 432 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6819 (ptt180) REVERT: 2 78 MET cc_start: 0.8135 (tpt) cc_final: 0.7271 (tpt) REVERT: 2 93 LYS cc_start: 0.9027 (mttm) cc_final: 0.8427 (tttm) REVERT: 2 112 ASN cc_start: 0.8146 (t0) cc_final: 0.7426 (t0) REVERT: 3 31 GLU cc_start: 0.8952 (tt0) cc_final: 0.8329 (tm-30) REVERT: 3 475 GLN cc_start: 0.6635 (mm110) cc_final: 0.6371 (tp40) REVERT: 3 476 LYS cc_start: 0.8453 (tttm) cc_final: 0.8212 (mttm) REVERT: 3 515 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7155 (ptm160) REVERT: 4 175 GLU cc_start: 0.8862 (tp30) cc_final: 0.8474 (mt-10) REVERT: 4 326 ASP cc_start: 0.8321 (t0) cc_final: 0.7992 (t0) REVERT: 4 342 MET cc_start: 0.8264 (tpt) cc_final: 0.7987 (tpt) REVERT: 4 343 GLU cc_start: 0.8813 (mp0) cc_final: 0.8426 (mp0) REVERT: 4 410 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8035 (mtm) REVERT: 5 178 ASP cc_start: 0.8539 (t0) cc_final: 0.8078 (t0) REVERT: 6 96 MET cc_start: 0.8431 (tpp) cc_final: 0.7966 (mmt) REVERT: 6 111 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8753 (ptt90) REVERT: 6 125 TYR cc_start: 0.9330 (t80) cc_final: 0.8856 (t80) REVERT: 6 156 LEU cc_start: 0.9493 (tp) cc_final: 0.9213 (tp) REVERT: A 1 MET cc_start: 0.6896 (tpp) cc_final: 0.5589 (ptt) REVERT: A 87 MET cc_start: 0.8241 (tmt) cc_final: 0.7974 (tmt) REVERT: H 1 MET cc_start: 0.6372 (ttp) cc_final: 0.5516 (mmt) REVERT: H 30 TYR cc_start: 0.8843 (m-80) cc_final: 0.8535 (m-80) REVERT: H 235 ASN cc_start: 0.8858 (t0) cc_final: 0.8576 (t0) REVERT: H 258 ASN cc_start: 0.7986 (t0) cc_final: 0.7557 (t0) REVERT: H 286 MET cc_start: 0.9112 (tpp) cc_final: 0.8819 (mmm) REVERT: J 2 MET cc_start: 0.8402 (tpt) cc_final: 0.7934 (mtt) REVERT: J 87 LYS cc_start: 0.8003 (ptpt) cc_final: 0.6653 (tmtt) REVERT: J 143 ILE cc_start: 0.9168 (mt) cc_final: 0.8877 (mt) REVERT: L 3 LEU cc_start: 0.8672 (tp) cc_final: 0.8270 (tt) REVERT: L 79 SER cc_start: 0.7497 (p) cc_final: 0.6820 (m) REVERT: L 82 MET cc_start: 0.8305 (mmt) cc_final: 0.7867 (mmt) REVERT: L 128 MET cc_start: 0.8204 (tpt) cc_final: 0.7631 (tmm) REVERT: L 270 ASN cc_start: 0.8754 (t0) cc_final: 0.8535 (t0) REVERT: L 354 GLN cc_start: 0.6503 (mt0) cc_final: 0.5850 (tt0) REVERT: L 386 LEU cc_start: 0.7193 (mt) cc_final: 0.6732 (tp) REVERT: L 445 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: L 589 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.7983 (mt) REVERT: M 10 MET cc_start: 0.8096 (ttm) cc_final: 0.7840 (ttm) REVERT: M 12 MET cc_start: 0.8403 (mmp) cc_final: 0.8055 (tmm) REVERT: M 22 MET cc_start: 0.8690 (mmp) cc_final: 0.7832 (mtt) REVERT: M 141 GLU cc_start: 0.8318 (pm20) cc_final: 0.8073 (pt0) REVERT: M 222 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7490 (mm-30) REVERT: M 243 MET cc_start: 0.9302 (mtp) cc_final: 0.8967 (mtp) REVERT: M 263 MET cc_start: 0.8377 (mmt) cc_final: 0.8103 (mmt) REVERT: M 271 MET cc_start: 0.7856 (mmp) cc_final: 0.7655 (mmm) REVERT: M 325 MET cc_start: 0.9131 (tpt) cc_final: 0.8923 (tpt) REVERT: M 374 ASN cc_start: 0.8564 (m-40) cc_final: 0.8140 (m-40) REVERT: N 36 ASN cc_start: 0.8337 (t0) cc_final: 0.7950 (t0) REVERT: N 77 ASN cc_start: 0.8739 (t0) cc_final: 0.8507 (t0) REVERT: N 213 SER cc_start: 0.9298 (m) cc_final: 0.8853 (t) REVERT: N 268 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: N 329 MET cc_start: 0.8330 (mtm) cc_final: 0.8077 (mtm) REVERT: V 38 TYR cc_start: 0.7540 (m-80) cc_final: 0.7278 (m-80) REVERT: V 117 MET cc_start: 0.7801 (mtp) cc_final: 0.7458 (mtp) REVERT: W 28 TYR cc_start: 0.7868 (m-10) cc_final: 0.7565 (m-10) REVERT: W 119 ASP cc_start: 0.8399 (p0) cc_final: 0.7661 (t0) REVERT: X 49 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7816 (mm-30) REVERT: X 51 ILE cc_start: 0.8687 (tt) cc_final: 0.8433 (mm) REVERT: Y 18 LYS cc_start: 0.8055 (mmmm) cc_final: 0.7468 (mttp) REVERT: Y 51 ASP cc_start: 0.7787 (t0) cc_final: 0.7504 (t70) REVERT: Z 42 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.6904 (tmt170) REVERT: Z 81 VAL cc_start: 0.8246 (m) cc_final: 0.8014 (t) REVERT: Z 100 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7658 (mm-30) REVERT: Z 113 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8184 (tm-30) REVERT: Z 123 ASN cc_start: 0.7238 (m110) cc_final: 0.6936 (t0) REVERT: a 45 ASP cc_start: 0.8459 (t0) cc_final: 0.8198 (t0) REVERT: c 51 ASN cc_start: 0.8855 (t160) cc_final: 0.8621 (t0) REVERT: c 90 GLU cc_start: 0.8371 (pm20) cc_final: 0.7847 (mm-30) REVERT: c 97 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8216 (tm-30) REVERT: d 127 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8026 (mm-30) REVERT: d 162 GLU cc_start: 0.7110 (mp0) cc_final: 0.6419 (tm-30) REVERT: d 270 PHE cc_start: 0.5243 (OUTLIER) cc_final: 0.4712 (t80) REVERT: d 271 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.3456 (mm-30) REVERT: d 281 ARG cc_start: 0.8763 (ptp90) cc_final: 0.7853 (ptt90) REVERT: e 39 ARG cc_start: 0.7965 (mtt180) cc_final: 0.6204 (mmt-90) REVERT: e 58 SER cc_start: 0.9121 (t) cc_final: 0.8547 (p) REVERT: e 59 ASP cc_start: 0.7559 (m-30) cc_final: 0.7249 (t70) REVERT: e 61 GLN cc_start: 0.7584 (mt0) cc_final: 0.6942 (mm110) REVERT: f 43 TYR cc_start: 0.8376 (t80) cc_final: 0.7962 (t80) REVERT: f 53 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8521 (tm-30) REVERT: f 57 ILE cc_start: 0.8620 (mt) cc_final: 0.8138 (mt) REVERT: f 92 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8493 (mtmm) REVERT: h 6 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8646 (tp) REVERT: h 8 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: h 39 LYS cc_start: 0.9162 (tptm) cc_final: 0.7867 (pttt) REVERT: i 12 GLN cc_start: 0.8670 (pt0) cc_final: 0.8148 (tp40) REVERT: i 37 THR cc_start: 0.9086 (m) cc_final: 0.8740 (p) REVERT: i 53 LYS cc_start: 0.7702 (mmtm) cc_final: 0.7002 (ptpp) REVERT: j 54 MET cc_start: 0.7435 (mtt) cc_final: 0.6749 (tmm) REVERT: k 37 LYS cc_start: 0.7281 (pttp) cc_final: 0.6696 (mmtt) REVERT: k 201 ASP cc_start: 0.6655 (m-30) cc_final: 0.6409 (m-30) REVERT: k 238 ILE cc_start: 0.7337 (mt) cc_final: 0.7112 (tp) REVERT: l 5 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9045 (p) REVERT: l 53 LYS cc_start: 0.8479 (pttm) cc_final: 0.8098 (tptt) REVERT: l 63 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6906 (ttm-80) REVERT: m 9 LYS cc_start: 0.7162 (ttpp) cc_final: 0.6520 (mptt) REVERT: m 15 GLU cc_start: 0.8614 (mp0) cc_final: 0.8181 (mp0) REVERT: m 39 LYS cc_start: 0.8241 (ttpm) cc_final: 0.7969 (ptpp) REVERT: o 8 ARG cc_start: 0.7669 (mpt-90) cc_final: 0.6146 (mtm110) REVERT: o 11 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7730 (tp) REVERT: o 45 ASP cc_start: 0.8626 (t70) cc_final: 0.8322 (t0) REVERT: o 95 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8289 (mptt) REVERT: o 103 GLU cc_start: 0.5955 (mm-30) cc_final: 0.5686 (tm-30) REVERT: p 34 GLU cc_start: 0.7510 (tt0) cc_final: 0.7194 (tt0) REVERT: p 60 GLU cc_start: 0.8007 (tt0) cc_final: 0.7747 (tp30) REVERT: p 79 PHE cc_start: 0.6492 (t80) cc_final: 0.6174 (t80) REVERT: p 92 PHE cc_start: 0.7885 (m-80) cc_final: 0.7656 (m-80) REVERT: p 102 TYR cc_start: 0.6936 (t80) cc_final: 0.5979 (t80) REVERT: q 9 MET cc_start: 0.8263 (mmm) cc_final: 0.8043 (mmt) REVERT: q 26 ARG cc_start: 0.7775 (tmt170) cc_final: 0.7236 (mtt90) REVERT: q 59 LEU cc_start: 0.7819 (mt) cc_final: 0.7353 (tt) REVERT: q 130 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7815 (mm-30) REVERT: r 75 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6233 (mt) REVERT: r 109 ILE cc_start: 0.7796 (mm) cc_final: 0.7520 (mp) REVERT: r 121 GLU cc_start: 0.7483 (tp30) cc_final: 0.7017 (tm-30) REVERT: s 28 TYR cc_start: 0.6856 (t80) cc_final: 0.6482 (t80) REVERT: s 34 LYS cc_start: 0.6378 (ptpt) cc_final: 0.5606 (tppt) REVERT: s 71 ASP cc_start: 0.7467 (m-30) cc_final: 0.7161 (p0) REVERT: s 117 ARG cc_start: 0.2745 (ttp-170) cc_final: 0.1237 (mtp-110) REVERT: t 20 LYS cc_start: 0.8437 (tmmt) cc_final: 0.7601 (ttmm) REVERT: t 50 HIS cc_start: 0.7177 (t-90) cc_final: 0.6664 (t-170) REVERT: t 139 LEU cc_start: 0.8314 (tp) cc_final: 0.7982 (mt) REVERT: t 174 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7705 (mtm110) REVERT: u 14 PHE cc_start: 0.6234 (t80) cc_final: 0.5424 (p90) REVERT: v 32 GLU cc_start: 0.6944 (mp0) cc_final: 0.6584 (mp0) REVERT: v 42 MET cc_start: 0.7787 (mmm) cc_final: 0.6906 (mpp) REVERT: v 91 THR cc_start: 0.7154 (p) cc_final: 0.6926 (t) REVERT: v 102 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6871 (p) REVERT: v 105 LEU cc_start: 0.6939 (tp) cc_final: 0.6719 (tp) REVERT: w 26 TRP cc_start: 0.5185 (p-90) cc_final: 0.4619 (p-90) REVERT: w 36 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7381 (t0) REVERT: w 86 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8052 (tp40) REVERT: w 122 GLU cc_start: 0.7180 (pm20) cc_final: 0.6132 (mm-30) REVERT: y 25 TYR cc_start: 0.8143 (t80) cc_final: 0.6977 (m-10) REVERT: z 25 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7335 (ptt90) REVERT: z 69 ILE cc_start: 0.7794 (pt) cc_final: 0.7396 (mt) outliers start: 284 outliers final: 231 residues processed: 1677 average time/residue: 0.6462 time to fit residues: 1860.4241 Evaluate side-chains 1722 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1471 time to evaluate : 6.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 122 CYS Chi-restraints excluded: chain 1 residue 145 GLU Chi-restraints excluded: chain 1 residue 149 LEU Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 1 residue 248 GLU Chi-restraints excluded: chain 1 residue 266 CYS Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 379 PHE Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 2 residue 169 ILE Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 118 ASP Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 221 GLU Chi-restraints excluded: chain 3 residue 241 SER Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 357 ASP Chi-restraints excluded: chain 3 residue 473 ILE Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 617 ASP Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 623 LEU Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 3 residue 678 SER Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 185 SER Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 410 MET Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 16 ASP Chi-restraints excluded: chain 5 residue 83 ILE Chi-restraints excluded: chain 5 residue 201 SER Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 290 SER Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 37 MET Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 136 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain h residue 54 CYS Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 100 VAL Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 47 GLN Chi-restraints excluded: chain j residue 50 ILE Chi-restraints excluded: chain j residue 62 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain k residue 267 LEU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 53 GLN Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 69 LEU Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 69 VAL Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 97 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 9.9990 chunk 740 optimal weight: 30.0000 chunk 675 optimal weight: 30.0000 chunk 720 optimal weight: 6.9990 chunk 433 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 565 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 650 optimal weight: 0.9980 chunk 681 optimal weight: 2.9990 chunk 717 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 55 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69560 Z= 0.549 Angle : 1.588 50.628 94035 Z= 1.018 Chirality : 0.308 6.387 10182 Planarity : 0.004 0.060 11744 Dihedral : 10.953 158.969 10516 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.69 % Favored : 95.30 % Rotamer: Outliers : 3.67 % Allowed : 18.51 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.10), residues: 8122 helix: 0.65 (0.08), residues: 4195 sheet: -0.79 (0.27), residues: 386 loop : -0.88 (0.11), residues: 3541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP p 100 HIS 0.008 0.001 HIS N 112 PHE 0.031 0.002 PHE M 122 TYR 0.045 0.002 TYR p 46 ARG 0.009 0.000 ARG 4 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1552 time to evaluate : 6.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 107 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: 1 145 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: 1 149 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8932 (mp) REVERT: 1 228 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9215 (p) REVERT: 1 281 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: 1 317 MET cc_start: 0.9070 (mmm) cc_final: 0.8821 (tpp) REVERT: 1 432 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6772 (ptt180) REVERT: 2 43 LYS cc_start: 0.9039 (tttt) cc_final: 0.8483 (ttmm) REVERT: 2 78 MET cc_start: 0.8009 (tpt) cc_final: 0.7281 (tpt) REVERT: 2 93 LYS cc_start: 0.9016 (mttm) cc_final: 0.8446 (tttm) REVERT: 2 112 ASN cc_start: 0.8111 (t0) cc_final: 0.7382 (t0) REVERT: 3 31 GLU cc_start: 0.8942 (tt0) cc_final: 0.8344 (tm-30) REVERT: 3 121 MET cc_start: 0.8890 (mmm) cc_final: 0.8519 (mmm) REVERT: 3 259 ASN cc_start: 0.9194 (p0) cc_final: 0.8504 (p0) REVERT: 3 475 GLN cc_start: 0.6413 (mm110) cc_final: 0.6159 (tp40) REVERT: 3 476 LYS cc_start: 0.8370 (tttm) cc_final: 0.8115 (mmtp) REVERT: 3 515 ARG cc_start: 0.7640 (mtt-85) cc_final: 0.7143 (ptm160) REVERT: 3 568 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7705 (mt-10) REVERT: 4 171 PHE cc_start: 0.8939 (m-10) cc_final: 0.8674 (m-10) REVERT: 4 175 GLU cc_start: 0.8854 (tp30) cc_final: 0.8463 (mt-10) REVERT: 4 232 ASN cc_start: 0.9059 (t0) cc_final: 0.8511 (t0) REVERT: 4 326 ASP cc_start: 0.8279 (t0) cc_final: 0.7952 (t0) REVERT: 4 342 MET cc_start: 0.8126 (tpt) cc_final: 0.7837 (tpt) REVERT: 4 343 GLU cc_start: 0.8793 (mp0) cc_final: 0.8350 (mp0) REVERT: 4 410 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: 6 96 MET cc_start: 0.8398 (tpp) cc_final: 0.8032 (mmt) REVERT: 6 111 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8733 (ptt90) REVERT: 6 125 TYR cc_start: 0.9318 (t80) cc_final: 0.8721 (t80) REVERT: 6 156 LEU cc_start: 0.9461 (tp) cc_final: 0.9147 (tp) REVERT: 9 14 MET cc_start: 0.7675 (tpt) cc_final: 0.7385 (tpt) REVERT: 9 93 THR cc_start: 0.9371 (m) cc_final: 0.8930 (t) REVERT: A 1 MET cc_start: 0.6843 (tpp) cc_final: 0.5591 (ptt) REVERT: A 87 MET cc_start: 0.8247 (tmt) cc_final: 0.7989 (tmt) REVERT: H 1 MET cc_start: 0.6308 (ttp) cc_final: 0.5648 (mmt) REVERT: H 30 TYR cc_start: 0.8772 (m-80) cc_final: 0.8426 (m-80) REVERT: H 235 ASN cc_start: 0.8833 (t0) cc_final: 0.8630 (t0) REVERT: H 258 ASN cc_start: 0.7950 (t0) cc_final: 0.7517 (t0) REVERT: J 2 MET cc_start: 0.8387 (tpt) cc_final: 0.7943 (mtt) REVERT: J 87 LYS cc_start: 0.7995 (ptpt) cc_final: 0.6555 (tmtt) REVERT: J 111 LYS cc_start: 0.7475 (tppt) cc_final: 0.7000 (tppt) REVERT: J 143 ILE cc_start: 0.9158 (mt) cc_final: 0.8743 (mt) REVERT: L 3 LEU cc_start: 0.8676 (tp) cc_final: 0.8233 (tt) REVERT: L 79 SER cc_start: 0.7420 (p) cc_final: 0.6712 (m) REVERT: L 82 MET cc_start: 0.8292 (mmt) cc_final: 0.7911 (mmt) REVERT: L 128 MET cc_start: 0.8159 (tpt) cc_final: 0.7609 (tmm) REVERT: L 268 GLU cc_start: 0.8477 (pt0) cc_final: 0.8223 (pm20) REVERT: L 270 ASN cc_start: 0.8729 (t0) cc_final: 0.8515 (t0) REVERT: L 354 GLN cc_start: 0.6438 (mt0) cc_final: 0.5726 (tt0) REVERT: L 588 PHE cc_start: 0.8959 (m-80) cc_final: 0.8685 (m-80) REVERT: L 589 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.7944 (mt) REVERT: M 10 MET cc_start: 0.8094 (ttm) cc_final: 0.7847 (ttm) REVERT: M 12 MET cc_start: 0.8319 (mmp) cc_final: 0.7971 (tmm) REVERT: M 22 MET cc_start: 0.8603 (mmp) cc_final: 0.7698 (mtt) REVERT: M 141 GLU cc_start: 0.8285 (pm20) cc_final: 0.8067 (pt0) REVERT: M 222 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7444 (mm-30) REVERT: M 243 MET cc_start: 0.9290 (mtp) cc_final: 0.9000 (mtp) REVERT: M 263 MET cc_start: 0.8362 (mmt) cc_final: 0.8095 (mmt) REVERT: M 271 MET cc_start: 0.7837 (mmp) cc_final: 0.7629 (mmm) REVERT: M 279 GLN cc_start: 0.8857 (tp40) cc_final: 0.8451 (tp40) REVERT: M 325 MET cc_start: 0.9277 (tpt) cc_final: 0.8878 (tpt) REVERT: M 374 ASN cc_start: 0.8475 (m-40) cc_final: 0.8083 (m-40) REVERT: N 36 ASN cc_start: 0.8241 (t0) cc_final: 0.7848 (t0) REVERT: N 77 ASN cc_start: 0.8750 (t0) cc_final: 0.8434 (t0) REVERT: N 213 SER cc_start: 0.9298 (m) cc_final: 0.8846 (t) REVERT: N 268 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: N 329 MET cc_start: 0.8346 (mtm) cc_final: 0.8088 (mtm) REVERT: V 38 TYR cc_start: 0.7469 (m-80) cc_final: 0.7194 (m-80) REVERT: V 117 MET cc_start: 0.7782 (mtp) cc_final: 0.7480 (mtp) REVERT: W 28 TYR cc_start: 0.7822 (m-10) cc_final: 0.7409 (m-10) REVERT: W 91 MET cc_start: 0.7867 (mmt) cc_final: 0.7543 (mmm) REVERT: W 119 ASP cc_start: 0.8418 (p0) cc_final: 0.7710 (t0) REVERT: X 49 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7811 (mm-30) REVERT: X 51 ILE cc_start: 0.8717 (tt) cc_final: 0.8466 (mm) REVERT: Y 18 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7476 (mttp) REVERT: Y 51 ASP cc_start: 0.7819 (t0) cc_final: 0.7321 (t70) REVERT: Z 42 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.6865 (tmt170) REVERT: Z 81 VAL cc_start: 0.8233 (m) cc_final: 0.7996 (t) REVERT: Z 113 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8173 (tm-30) REVERT: Z 123 ASN cc_start: 0.7195 (m110) cc_final: 0.6922 (t0) REVERT: a 45 ASP cc_start: 0.8510 (t0) cc_final: 0.8273 (t0) REVERT: c 36 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7769 (mtp-110) REVERT: c 51 ASN cc_start: 0.8838 (t160) cc_final: 0.8558 (t0) REVERT: c 52 THR cc_start: 0.9338 (p) cc_final: 0.9040 (t) REVERT: c 90 GLU cc_start: 0.8342 (pm20) cc_final: 0.7807 (mm-30) REVERT: c 97 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8261 (tm-30) REVERT: d 32 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7420 (ttm-80) REVERT: d 127 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8052 (mm-30) REVERT: d 162 GLU cc_start: 0.6895 (mp0) cc_final: 0.6369 (tm-30) REVERT: d 270 PHE cc_start: 0.5039 (OUTLIER) cc_final: 0.4583 (t80) REVERT: d 271 GLU cc_start: 0.5376 (OUTLIER) cc_final: 0.3443 (mm-30) REVERT: d 281 ARG cc_start: 0.8751 (ptp90) cc_final: 0.7843 (ptt90) REVERT: e 39 ARG cc_start: 0.7931 (mtt180) cc_final: 0.6182 (mmt-90) REVERT: e 58 SER cc_start: 0.9099 (t) cc_final: 0.8520 (p) REVERT: e 59 ASP cc_start: 0.7512 (m-30) cc_final: 0.7210 (t70) REVERT: e 61 GLN cc_start: 0.7550 (mt0) cc_final: 0.6959 (mm110) REVERT: f 43 TYR cc_start: 0.8359 (t80) cc_final: 0.7968 (t80) REVERT: f 53 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8505 (tm-30) REVERT: f 57 ILE cc_start: 0.8605 (mt) cc_final: 0.8130 (mt) REVERT: f 94 ILE cc_start: 0.8725 (mt) cc_final: 0.8521 (mp) REVERT: h 6 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8628 (tp) REVERT: h 8 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: h 39 LYS cc_start: 0.9171 (tptm) cc_final: 0.8161 (ttpt) REVERT: i 12 GLN cc_start: 0.8673 (pt0) cc_final: 0.8150 (tp40) REVERT: i 37 THR cc_start: 0.9083 (m) cc_final: 0.8733 (p) REVERT: i 53 LYS cc_start: 0.7690 (mmtm) cc_final: 0.6982 (ptpp) REVERT: j 49 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7651 (mt-10) REVERT: j 54 MET cc_start: 0.7422 (mtt) cc_final: 0.6721 (tmm) REVERT: k 37 LYS cc_start: 0.7233 (pttp) cc_final: 0.6612 (mmtt) REVERT: k 201 ASP cc_start: 0.6609 (m-30) cc_final: 0.6369 (m-30) REVERT: k 238 ILE cc_start: 0.7320 (mt) cc_final: 0.7088 (tp) REVERT: l 5 VAL cc_start: 0.9259 (m) cc_final: 0.9002 (p) REVERT: l 53 LYS cc_start: 0.8461 (pttm) cc_final: 0.8015 (tptt) REVERT: m 9 LYS cc_start: 0.7168 (ttpp) cc_final: 0.6524 (mptt) REVERT: m 15 GLU cc_start: 0.8563 (mp0) cc_final: 0.8114 (mp0) REVERT: m 39 LYS cc_start: 0.8192 (ttpm) cc_final: 0.7921 (ptpp) REVERT: o 8 ARG cc_start: 0.7672 (mpt-90) cc_final: 0.6172 (mtm110) REVERT: o 11 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7676 (tp) REVERT: o 45 ASP cc_start: 0.8618 (t70) cc_final: 0.8289 (t0) REVERT: o 95 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8301 (mptt) REVERT: o 103 GLU cc_start: 0.5983 (mm-30) cc_final: 0.5688 (tm-30) REVERT: p 34 GLU cc_start: 0.7531 (tt0) cc_final: 0.7263 (tt0) REVERT: p 60 GLU cc_start: 0.7984 (tt0) cc_final: 0.7742 (tp30) REVERT: p 79 PHE cc_start: 0.6478 (t80) cc_final: 0.6169 (t80) REVERT: p 92 PHE cc_start: 0.7853 (m-80) cc_final: 0.7639 (m-80) REVERT: p 102 TYR cc_start: 0.6933 (t80) cc_final: 0.5974 (t80) REVERT: q 9 MET cc_start: 0.8268 (mmm) cc_final: 0.8049 (mmt) REVERT: q 26 ARG cc_start: 0.7748 (tmt170) cc_final: 0.7230 (mtt90) REVERT: q 59 LEU cc_start: 0.7824 (mt) cc_final: 0.7378 (tt) REVERT: q 130 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7833 (mm-30) REVERT: r 75 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6261 (mt) REVERT: r 109 ILE cc_start: 0.7764 (mm) cc_final: 0.7489 (mp) REVERT: r 121 GLU cc_start: 0.7481 (tp30) cc_final: 0.7035 (tm-30) REVERT: s 21 MET cc_start: 0.7502 (ptt) cc_final: 0.7093 (ptt) REVERT: s 28 TYR cc_start: 0.6831 (t80) cc_final: 0.6477 (t80) REVERT: s 34 LYS cc_start: 0.6425 (ptpt) cc_final: 0.5644 (tppt) REVERT: s 71 ASP cc_start: 0.7462 (m-30) cc_final: 0.7175 (p0) REVERT: s 117 ARG cc_start: 0.2787 (ttp-170) cc_final: 0.0942 (mtp-110) REVERT: t 50 HIS cc_start: 0.7169 (t-90) cc_final: 0.6658 (t-170) REVERT: t 139 LEU cc_start: 0.8327 (tp) cc_final: 0.8045 (mt) REVERT: t 174 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7683 (mtm110) REVERT: u 14 PHE cc_start: 0.6215 (t80) cc_final: 0.5398 (p90) REVERT: v 7 ASP cc_start: 0.6953 (p0) cc_final: 0.6300 (m-30) REVERT: v 32 GLU cc_start: 0.6962 (mp0) cc_final: 0.6601 (mp0) REVERT: v 42 MET cc_start: 0.7747 (mmm) cc_final: 0.6845 (mpp) REVERT: v 102 CYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6899 (p) REVERT: v 105 LEU cc_start: 0.6831 (tp) cc_final: 0.6598 (tp) REVERT: w 26 TRP cc_start: 0.5050 (p-90) cc_final: 0.4485 (p-90) REVERT: w 36 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7307 (t0) REVERT: w 86 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8039 (tp40) REVERT: w 122 GLU cc_start: 0.7169 (pm20) cc_final: 0.6130 (mm-30) REVERT: y 25 TYR cc_start: 0.8125 (t80) cc_final: 0.6944 (m-10) REVERT: z 25 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7283 (ptt90) REVERT: z 69 ILE cc_start: 0.7638 (pt) cc_final: 0.7272 (mt) outliers start: 264 outliers final: 210 residues processed: 1697 average time/residue: 0.6447 time to fit residues: 1883.9341 Evaluate side-chains 1692 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1464 time to evaluate : 5.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 122 CYS Chi-restraints excluded: chain 1 residue 145 GLU Chi-restraints excluded: chain 1 residue 149 LEU Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 1 residue 248 GLU Chi-restraints excluded: chain 1 residue 266 CYS Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 373 ASN Chi-restraints excluded: chain 1 residue 379 PHE Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 2 residue 169 ILE Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 118 ASP Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 221 GLU Chi-restraints excluded: chain 3 residue 241 SER Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 357 ASP Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 623 LEU Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 185 SER Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 410 MET Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 83 ILE Chi-restraints excluded: chain 5 residue 201 SER Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 37 MET Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 98 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 136 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 270 PHE Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 13 LEU Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 62 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain k residue 267 LEU Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 89 ASN Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 53 GLN Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 20 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain u residue 66 ILE Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 69 LEU Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 6.9990 chunk 761 optimal weight: 20.0000 chunk 464 optimal weight: 9.9990 chunk 361 optimal weight: 0.0060 chunk 529 optimal weight: 20.0000 chunk 798 optimal weight: 20.0000 chunk 735 optimal weight: 7.9990 chunk 636 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 491 optimal weight: 20.0000 chunk 390 optimal weight: 6.9990 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN M 374 ASN N 222 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 58 GLN v 55 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.239 69560 Z= 0.567 Angle : 1.602 50.673 94035 Z= 1.024 Chirality : 0.308 6.388 10182 Planarity : 0.004 0.066 11744 Dihedral : 10.946 158.270 10516 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.00 % Favored : 94.99 % Rotamer: Outliers : 3.56 % Allowed : 19.03 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.09), residues: 8122 helix: 0.62 (0.08), residues: 4192 sheet: -0.79 (0.27), residues: 385 loop : -0.88 (0.11), residues: 3545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP z 2 HIS 0.008 0.001 HIS N 112 PHE 0.030 0.002 PHE z 17 TYR 0.044 0.002 TYR Z 142 ARG 0.009 0.000 ARG 4 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1742 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1486 time to evaluate : 6.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 107 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: 1 145 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: 1 228 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9218 (p) REVERT: 1 281 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: 1 317 MET cc_start: 0.9070 (mmm) cc_final: 0.8839 (tpp) REVERT: 1 432 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6787 (ptt180) REVERT: 2 78 MET cc_start: 0.8011 (tpt) cc_final: 0.7262 (tpt) REVERT: 2 93 LYS cc_start: 0.9056 (mttm) cc_final: 0.8470 (tttm) REVERT: 2 112 ASN cc_start: 0.8115 (t0) cc_final: 0.7400 (t0) REVERT: 3 121 MET cc_start: 0.8899 (mmm) cc_final: 0.8506 (mmm) REVERT: 3 259 ASN cc_start: 0.9188 (p0) cc_final: 0.8503 (p0) REVERT: 3 475 GLN cc_start: 0.6407 (mm110) cc_final: 0.5990 (tp40) REVERT: 3 476 LYS cc_start: 0.8430 (tttm) cc_final: 0.8130 (mmtp) REVERT: 3 515 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7124 (ptm160) REVERT: 4 171 PHE cc_start: 0.8932 (m-10) cc_final: 0.8588 (m-10) REVERT: 4 175 GLU cc_start: 0.8866 (tp30) cc_final: 0.8454 (mt-10) REVERT: 4 232 ASN cc_start: 0.9060 (t0) cc_final: 0.8525 (t0) REVERT: 4 326 ASP cc_start: 0.8296 (t0) cc_final: 0.7862 (t70) REVERT: 4 343 GLU cc_start: 0.8841 (mp0) cc_final: 0.8433 (mp0) REVERT: 6 96 MET cc_start: 0.8404 (tpp) cc_final: 0.8152 (mmt) REVERT: 6 111 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8496 (ptt90) REVERT: 6 125 TYR cc_start: 0.9338 (t80) cc_final: 0.8823 (t80) REVERT: 6 156 LEU cc_start: 0.9452 (tp) cc_final: 0.9214 (tp) REVERT: 6 168 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8386 (tttt) REVERT: 9 14 MET cc_start: 0.7619 (tpt) cc_final: 0.7325 (tpt) REVERT: 9 93 THR cc_start: 0.9354 (m) cc_final: 0.8987 (t) REVERT: A 1 MET cc_start: 0.6903 (tpp) cc_final: 0.5630 (ptt) REVERT: H 1 MET cc_start: 0.6321 (ttp) cc_final: 0.5623 (mmt) REVERT: H 30 TYR cc_start: 0.8830 (m-80) cc_final: 0.8516 (m-80) REVERT: H 70 MET cc_start: 0.8839 (ttp) cc_final: 0.7927 (ttp) REVERT: H 121 TRP cc_start: 0.7968 (t60) cc_final: 0.7614 (t60) REVERT: H 235 ASN cc_start: 0.8878 (t0) cc_final: 0.8652 (t0) REVERT: H 258 ASN cc_start: 0.8033 (t0) cc_final: 0.7615 (t0) REVERT: J 2 MET cc_start: 0.8431 (tpt) cc_final: 0.7959 (mtt) REVERT: J 28 TYR cc_start: 0.8187 (m-80) cc_final: 0.7726 (m-10) REVERT: J 55 MET cc_start: 0.9211 (mmp) cc_final: 0.8956 (mmm) REVERT: J 87 LYS cc_start: 0.8009 (ptpt) cc_final: 0.6651 (tmtt) REVERT: J 111 LYS cc_start: 0.7442 (tppt) cc_final: 0.6998 (tppt) REVERT: J 139 GLU cc_start: 0.8034 (pm20) cc_final: 0.7815 (pm20) REVERT: J 143 ILE cc_start: 0.9223 (mt) cc_final: 0.8946 (mt) REVERT: L 79 SER cc_start: 0.7504 (p) cc_final: 0.6753 (m) REVERT: L 82 MET cc_start: 0.8311 (mmt) cc_final: 0.7871 (mmt) REVERT: L 128 MET cc_start: 0.8185 (tpt) cc_final: 0.7695 (tmm) REVERT: L 224 SER cc_start: 0.9108 (m) cc_final: 0.8769 (t) REVERT: L 268 GLU cc_start: 0.8465 (pt0) cc_final: 0.8198 (pm20) REVERT: L 270 ASN cc_start: 0.8753 (t0) cc_final: 0.8552 (t0) REVERT: L 314 MET cc_start: 0.8014 (tpp) cc_final: 0.7463 (tpp) REVERT: M 10 MET cc_start: 0.8133 (ttm) cc_final: 0.7861 (ttm) REVERT: M 12 MET cc_start: 0.8329 (mmp) cc_final: 0.7974 (tmm) REVERT: M 22 MET cc_start: 0.8649 (mmp) cc_final: 0.7808 (mtt) REVERT: M 141 GLU cc_start: 0.8314 (pm20) cc_final: 0.8084 (pt0) REVERT: M 222 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7388 (mm-30) REVERT: M 243 MET cc_start: 0.9298 (mtp) cc_final: 0.9000 (mtp) REVERT: M 263 MET cc_start: 0.8369 (mmt) cc_final: 0.8069 (mmt) REVERT: M 271 MET cc_start: 0.7855 (mmp) cc_final: 0.7642 (mmm) REVERT: M 279 GLN cc_start: 0.8869 (tp40) cc_final: 0.8461 (tp40) REVERT: M 325 MET cc_start: 0.9312 (tpt) cc_final: 0.8983 (tpt) REVERT: M 374 ASN cc_start: 0.8543 (m110) cc_final: 0.8155 (m-40) REVERT: N 36 ASN cc_start: 0.8222 (t0) cc_final: 0.7832 (t0) REVERT: N 77 ASN cc_start: 0.8736 (t0) cc_final: 0.8398 (t0) REVERT: N 213 SER cc_start: 0.9314 (m) cc_final: 0.8854 (t) REVERT: N 268 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: N 329 MET cc_start: 0.8359 (mtm) cc_final: 0.8106 (mtm) REVERT: V 38 TYR cc_start: 0.7569 (m-80) cc_final: 0.7179 (m-80) REVERT: V 117 MET cc_start: 0.7775 (mtp) cc_final: 0.7483 (mtp) REVERT: W 91 MET cc_start: 0.7897 (mmt) cc_final: 0.7560 (mmm) REVERT: W 119 ASP cc_start: 0.8461 (p0) cc_final: 0.7731 (t0) REVERT: X 49 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7818 (mm-30) REVERT: Y 18 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7594 (mppt) REVERT: Y 51 ASP cc_start: 0.7818 (t0) cc_final: 0.7519 (t70) REVERT: Z 42 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.6835 (tmt170) REVERT: Z 81 VAL cc_start: 0.8266 (m) cc_final: 0.8032 (t) REVERT: Z 123 ASN cc_start: 0.7153 (m110) cc_final: 0.6879 (t0) REVERT: a 45 ASP cc_start: 0.8532 (t0) cc_final: 0.8324 (t0) REVERT: c 36 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7756 (mtp-110) REVERT: c 51 ASN cc_start: 0.8877 (t160) cc_final: 0.8611 (t0) REVERT: c 52 THR cc_start: 0.9353 (p) cc_final: 0.9064 (t) REVERT: c 90 GLU cc_start: 0.8331 (pm20) cc_final: 0.7830 (mm-30) REVERT: c 97 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8225 (tm-30) REVERT: d 127 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8009 (mm-30) REVERT: d 162 GLU cc_start: 0.7017 (mp0) cc_final: 0.6369 (tm-30) REVERT: d 270 PHE cc_start: 0.5028 (m-80) cc_final: 0.4575 (t80) REVERT: d 271 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.3445 (mm-30) REVERT: d 281 ARG cc_start: 0.8761 (ptp90) cc_final: 0.7851 (ptt90) REVERT: e 39 ARG cc_start: 0.7922 (mtt180) cc_final: 0.6275 (mmt-90) REVERT: e 58 SER cc_start: 0.9098 (t) cc_final: 0.8545 (p) REVERT: e 59 ASP cc_start: 0.7544 (m-30) cc_final: 0.7239 (t70) REVERT: e 61 GLN cc_start: 0.7516 (mt0) cc_final: 0.7027 (mm110) REVERT: f 43 TYR cc_start: 0.8412 (t80) cc_final: 0.8018 (t80) REVERT: f 53 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8500 (tm-30) REVERT: f 57 ILE cc_start: 0.8619 (mt) cc_final: 0.8139 (mt) REVERT: h 5 ARG cc_start: 0.7882 (tpp-160) cc_final: 0.7462 (ttp-170) REVERT: h 6 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8689 (tp) REVERT: h 8 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: h 39 LYS cc_start: 0.9185 (tptm) cc_final: 0.7892 (pttt) REVERT: i 12 GLN cc_start: 0.8689 (pt0) cc_final: 0.8164 (tp40) REVERT: i 37 THR cc_start: 0.9090 (m) cc_final: 0.8745 (p) REVERT: i 53 LYS cc_start: 0.7730 (mmtm) cc_final: 0.7023 (ptpp) REVERT: j 54 MET cc_start: 0.7380 (mtt) cc_final: 0.6717 (tmm) REVERT: k 37 LYS cc_start: 0.7283 (pttp) cc_final: 0.6719 (mmtt) REVERT: k 201 ASP cc_start: 0.6637 (m-30) cc_final: 0.6405 (m-30) REVERT: k 238 ILE cc_start: 0.7288 (mt) cc_final: 0.7086 (tp) REVERT: l 5 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9044 (p) REVERT: l 53 LYS cc_start: 0.8502 (pttm) cc_final: 0.8073 (tptt) REVERT: m 9 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6519 (mptt) REVERT: m 15 GLU cc_start: 0.8552 (mp0) cc_final: 0.8161 (mp0) REVERT: m 39 LYS cc_start: 0.8230 (ttpm) cc_final: 0.7952 (ptpp) REVERT: o 8 ARG cc_start: 0.7680 (mpt-90) cc_final: 0.6181 (mtm110) REVERT: o 11 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7723 (tp) REVERT: o 45 ASP cc_start: 0.8634 (t70) cc_final: 0.8288 (t0) REVERT: o 95 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8294 (mptt) REVERT: o 103 GLU cc_start: 0.6009 (mm-30) cc_final: 0.5652 (tm-30) REVERT: p 34 GLU cc_start: 0.7555 (tt0) cc_final: 0.7287 (tt0) REVERT: p 60 GLU cc_start: 0.8033 (tt0) cc_final: 0.7769 (tp30) REVERT: p 79 PHE cc_start: 0.6388 (t80) cc_final: 0.6103 (t80) REVERT: p 92 PHE cc_start: 0.7860 (m-80) cc_final: 0.7639 (m-80) REVERT: p 102 TYR cc_start: 0.6942 (t80) cc_final: 0.5981 (t80) REVERT: q 26 ARG cc_start: 0.7863 (tmt170) cc_final: 0.7351 (mtt90) REVERT: q 59 LEU cc_start: 0.7927 (mt) cc_final: 0.7450 (tt) REVERT: q 130 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7846 (mm-30) REVERT: r 75 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6269 (mt) REVERT: r 109 ILE cc_start: 0.7775 (mm) cc_final: 0.7500 (mp) REVERT: s 21 MET cc_start: 0.7552 (ptt) cc_final: 0.7110 (ptt) REVERT: s 28 TYR cc_start: 0.6840 (t80) cc_final: 0.6473 (t80) REVERT: s 34 LYS cc_start: 0.6431 (ptpt) cc_final: 0.5545 (tppt) REVERT: s 71 ASP cc_start: 0.7532 (m-30) cc_final: 0.7254 (p0) REVERT: s 117 ARG cc_start: 0.2671 (ttp-170) cc_final: 0.1101 (mtp-110) REVERT: t 50 HIS cc_start: 0.7193 (t-90) cc_final: 0.6675 (t-170) REVERT: t 139 LEU cc_start: 0.8305 (tp) cc_final: 0.8008 (mt) REVERT: t 174 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7701 (mtm110) REVERT: u 14 PHE cc_start: 0.6245 (t80) cc_final: 0.5381 (p90) REVERT: v 7 ASP cc_start: 0.6863 (p0) cc_final: 0.6282 (m-30) REVERT: v 32 GLU cc_start: 0.6952 (mp0) cc_final: 0.6599 (mp0) REVERT: v 42 MET cc_start: 0.7723 (mmm) cc_final: 0.6823 (mpp) REVERT: v 102 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7036 (p) REVERT: w 26 TRP cc_start: 0.5186 (p-90) cc_final: 0.4610 (p-90) REVERT: w 36 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7374 (t0) REVERT: w 86 GLN cc_start: 0.8593 (tm-30) cc_final: 0.7875 (mm-40) REVERT: w 122 GLU cc_start: 0.7190 (pm20) cc_final: 0.6106 (mm-30) REVERT: y 25 TYR cc_start: 0.8147 (t80) cc_final: 0.6945 (m-10) REVERT: z 25 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7251 (ptt90) REVERT: z 69 ILE cc_start: 0.7576 (pt) cc_final: 0.7184 (mt) outliers start: 256 outliers final: 221 residues processed: 1630 average time/residue: 0.6387 time to fit residues: 1787.0197 Evaluate side-chains 1686 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1450 time to evaluate : 6.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 122 CYS Chi-restraints excluded: chain 1 residue 145 GLU Chi-restraints excluded: chain 1 residue 162 ILE Chi-restraints excluded: chain 1 residue 185 ILE Chi-restraints excluded: chain 1 residue 225 VAL Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 1 residue 248 GLU Chi-restraints excluded: chain 1 residue 266 CYS Chi-restraints excluded: chain 1 residue 281 GLU Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 373 ASN Chi-restraints excluded: chain 1 residue 379 PHE Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 432 ARG Chi-restraints excluded: chain 2 residue 109 MET Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 168 ASP Chi-restraints excluded: chain 2 residue 169 ILE Chi-restraints excluded: chain 3 residue 81 THR Chi-restraints excluded: chain 3 residue 118 ASP Chi-restraints excluded: chain 3 residue 146 VAL Chi-restraints excluded: chain 3 residue 221 GLU Chi-restraints excluded: chain 3 residue 241 SER Chi-restraints excluded: chain 3 residue 351 THR Chi-restraints excluded: chain 3 residue 357 ASP Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 536 ASP Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 621 ASN Chi-restraints excluded: chain 3 residue 623 LEU Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 635 ASP Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 3 residue 670 ASP Chi-restraints excluded: chain 4 residue 47 LEU Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 185 SER Chi-restraints excluded: chain 4 residue 219 SER Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 420 THR Chi-restraints excluded: chain 5 residue 77 ASP Chi-restraints excluded: chain 5 residue 83 ILE Chi-restraints excluded: chain 5 residue 201 SER Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 111 ARG Chi-restraints excluded: chain 9 residue 39 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 84 GLU Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 140 SER Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 507 THR Chi-restraints excluded: chain L residue 519 THR Chi-restraints excluded: chain L residue 531 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 354 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 281 LEU Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 37 MET Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 41 ASP Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 90 GLN Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 90 VAL Chi-restraints excluded: chain d residue 136 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 254 LEU Chi-restraints excluded: chain d residue 271 GLU Chi-restraints excluded: chain d residue 280 THR Chi-restraints excluded: chain d residue 284 VAL Chi-restraints excluded: chain d residue 302 ASP Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain d residue 316 GLU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain f residue 13 LEU Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 21 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 8 GLN Chi-restraints excluded: chain h residue 54 CYS Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain i residue 96 ASP Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 120 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 39 ASP Chi-restraints excluded: chain j residue 62 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 127 SER Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 91 TYR Chi-restraints excluded: chain m residue 27 LEU Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 72 TRP Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 37 LEU Chi-restraints excluded: chain o residue 87 ASP Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain q residue 50 MET Chi-restraints excluded: chain q residue 89 ASN Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 53 GLN Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 41 CYS Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 113 MET Chi-restraints excluded: chain t residue 150 THR Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 20 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain u residue 66 ILE Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 69 LEU Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 69 VAL Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 97 VAL Chi-restraints excluded: chain w residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 4.9990 chunk 677 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 586 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 637 optimal weight: 30.0000 chunk 266 optimal weight: 9.9990 chunk 654 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN L 116 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 GLN N 222 ASN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 148 HIS ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 55 GLN ** v 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 ASN ** z 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121048 restraints weight = 135505.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123087 restraints weight = 72943.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124520 restraints weight = 46746.271| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 69560 Z= 0.552 Angle : 1.598 50.627 94035 Z= 1.021 Chirality : 0.308 6.383 10182 Planarity : 0.004 0.060 11744 Dihedral : 10.743 158.292 10516 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.36 % Favored : 95.63 % Rotamer: Outliers : 3.44 % Allowed : 19.27 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 8122 helix: 0.68 (0.08), residues: 4198 sheet: -0.79 (0.27), residues: 376 loop : -0.82 (0.11), residues: 3548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP z 2 HIS 0.008 0.001 HIS t 168 PHE 0.030 0.002 PHE M 122 TYR 0.046 0.002 TYR Z 142 ARG 0.011 0.000 ARG g 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25460.26 seconds wall clock time: 443 minutes 19.92 seconds (26599.92 seconds total)