Starting phenix.real_space_refine on Fri Feb 16 12:14:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkl_11253/02_2024/6zkl_11253_updated.pdb" } resolution = 3.1 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= 0.003 sd= 0.032 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 46 5.49 5 S 466 5.16 5 C 43687 2.51 5 N 11154 2.21 5 O 12109 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 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 642": "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 "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "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 437": "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 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "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 "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 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 58": "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 27": "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 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 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" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67492 Number of models: 1 Model: "" Number of chains: 71 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: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3427 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 397} Chain breaks: 1 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: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2498 Classifications: {'peptide': 314} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 291} Chain breaks: 1 Chain: "J" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1264 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 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: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 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: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'3PE': 1, '970': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'970': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "K" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 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: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "l" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "o" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 165 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 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: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 105.894 53.285 241.223 1.00 25.70 S ATOM 2676 SG CYS 1 359 113.062 53.803 241.891 1.00 42.93 S ATOM 4116 SG CYS 2 103 104.173 48.823 260.348 1.00 79.54 S ATOM 4150 SG CYS 2 108 102.170 46.590 262.597 1.00 55.04 S ATOM 4430 SG CYS 2 144 105.646 45.307 256.857 1.00 61.98 S ATOM 4453 SG CYS 2 148 103.926 42.308 258.384 1.00 97.99 S ATOM 5793 SG CYS 3 114 107.662 71.198 225.939 1.00 32.51 S ATOM 5732 SG CYS 3 105 102.324 74.558 227.956 1.00 36.29 S ATOM 5753 SG CYS 3 108 108.399 76.537 229.418 1.00 30.63 S ATOM 6125 SG CYS 3 156 115.118 64.203 230.758 1.00 27.88 S ATOM 6102 SG CYS 3 153 113.108 67.300 236.374 1.00 30.58 S ATOM 6149 SG CYS 3 159 119.140 68.016 234.547 1.00 62.59 S ATOM 6479 SG CYS 3 203 114.835 70.432 230.787 1.00 76.43 S ATOM 5238 SG CYS 3 41 114.305 57.519 229.076 1.00 48.81 S ATOM 5324 SG CYS 3 52 110.517 58.442 228.240 1.00 42.66 S ATOM 5349 SG CYS 3 55 111.069 53.324 224.998 1.00 27.68 S ATOM 5450 SG CYS 3 69 114.709 53.563 226.419 1.00 34.00 S ATOM 16378 SG CYS 6 149 88.418 93.777 208.286 1.00 33.23 S ATOM 15644 SG CYS 6 54 85.135 93.438 202.442 1.00 82.29 S ATOM 17596 SG CYS 9 119 91.222 88.285 213.898 1.00 27.32 S ATOM 17570 SG CYS 9 116 92.749 94.726 214.483 1.00 44.58 S ATOM 17617 SG CYS 9 122 93.471 90.579 219.416 1.00 27.48 S ATOM 17344 SG CYS 9 87 97.367 90.195 214.098 1.00 32.76 S ATOM 17646 SG CYS 9 126 95.985 87.508 226.674 1.00 66.01 S ATOM 17317 SG CYS 9 83 99.351 89.240 221.488 1.00 29.44 S ATOM 17275 SG CYS 9 77 101.715 91.032 227.167 1.00 45.21 S ATOM 17294 SG CYS 9 80 100.938 84.434 225.573 1.00 41.81 S ATOM 41188 SG CYS b 59 97.738 83.683 242.088 1.00 38.78 S ATOM 41366 SG CYS b 84 100.705 83.705 239.676 1.00 29.82 S ATOM 41388 SG CYS b 87 99.079 86.642 240.567 1.00 35.15 S Time building chain proxies: 28.79, per 1000 atoms: 0.43 Number of scatterers: 67492 At special positions: 0 Unit cell: (178.248, 196.285, 291.775, 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 466 16.00 P 46 15.00 O 12109 8.00 N 11154 7.00 C 43687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 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: 22.08 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " 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 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 501 " - 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="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 502 " pdb="FE4 SF4 6 502 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 502 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 502 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 502 " - 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="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " 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 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " Number of angles added : 3 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 30 sheets defined 50.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.78 Creating SS restraints... Processing helix chain '1' and resid 33 through 39 removed outlier: 3.939A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 62 removed outlier: 3.864A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.779A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.633A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 107 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' 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 237 removed outlier: 4.662A pdb=" N SER 1 231 " --> pdb=" O THR 1 227 " (cutoff:3.500A) Proline residue: 1 232 - end of helix Processing helix chain '1' and resid 239 through 244 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: 4.644A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 387 through 399 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: 3.698A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 3.579A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.596A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 110 Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 33 removed outlier: 4.127A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 123 Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 196 through 202 removed outlier: 3.763A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE 3 202 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 272 removed outlier: 5.052A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 309 removed outlier: 3.568A pdb=" N SER 3 309 " --> pdb=" O GLY 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 325 through 336 Processing helix chain '3' and resid 359 through 362 Processing helix chain '3' and resid 369 through 371 No H-bonds generated for 'chain '3' and resid 369 through 371' 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 433 removed outlier: 4.326A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.964A 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 478 Processing helix chain '3' and resid 499 through 505 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 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 650 Processing helix chain '3' and resid 669 through 672 No H-bonds generated for 'chain '3' and resid 669 through 672' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 15 removed outlier: 3.967A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 4.680A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 100 Processing helix chain '4' and resid 103 through 105 No H-bonds generated for 'chain '4' and resid 103 through 105' Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.660A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.169A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 215 Processing helix chain '4' and resid 218 through 229 Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 261 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: 4.655A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.816A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 3.954A 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: 3.952A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 3.505A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 138 removed outlier: 3.759A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (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 42 Processing helix chain '6' and resid 54 through 63 removed outlier: 3.650A 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 97 through 105 Processing helix chain '6' and resid 117 through 121 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 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' 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 121 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 175 removed outlier: 5.755A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.497A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.636A 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 2 through 32 Proline residue: H 12 - end of helix removed outlier: 3.891A 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 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.052A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.792A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 220 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.955A pdb=" N ILE J 5 " --> pdb=" O MET J 2 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU J 9 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.893A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 75 removed outlier: 4.039A pdb=" N LEU J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.035A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.670A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.888A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.651A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.707A 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 57 removed outlier: 4.259A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.804A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 4.016A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 137 through 157 removed outlier: 3.962A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.995A 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 231 through 235 Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.366A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (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: 4.389A 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: 4.957A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.902A 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 389 through 400 removed outlier: 5.359A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.616A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.942A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.856A 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 506 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 4.004A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.832A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.951A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN L 546 " --> pdb=" O THR L 543 " (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: 4.125A 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 42 removed outlier: 4.124A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.734A 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 107 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.296A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.436A 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 171 removed outlier: 4.135A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.339A pdb=" N MET M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) 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: 4.957A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 No H-bonds generated for 'chain 'M' and resid 216 through 219' Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.649A 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: 3.900A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.172A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.143A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.019A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'M' and resid 456 through 458 No H-bonds generated for 'chain 'M' and resid 456 through 458' 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 105 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 135 removed outlier: 3.983A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'N' and resid 151 through 171 removed outlier: 4.197A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.895A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 259 through 270 removed outlier: 4.539A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.716A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.626A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 removed outlier: 3.501A pdb=" N THR N 334 " --> pdb=" O THR N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.801A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 8 Processing helix chain 'V' and resid 18 through 42 Processing helix chain 'V' and resid 48 through 79 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 15 through 46 removed outlier: 4.717A 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 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' 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 69 removed outlier: 4.976A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) 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 56 through 76 removed outlier: 3.708A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.776A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 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 120 removed outlier: 4.320A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'a' and resid 42 through 45 removed outlier: 3.550A pdb=" N ASP a 45 " --> pdb=" O GLN a 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 42 through 45' Processing helix chain 'a' and resid 50 through 58 Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.722A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) 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 31 removed outlier: 4.508A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) 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: 4.463A 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 119 through 122 Processing helix chain 'd' and resid 29 through 39 removed outlier: 4.029A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 62 removed outlier: 4.844A 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 124 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 182 No H-bonds generated for 'chain 'd' and resid 179 through 182' Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 through 303' Processing helix chain 'd' and resid 314 through 318 Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.721A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU e 37 " --> 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: 4.201A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 64 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.755A 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: 4.235A 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 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'i' and resid 2 through 17 removed outlier: 3.806A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.035A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.876A 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 35 through 45 removed outlier: 3.904A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS k 45 " --> pdb=" O VAL k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 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 removed outlier: 3.732A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.341A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.805A 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 209 Processing helix chain 'k' and resid 211 through 217 removed outlier: 5.375A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 3.782A 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 296 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 9 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 48 through 54 removed outlier: 3.887A 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 87 Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.733A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 37 Processing helix chain 'n' and resid 45 through 52 removed outlier: 4.664A pdb=" N TRP n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ARG n 51 " --> pdb=" O ASN n 47 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR n 52 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 2 through 4 No H-bonds generated for 'chain 'o' and resid 2 through 4' Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.735A 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 95 removed outlier: 4.154A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 15 through 17 No H-bonds generated for 'chain 'p' and resid 15 through 17' Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.876A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 70 Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix 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 136 Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 68 through 72 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 120 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 57 through 72 Processing helix chain 't' and resid 100 through 105 removed outlier: 3.500A pdb=" N ASP t 105 " --> pdb=" O CYS t 102 " (cutoff:3.500A) 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 142 removed outlier: 4.291A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU t 142 " --> pdb=" O GLN t 138 " (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 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' 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 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 86 through 102 removed outlier: 3.645A pdb=" N ALA w 102 " --> pdb=" O LYS w 98 " (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 45 Processing helix chain 'y' and resid 11 through 33 removed outlier: 3.678A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU y 15 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 3.519A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 30 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 6.015A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 253 through 258 Processing sheet with id= C, first strand: chain '1' and resid 306 through 308 removed outlier: 7.265A pdb=" N MET 1 337 " --> pdb=" O LEU 1 295 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL 1 297 " --> pdb=" O ILE 1 335 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE 1 335 " --> pdb=" O VAL 1 297 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 137 through 142 removed outlier: 6.537A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 9 through 13 Processing sheet with id= F, first strand: chain '3' and resid 146 through 148 Processing sheet with id= G, first strand: chain '3' and resid 173 through 175 Processing sheet with id= H, first strand: chain '3' and resid 226 through 228 removed outlier: 3.582A pdb=" N ARG 3 249 " --> pdb=" O SER 3 241 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG 3 243 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL 3 247 " --> pdb=" O ARG 3 243 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 283 through 285 Processing sheet with id= J, first strand: chain '3' and resid 343 through 345 removed outlier: 8.968A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 490 through 493 removed outlier: 8.204A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '3' and resid 572 through 574 Processing sheet with id= M, first strand: chain '4' and resid 361 through 368 Processing sheet with id= N, first strand: chain '4' and resid 63 through 69 removed outlier: 3.604A pdb=" N LYS 4 75 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 74 through 79 removed outlier: 6.605A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 172 through 177 Processing sheet with id= Q, first strand: chain '6' and resid 85 through 89 removed outlier: 6.499A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '9' and resid 65 through 67 Processing sheet with id= S, first strand: chain '9' and resid 92 through 98 removed outlier: 6.112A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= U, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= V, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.698A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= X, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= Y, first strand: chain 'c' and resid 102 through 106 removed outlier: 4.306A pdb=" N VAL c 39 " --> pdb=" O GLU c 106 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.451A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 51 through 57 removed outlier: 3.630A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'i' and resid 60 through 63 removed outlier: 3.926A pdb=" N GLY i 40 " --> pdb=" O TYR i 48 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.574A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 2780 hydrogen bonds defined for protein. 7875 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: 23.44 Time building geometry restraints manager: 24.20 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: 28403 1.43 - 1.66: 39909 1.66 - 1.90: 759 1.90 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69151 Sorted by residual: bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.331 0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.606 0.227 3.80e-02 6.93e+02 3.57e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.12e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" C13 ZMP g 201 " pdb=" N1 ZMP g 201 " ideal model delta sigma weight residual 1.451 1.341 0.110 2.00e-02 2.50e+03 3.05e+01 ... (remaining 69146 not shown) Histogram of bond angle deviations from ideal: 62.23 - 77.25: 74 77.25 - 92.27: 8 92.27 - 107.29: 3456 107.29 - 122.31: 79599 122.31 - 137.34: 10327 Bond angle restraints: 93464 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 74.46 46.14 3.00e+00 1.11e-01 2.37e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 70.75 38.55 3.00e+00 1.11e-01 1.65e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.04 14.29 1.14e+00 7.69e-01 1.57e+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 89.96 14.37 1.20e+00 6.94e-01 1.43e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 130.83 -23.09 1.95e+00 2.62e-01 1.40e+02 ... (remaining 93459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 41226 34.35 - 68.71: 806 68.71 - 103.06: 68 103.06 - 137.41: 9 137.41 - 171.77: 3 Dihedral angle restraints: 42112 sinusoidal: 18336 harmonic: 23776 Sorted by residual: 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 -130.40 -49.60 0 5.00e+00 4.00e-02 9.84e+01 dihedral pdb=" CA VAL A 29 " pdb=" C VAL A 29 " pdb=" N TYR A 30 " pdb=" CA TYR A 30 " ideal model delta harmonic sigma weight residual -180.00 -134.65 -45.35 0 5.00e+00 4.00e-02 8.22e+01 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 -138.34 -41.66 0 5.00e+00 4.00e-02 6.94e+01 ... (remaining 42109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.233: 10091 4.233 - 8.467: 5 8.467 - 12.700: 0 12.700 - 16.933: 0 16.933 - 21.166: 24 Chirality restraints: 10120 Sorted by residual: chirality pdb="FE1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S3 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.17 2.00e-01 2.50e+01 1.12e+04 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 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " pdb=" S4 SF4 9 402 " both_signs ideal model delta sigma weight residual False -10.55 10.60 -21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10117 not shown) Planarity restraints: 11650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 970 H 501 " -0.047 2.00e-02 2.50e+03 5.31e-02 7.04e+01 pdb=" C06 970 H 501 " 0.012 2.00e-02 2.50e+03 pdb=" C07 970 H 501 " 0.010 2.00e-02 2.50e+03 pdb=" C09 970 H 501 " 0.032 2.00e-02 2.50e+03 pdb=" C10 970 H 501 " 0.042 2.00e-02 2.50e+03 pdb=" C11 970 H 501 " 0.029 2.00e-02 2.50e+03 pdb=" C12 970 H 501 " 0.033 2.00e-02 2.50e+03 pdb=" C24 970 H 501 " -0.121 2.00e-02 2.50e+03 pdb=" O08 970 H 501 " -0.051 2.00e-02 2.50e+03 pdb=" O13 970 H 501 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 970 6 501 " -0.011 2.00e-02 2.50e+03 4.40e-02 4.84e+01 pdb=" C18 970 6 501 " 0.002 2.00e-02 2.50e+03 pdb=" C19 970 6 501 " 0.012 2.00e-02 2.50e+03 pdb=" C20 970 6 501 " -0.014 2.00e-02 2.50e+03 pdb=" C21 970 6 501 " -0.020 2.00e-02 2.50e+03 pdb=" C22 970 6 501 " -0.001 2.00e-02 2.50e+03 pdb=" C23 970 6 501 " 0.079 2.00e-02 2.50e+03 pdb=" O16 970 6 501 " -0.063 2.00e-02 2.50e+03 pdb=" O26 970 6 501 " -0.056 2.00e-02 2.50e+03 pdb=" O28 970 6 501 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 970 6 501 " 0.025 2.00e-02 2.50e+03 3.39e-02 2.87e+01 pdb=" C06 970 6 501 " 0.000 2.00e-02 2.50e+03 pdb=" C07 970 6 501 " 0.016 2.00e-02 2.50e+03 pdb=" C09 970 6 501 " 0.043 2.00e-02 2.50e+03 pdb=" C10 970 6 501 " 0.028 2.00e-02 2.50e+03 pdb=" C11 970 6 501 " -0.006 2.00e-02 2.50e+03 pdb=" C12 970 6 501 " -0.002 2.00e-02 2.50e+03 pdb=" C24 970 6 501 " -0.047 2.00e-02 2.50e+03 pdb=" O08 970 6 501 " -0.073 2.00e-02 2.50e+03 pdb=" O13 970 6 501 " 0.017 2.00e-02 2.50e+03 ... (remaining 11647 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 19730 2.82 - 3.40: 73322 3.40 - 3.98: 139379 3.98 - 4.56: 194904 4.56 - 5.14: 281876 Nonbonded interactions: 709211 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.242 2.440 nonbonded pdb=" OG SER 5 119 " pdb=" OE2 GLU 5 131 " model vdw 2.252 2.440 nonbonded pdb=" O ILE L 556 " pdb=" OG1 THR L 560 " model vdw 2.258 2.440 nonbonded pdb=" O GLU c 28 " pdb=" OG1 THR c 32 " model vdw 2.259 2.440 nonbonded pdb=" OG SER k 22 " pdb=" O GLY k 119 " model vdw 2.261 2.440 ... (remaining 709206 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 individual isotropic 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: 0.440 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: 0.080 Extract box with map and model: 5.170 Check model and map are aligned: 0.740 Set scattering table: 0.480 Process input model: 164.300 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.280 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 0.227 69151 Z= 0.423 Angle : 1.010 46.142 93464 Z= 0.534 Chirality : 1.027 21.166 10120 Planarity : 0.008 0.088 11650 Dihedral : 13.003 171.768 26757 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.99 (0.08), residues: 8043 helix: -1.91 (0.06), residues: 4240 sheet: -1.43 (0.26), residues: 368 loop : -1.99 (0.09), residues: 3435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP 1 371 HIS 0.018 0.002 HIS Z 55 PHE 0.060 0.003 PHE J 17 TYR 0.073 0.003 TYR 6 125 ARG 0.023 0.001 ARG Y 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2293 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2288 time to evaluate : 5.836 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: 1 436 GLN cc_start: 0.6913 (pt0) cc_final: 0.6701 (tm-30) REVERT: 2 18 GLU cc_start: 0.7358 (mp0) cc_final: 0.7119 (mp0) REVERT: 2 134 ASP cc_start: 0.7171 (p0) cc_final: 0.6681 (m-30) REVERT: 3 14 ASP cc_start: 0.7790 (m-30) cc_final: 0.7509 (m-30) REVERT: 3 190 MET cc_start: 0.7769 (ttm) cc_final: 0.7502 (mmm) REVERT: 3 256 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7758 (tp30) REVERT: 3 288 LYS cc_start: 0.7269 (mtmp) cc_final: 0.6905 (mttm) REVERT: 3 306 MET cc_start: 0.7735 (tpt) cc_final: 0.7463 (tpt) REVERT: 3 340 SER cc_start: 0.7733 (t) cc_final: 0.6692 (p) REVERT: 3 431 ASP cc_start: 0.6832 (m-30) cc_final: 0.6278 (t70) REVERT: 3 595 GLU cc_start: 0.7478 (tt0) cc_final: 0.7189 (tt0) REVERT: 3 654 GLN cc_start: 0.6274 (tp-100) cc_final: 0.5939 (tt0) REVERT: 3 657 LEU cc_start: 0.6037 (mt) cc_final: 0.5823 (mt) REVERT: 4 50 ASN cc_start: 0.8027 (t0) cc_final: 0.7785 (m110) REVERT: 4 59 HIS cc_start: 0.7533 (m-70) cc_final: 0.6901 (m-70) REVERT: 4 65 VAL cc_start: 0.8088 (t) cc_final: 0.7757 (m) REVERT: 4 74 ARG cc_start: 0.7337 (mmt-90) cc_final: 0.7123 (mmm-85) REVERT: 4 75 LYS cc_start: 0.8042 (tttm) cc_final: 0.7628 (tptp) REVERT: 4 259 MET cc_start: 0.8755 (mmm) cc_final: 0.8498 (mmm) REVERT: 4 282 GLU cc_start: 0.7579 (tt0) cc_final: 0.7289 (tt0) REVERT: 4 338 MET cc_start: 0.8731 (tmm) cc_final: 0.8258 (tmm) REVERT: 4 410 MET cc_start: 0.7907 (mtm) cc_final: 0.7589 (mtp) REVERT: 5 15 ASN cc_start: 0.7241 (t0) cc_final: 0.7039 (t0) REVERT: 5 124 TYR cc_start: 0.8772 (m-80) cc_final: 0.8541 (m-80) REVERT: 5 200 ASN cc_start: 0.8133 (m-40) cc_final: 0.7928 (m-40) REVERT: 6 32 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7779 (mmtt) REVERT: 6 70 ASP cc_start: 0.8448 (t70) cc_final: 0.8246 (t0) REVERT: 6 79 SER cc_start: 0.8182 (t) cc_final: 0.7877 (t) REVERT: 6 143 ASP cc_start: 0.7795 (m-30) cc_final: 0.7542 (m-30) REVERT: 6 166 LYS cc_start: 0.8634 (tttt) cc_final: 0.8349 (ttpp) REVERT: 6 171 LYS cc_start: 0.7889 (mttp) cc_final: 0.7661 (mttm) REVERT: 6 174 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.8070 (mmm-85) REVERT: 6 178 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7234 (mtp-110) REVERT: 9 14 MET cc_start: 0.6861 (tpt) cc_final: 0.6595 (tpp) REVERT: 9 15 LYS cc_start: 0.7066 (tptp) cc_final: 0.6815 (tptp) REVERT: 9 110 ASP cc_start: 0.8644 (m-30) cc_final: 0.8426 (m-30) REVERT: 9 113 MET cc_start: 0.8783 (mmm) cc_final: 0.8580 (mmm) REVERT: A 13 LEU cc_start: 0.7557 (tp) cc_final: 0.7231 (tp) REVERT: A 49 LEU cc_start: 0.5788 (tp) cc_final: 0.5574 (tt) REVERT: A 53 MET cc_start: 0.7309 (tpt) cc_final: 0.6990 (tpt) REVERT: A 113 TRP cc_start: 0.6515 (m-10) cc_final: 0.5940 (m-10) REVERT: H 108 MET cc_start: 0.8234 (mmp) cc_final: 0.7979 (mmm) REVERT: H 192 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7669 (tp30) REVERT: H 194 ASN cc_start: 0.7610 (m-40) cc_final: 0.7187 (m110) REVERT: H 251 MET cc_start: 0.7646 (mtp) cc_final: 0.7299 (mtt) REVERT: H 253 GLU cc_start: 0.7202 (mp0) cc_final: 0.6976 (mp0) REVERT: H 283 ASP cc_start: 0.7904 (p0) cc_final: 0.7658 (p0) REVERT: J 36 SER cc_start: 0.8161 (m) cc_final: 0.7955 (t) REVERT: J 59 ILE cc_start: 0.7882 (mm) cc_final: 0.7660 (mm) REVERT: J 65 MET cc_start: 0.8237 (mmm) cc_final: 0.8026 (mmp) REVERT: J 173 ARG cc_start: 0.6412 (ttp-170) cc_final: 0.5978 (ttp-170) REVERT: K 8 ILE cc_start: 0.7900 (mm) cc_final: 0.7446 (mt) REVERT: K 50 ASN cc_start: 0.7854 (t160) cc_final: 0.7547 (t0) REVERT: K 91 GLN cc_start: 0.7011 (pm20) cc_final: 0.6660 (pp30) REVERT: L 90 VAL cc_start: 0.7583 (t) cc_final: 0.7379 (m) REVERT: L 95 PHE cc_start: 0.7478 (t80) cc_final: 0.7184 (t80) REVERT: L 108 MET cc_start: 0.7174 (mmm) cc_final: 0.6500 (tpp) REVERT: L 214 MET cc_start: 0.7392 (mmp) cc_final: 0.6801 (tmm) REVERT: L 235 SER cc_start: 0.7425 (m) cc_final: 0.7150 (p) REVERT: L 291 CYS cc_start: 0.7086 (m) cc_final: 0.6800 (m) REVERT: L 317 ILE cc_start: 0.8424 (mt) cc_final: 0.8218 (mt) REVERT: L 340 PHE cc_start: 0.7395 (m-80) cc_final: 0.6647 (m-80) REVERT: L 385 PHE cc_start: 0.6650 (m-80) cc_final: 0.6239 (m-80) REVERT: L 462 LEU cc_start: 0.7177 (mt) cc_final: 0.6953 (mt) REVERT: L 475 MET cc_start: 0.7065 (mmm) cc_final: 0.6478 (mmt) REVERT: L 480 MET cc_start: 0.5050 (mtp) cc_final: 0.4748 (mtm) REVERT: L 507 THR cc_start: 0.6535 (p) cc_final: 0.5953 (m) REVERT: L 520 PHE cc_start: 0.5608 (t80) cc_final: 0.4959 (t80) REVERT: L 528 TYR cc_start: 0.5556 (m-10) cc_final: 0.5239 (m-10) REVERT: L 533 MET cc_start: 0.6327 (mmm) cc_final: 0.6110 (mmp) REVERT: L 544 MET cc_start: 0.4957 (tmm) cc_final: 0.4354 (mmm) REVERT: M 70 MET cc_start: 0.7538 (mtm) cc_final: 0.7306 (mtm) REVERT: M 89 LEU cc_start: 0.7665 (tm) cc_final: 0.7261 (tp) REVERT: M 269 MET cc_start: 0.7197 (ptt) cc_final: 0.6803 (ptt) REVERT: N 11 MET cc_start: 0.7686 (mmp) cc_final: 0.7328 (tmm) REVERT: N 114 TRP cc_start: 0.8016 (p-90) cc_final: 0.7792 (p-90) REVERT: N 151 LEU cc_start: 0.7638 (tp) cc_final: 0.7136 (tt) REVERT: N 154 ILE cc_start: 0.8294 (tp) cc_final: 0.8077 (tt) REVERT: N 167 TRP cc_start: 0.6841 (m-90) cc_final: 0.6531 (m-10) REVERT: N 276 ILE cc_start: 0.7616 (mm) cc_final: 0.7178 (mt) REVERT: V 5 LEU cc_start: 0.2599 (mp) cc_final: 0.2125 (mt) REVERT: V 39 SER cc_start: 0.2475 (t) cc_final: 0.2018 (m) REVERT: V 137 GLU cc_start: 0.6258 (tp30) cc_final: 0.6003 (mp0) REVERT: W 6 LYS cc_start: 0.4641 (pttp) cc_final: 0.4275 (ptpp) REVERT: W 27 PHE cc_start: 0.7226 (t80) cc_final: 0.7002 (t80) REVERT: W 36 VAL cc_start: 0.7824 (t) cc_final: 0.7448 (p) REVERT: W 59 TYR cc_start: 0.4835 (t80) cc_final: 0.4547 (t80) REVERT: W 125 TYR cc_start: 0.7631 (m-80) cc_final: 0.7351 (m-80) REVERT: W 130 LYS cc_start: 0.7858 (pttp) cc_final: 0.7588 (ptpt) REVERT: X 15 VAL cc_start: 0.6708 (t) cc_final: 0.6445 (p) REVERT: X 52 MET cc_start: 0.6545 (mtp) cc_final: 0.5991 (mtt) REVERT: X 66 ASP cc_start: 0.5794 (m-30) cc_final: 0.5556 (m-30) REVERT: Y 3 ILE cc_start: 0.7019 (mm) cc_final: 0.6540 (pt) REVERT: Y 141 TYR cc_start: 0.7515 (m-80) cc_final: 0.7306 (m-80) REVERT: Z 7 ASP cc_start: 0.6300 (m-30) cc_final: 0.6081 (m-30) REVERT: Z 60 TYR cc_start: 0.5240 (p90) cc_final: 0.4915 (p90) REVERT: Z 162 MET cc_start: 0.6924 (mtp) cc_final: 0.6596 (ttt) REVERT: a 38 TYR cc_start: 0.8033 (t80) cc_final: 0.7810 (t80) REVERT: a 45 ASP cc_start: 0.7332 (m-30) cc_final: 0.7064 (p0) REVERT: a 53 ASP cc_start: 0.7440 (m-30) cc_final: 0.7117 (m-30) REVERT: a 65 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7117 (mm110) REVERT: c 18 ASP cc_start: 0.7354 (t70) cc_final: 0.6703 (p0) REVERT: c 22 LEU cc_start: 0.8236 (mt) cc_final: 0.7966 (mt) REVERT: c 66 GLU cc_start: 0.8632 (tt0) cc_final: 0.8324 (tm-30) REVERT: d 10 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7332 (mtpp) REVERT: d 32 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7284 (ttm110) REVERT: d 219 LYS cc_start: 0.7666 (mttt) cc_final: 0.6908 (ttpt) REVERT: d 238 LEU cc_start: 0.8137 (tp) cc_final: 0.7731 (tp) REVERT: d 313 LYS cc_start: 0.7088 (mmtm) cc_final: 0.6475 (mmtt) REVERT: e 34 ASP cc_start: 0.7351 (m-30) cc_final: 0.6883 (m-30) REVERT: e 59 ASP cc_start: 0.6877 (m-30) cc_final: 0.6518 (m-30) REVERT: f 24 LYS cc_start: 0.7234 (mttt) cc_final: 0.6946 (mtmt) REVERT: f 39 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7710 (mtpp) REVERT: f 58 VAL cc_start: 0.8401 (t) cc_final: 0.8158 (t) REVERT: f 61 GLU cc_start: 0.6797 (tp30) cc_final: 0.6538 (tp30) REVERT: f 63 ASP cc_start: 0.6350 (t0) cc_final: 0.6083 (t0) REVERT: g 22 ARG cc_start: 0.6949 (mmm160) cc_final: 0.6404 (mtm110) REVERT: g 24 MET cc_start: 0.7035 (mmm) cc_final: 0.6757 (tpt) REVERT: g 33 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7821 (mm-30) REVERT: g 41 GLU cc_start: 0.7520 (tp30) cc_final: 0.7303 (tp30) REVERT: g 48 LEU cc_start: 0.8441 (pp) cc_final: 0.8128 (tp) REVERT: g 50 GLN cc_start: 0.7789 (pt0) cc_final: 0.7557 (mm-40) REVERT: g 118 LEU cc_start: 0.8097 (tp) cc_final: 0.7685 (tp) REVERT: h 17 ARG cc_start: 0.7140 (mmm-85) cc_final: 0.6933 (mtt90) REVERT: h 39 LYS cc_start: 0.8439 (tptm) cc_final: 0.8214 (tptp) REVERT: h 47 ARG cc_start: 0.6918 (mtm110) cc_final: 0.6643 (ttm110) REVERT: i 5 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7014 (mp10) REVERT: i 21 ARG cc_start: 0.6822 (ttm-80) cc_final: 0.6482 (tpt170) REVERT: i 51 ASP cc_start: 0.8090 (t0) cc_final: 0.7876 (t0) REVERT: i 53 LYS cc_start: 0.7496 (mmtm) cc_final: 0.7257 (mtpp) REVERT: i 76 ASP cc_start: 0.7882 (m-30) cc_final: 0.7648 (m-30) REVERT: i 78 ASP cc_start: 0.7872 (t0) cc_final: 0.7572 (t0) REVERT: j 18 VAL cc_start: 0.7093 (t) cc_final: 0.6764 (m) REVERT: j 21 LEU cc_start: 0.7282 (mt) cc_final: 0.6997 (mt) REVERT: j 24 LYS cc_start: 0.6941 (ttmp) cc_final: 0.6665 (mttt) REVERT: j 50 ILE cc_start: 0.8123 (mt) cc_final: 0.7863 (mt) REVERT: k 18 MET cc_start: 0.5990 (tpp) cc_final: 0.5739 (mmm) REVERT: k 63 THR cc_start: 0.7113 (p) cc_final: 0.6839 (p) REVERT: k 131 ASP cc_start: 0.5591 (t70) cc_final: 0.5340 (t70) REVERT: k 143 PHE cc_start: 0.5170 (m-10) cc_final: 0.4966 (m-10) REVERT: k 147 GLN cc_start: 0.6817 (mp10) cc_final: 0.5858 (mm-40) REVERT: k 214 MET cc_start: 0.7082 (mmm) cc_final: 0.6479 (tpp) REVERT: k 278 PHE cc_start: 0.6802 (m-80) cc_final: 0.6579 (m-80) REVERT: k 288 GLN cc_start: 0.7412 (tt0) cc_final: 0.7087 (tt0) REVERT: l 9 LEU cc_start: 0.8219 (mt) cc_final: 0.8006 (mp) REVERT: l 12 ASP cc_start: 0.6673 (t0) cc_final: 0.6406 (t0) REVERT: l 48 SER cc_start: 0.8105 (t) cc_final: 0.7883 (t) REVERT: l 79 LYS cc_start: 0.6948 (tttm) cc_final: 0.6677 (ttpt) REVERT: l 105 PRO cc_start: 0.5306 (Cg_endo) cc_final: 0.4951 (Cg_exo) REVERT: m 17 VAL cc_start: 0.8146 (t) cc_final: 0.7677 (m) REVERT: m 21 SER cc_start: 0.8474 (m) cc_final: 0.8263 (p) REVERT: m 22 PHE cc_start: 0.8348 (m-80) cc_final: 0.8105 (m-80) REVERT: m 43 MET cc_start: 0.7854 (mtp) cc_final: 0.7567 (mtp) REVERT: n 28 LEU cc_start: 0.6067 (mm) cc_final: 0.5637 (mt) REVERT: n 71 LYS cc_start: 0.6230 (ttmt) cc_final: 0.5910 (tptp) REVERT: o 1 MET cc_start: 0.5489 (ttp) cc_final: 0.5274 (ptm) REVERT: o 75 LEU cc_start: 0.8440 (mt) cc_final: 0.8214 (mt) REVERT: o 113 PHE cc_start: 0.6718 (t80) cc_final: 0.6517 (t80) REVERT: p 43 LYS cc_start: 0.6917 (tppt) cc_final: 0.6599 (tptt) REVERT: p 92 PHE cc_start: 0.5549 (m-10) cc_final: 0.5209 (m-10) REVERT: q 8 ASP cc_start: 0.7359 (t0) cc_final: 0.6977 (t70) REVERT: q 23 ASN cc_start: 0.7413 (t0) cc_final: 0.7175 (t0) REVERT: q 119 MET cc_start: 0.6616 (ttp) cc_final: 0.6224 (ttm) REVERT: q 120 MET cc_start: 0.7337 (tpp) cc_final: 0.7017 (tpp) REVERT: r 15 ARG cc_start: 0.5808 (ttm110) cc_final: 0.5557 (ttm110) REVERT: r 66 HIS cc_start: 0.3017 (t70) cc_final: 0.2543 (t-90) REVERT: r 87 TYR cc_start: 0.6655 (m-80) cc_final: 0.6282 (m-80) REVERT: r 89 VAL cc_start: 0.7232 (t) cc_final: 0.6986 (t) REVERT: s 34 LYS cc_start: 0.5367 (ptpt) cc_final: 0.5064 (ttpt) REVERT: s 38 MET cc_start: 0.6099 (tpt) cc_final: 0.5629 (tpp) REVERT: s 41 THR cc_start: 0.6811 (m) cc_final: 0.6576 (m) REVERT: s 81 HIS cc_start: 0.5733 (t-90) cc_final: 0.5507 (t-90) REVERT: t 26 LEU cc_start: 0.7964 (tp) cc_final: 0.7702 (mm) REVERT: t 33 ARG cc_start: 0.3500 (mmm160) cc_final: 0.2922 (mmt180) REVERT: t 172 ARG cc_start: 0.5973 (ptt-90) cc_final: 0.5504 (ptt180) REVERT: u 43 ASP cc_start: 0.5249 (m-30) cc_final: 0.4998 (m-30) REVERT: u 67 PRO cc_start: 0.3570 (Cg_exo) cc_final: 0.3339 (Cg_endo) REVERT: v 19 GLU cc_start: 0.5434 (tt0) cc_final: 0.4958 (tp30) REVERT: v 29 MET cc_start: 0.5915 (ptm) cc_final: 0.5664 (ptm) REVERT: v 33 ASP cc_start: 0.3967 (m-30) cc_final: 0.3693 (t0) REVERT: v 132 GLN cc_start: 0.5680 (mt0) cc_final: 0.5443 (mm110) REVERT: v 156 TYR cc_start: 0.4959 (m-80) cc_final: 0.4508 (m-80) REVERT: w 28 GLU cc_start: 0.6145 (tp30) cc_final: 0.5269 (pt0) REVERT: w 41 ASN cc_start: 0.6774 (t0) cc_final: 0.6557 (t0) REVERT: w 111 ASN cc_start: 0.6448 (m-40) cc_final: 0.6023 (p0) REVERT: x 14 TRP cc_start: 0.6011 (m100) cc_final: 0.5775 (m-10) REVERT: x 16 LYS cc_start: 0.6930 (ttmt) cc_final: 0.6633 (tptt) REVERT: x 27 LEU cc_start: 0.7812 (mt) cc_final: 0.7545 (mp) REVERT: y 8 ARG cc_start: 0.3991 (tpm170) cc_final: 0.3283 (ttt180) REVERT: y 41 SER cc_start: 0.7518 (p) cc_final: 0.7187 (t) REVERT: z 4 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7114 (mt-10) REVERT: z 25 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7225 (ptt90) outliers start: 5 outliers final: 3 residues processed: 2293 average time/residue: 0.7194 time to fit residues: 2660.2608 Evaluate side-chains 1400 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1397 time to evaluate : 5.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain V residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 0.1980 chunk 602 optimal weight: 10.0000 chunk 334 optimal weight: 40.0000 chunk 205 optimal weight: 9.9990 chunk 406 optimal weight: 2.9990 chunk 321 optimal weight: 30.0000 chunk 623 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 378 optimal weight: 20.0000 chunk 463 optimal weight: 8.9990 chunk 721 optimal weight: 20.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 150 GLN 1 200 GLN 1 324 GLN 1 373 ASN 2 150 ASN 2 155 GLN 3 82 ASN 3 179 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 437 HIS 3 546 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN 4 280 GLN 5 211 GLN 9 65 HIS H 157 ASN L 23 ASN L 135 ASN L 175 ASN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN L 270 ASN L 348 HIS L 446 ASN L 471 ASN L 509 HIS M 43 ASN M 81 GLN M 169 ASN M 188 ASN M 333 ASN N 235 ASN N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 ASN Y 15 GLN Y 29 HIS Z 99 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN Z 143 HIS ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 ASN b 32 GLN b 36 ASN d 37 HIS d 87 HIS d 288 HIS f 20 HIS f 49 GLN f 82 GLN g 25 ASN g 125 HIS h 8 GLN h 28 GLN k 141 GLN k 153 ASN k 258 ASN k 287 HIS ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN o 61 GLN p 116 GLN q 60 GLN q 111 HIS ** s 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN s 116 GLN t 77 GLN u 16 GLN v 55 GLN v 66 HIS v 136 ASN x 9 HIS y 13 HIS Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.267 69151 Z= 0.527 Angle : 1.596 50.867 93464 Z= 1.023 Chirality : 0.314 6.552 10120 Planarity : 0.006 0.084 11650 Dihedral : 13.892 171.726 10629 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.85 % Allowed : 7.79 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -1.25 (0.09), residues: 8043 helix: -0.28 (0.07), residues: 4242 sheet: -1.22 (0.25), residues: 378 loop : -1.39 (0.10), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 1 371 HIS 0.009 0.002 HIS a 44 PHE 0.030 0.002 PHE 4 171 TYR 0.032 0.002 TYR 6 125 ARG 0.007 0.001 ARG v 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1469 time to evaluate : 5.929 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: 1 82 MET cc_start: 0.8043 (mmm) cc_final: 0.7827 (mmm) REVERT: 1 354 TYR cc_start: 0.8565 (m-80) cc_final: 0.8150 (m-80) REVERT: 1 436 GLN cc_start: 0.7014 (pt0) cc_final: 0.6775 (tm-30) REVERT: 2 134 ASP cc_start: 0.7000 (p0) cc_final: 0.6733 (m-30) REVERT: 3 190 MET cc_start: 0.7662 (ttm) cc_final: 0.7440 (mmm) REVERT: 3 254 MET cc_start: 0.7646 (tmm) cc_final: 0.7433 (tmm) REVERT: 3 256 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7808 (tp30) REVERT: 3 288 LYS cc_start: 0.7320 (mtmp) cc_final: 0.7011 (mttm) REVERT: 3 306 MET cc_start: 0.7647 (tpt) cc_final: 0.7441 (tpt) REVERT: 3 340 SER cc_start: 0.7605 (t) cc_final: 0.6635 (p) REVERT: 3 431 ASP cc_start: 0.6956 (m-30) cc_final: 0.6354 (t70) REVERT: 3 654 GLN cc_start: 0.6361 (tp-100) cc_final: 0.5949 (tt0) REVERT: 4 50 ASN cc_start: 0.7942 (t0) cc_final: 0.7686 (m110) REVERT: 4 59 HIS cc_start: 0.7455 (m-70) cc_final: 0.6896 (m-70) REVERT: 4 65 VAL cc_start: 0.8145 (t) cc_final: 0.7775 (m) REVERT: 4 75 LYS cc_start: 0.8128 (tttm) cc_final: 0.7783 (mtpp) REVERT: 4 259 MET cc_start: 0.8827 (mmm) cc_final: 0.8510 (mmm) REVERT: 4 338 MET cc_start: 0.8731 (tmm) cc_final: 0.8337 (tmm) REVERT: 4 410 MET cc_start: 0.7927 (mtm) cc_final: 0.7673 (mtp) REVERT: 6 32 LYS cc_start: 0.8197 (mmpt) cc_final: 0.7960 (mmtt) REVERT: 6 79 SER cc_start: 0.8348 (t) cc_final: 0.8052 (t) REVERT: 6 178 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7252 (mtp-110) REVERT: 9 12 MET cc_start: 0.7490 (tpp) cc_final: 0.7189 (tpp) REVERT: 9 15 LYS cc_start: 0.7012 (tptp) cc_final: 0.6768 (tptp) REVERT: 9 110 ASP cc_start: 0.8294 (m-30) cc_final: 0.8072 (m-30) REVERT: 9 113 MET cc_start: 0.8731 (mmm) cc_final: 0.8394 (mmm) REVERT: A 49 LEU cc_start: 0.5668 (tp) cc_final: 0.5375 (tt) REVERT: A 113 TRP cc_start: 0.6389 (m-10) cc_final: 0.6066 (m-10) REVERT: H 194 ASN cc_start: 0.7737 (m-40) cc_final: 0.7439 (m-40) REVERT: H 251 MET cc_start: 0.7732 (mtp) cc_final: 0.7346 (mtt) REVERT: J 22 SER cc_start: 0.7049 (p) cc_final: 0.6815 (t) REVERT: J 65 MET cc_start: 0.8078 (mmm) cc_final: 0.7813 (mmp) REVERT: K 91 GLN cc_start: 0.7088 (pm20) cc_final: 0.6721 (pp30) REVERT: L 82 MET cc_start: 0.6835 (mmp) cc_final: 0.6545 (mmt) REVERT: L 95 PHE cc_start: 0.7537 (t80) cc_final: 0.7320 (t80) REVERT: L 108 MET cc_start: 0.7131 (mmm) cc_final: 0.6666 (tpp) REVERT: L 150 MET cc_start: 0.7467 (mmm) cc_final: 0.7254 (mmm) REVERT: L 214 MET cc_start: 0.7311 (mmp) cc_final: 0.6702 (ttt) REVERT: L 227 PHE cc_start: 0.7342 (t80) cc_final: 0.6725 (t80) REVERT: L 237 MET cc_start: 0.7013 (mmp) cc_final: 0.6457 (mmp) REVERT: L 340 PHE cc_start: 0.7441 (m-80) cc_final: 0.6709 (m-80) REVERT: L 475 MET cc_start: 0.7247 (mmm) cc_final: 0.6459 (mmt) REVERT: L 480 MET cc_start: 0.5218 (mtp) cc_final: 0.4726 (mtt) REVERT: L 520 PHE cc_start: 0.5438 (t80) cc_final: 0.4962 (t80) REVERT: L 571 MET cc_start: 0.4396 (ttp) cc_final: 0.4052 (ptm) REVERT: M 70 MET cc_start: 0.7549 (mtm) cc_final: 0.7333 (mtm) REVERT: M 86 LYS cc_start: 0.6923 (ptpt) cc_final: 0.6695 (mptt) REVERT: M 89 LEU cc_start: 0.7830 (tm) cc_final: 0.7609 (tp) REVERT: M 269 MET cc_start: 0.7294 (ptt) cc_final: 0.6915 (ptt) REVERT: M 396 MET cc_start: 0.8222 (mmt) cc_final: 0.7847 (mmt) REVERT: M 398 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6951 (tp) REVERT: M 433 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7332 (mt-10) REVERT: N 11 MET cc_start: 0.7692 (mmp) cc_final: 0.7375 (tmm) REVERT: N 47 LYS cc_start: 0.7288 (mmpt) cc_final: 0.7036 (mmmt) REVERT: N 167 TRP cc_start: 0.6933 (m-90) cc_final: 0.6570 (m-10) REVERT: N 276 ILE cc_start: 0.7462 (mm) cc_final: 0.7217 (mt) REVERT: N 282 MET cc_start: 0.6885 (mtp) cc_final: 0.6462 (mtm) REVERT: N 331 VAL cc_start: 0.8287 (t) cc_final: 0.8074 (p) REVERT: V 5 LEU cc_start: 0.2266 (mp) cc_final: 0.1705 (mt) REVERT: V 137 GLU cc_start: 0.6410 (tp30) cc_final: 0.5823 (mp0) REVERT: W 6 LYS cc_start: 0.4592 (pttp) cc_final: 0.4207 (ptpp) REVERT: W 36 VAL cc_start: 0.7756 (t) cc_final: 0.7468 (p) REVERT: W 114 MET cc_start: 0.7907 (mtt) cc_final: 0.7647 (mtt) REVERT: X 58 PHE cc_start: 0.5776 (m-80) cc_final: 0.5325 (m-80) REVERT: Y 3 ILE cc_start: 0.7062 (mm) cc_final: 0.6575 (pt) REVERT: Y 18 LYS cc_start: 0.7691 (mmmm) cc_final: 0.6989 (mtmm) REVERT: Y 72 GLN cc_start: 0.8536 (mm110) cc_final: 0.8330 (mm-40) REVERT: Z 36 PHE cc_start: 0.7609 (t80) cc_final: 0.7408 (t80) REVERT: Z 131 PHE cc_start: 0.7805 (t80) cc_final: 0.7442 (t80) REVERT: Z 162 MET cc_start: 0.7181 (mtp) cc_final: 0.6894 (ttt) REVERT: a 45 ASP cc_start: 0.7487 (m-30) cc_final: 0.7038 (p0) REVERT: a 53 ASP cc_start: 0.7430 (m-30) cc_final: 0.7196 (m-30) REVERT: c 18 ASP cc_start: 0.7371 (t70) cc_final: 0.6823 (p0) REVERT: c 66 GLU cc_start: 0.8658 (tt0) cc_final: 0.8401 (tm-30) REVERT: d 10 LYS cc_start: 0.7575 (mtpp) cc_final: 0.7338 (mtpt) REVERT: d 32 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7456 (ttm110) REVERT: d 219 LYS cc_start: 0.7754 (mttt) cc_final: 0.7075 (ttpt) REVERT: d 238 LEU cc_start: 0.8140 (tp) cc_final: 0.7845 (tt) REVERT: d 313 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6719 (mmtt) REVERT: e 38 LYS cc_start: 0.7928 (mttt) cc_final: 0.7642 (mppt) REVERT: e 67 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7095 (ttp-110) REVERT: e 88 ARG cc_start: 0.7191 (mtm-85) cc_final: 0.6779 (ttm110) REVERT: f 61 GLU cc_start: 0.6777 (tp30) cc_final: 0.6551 (tp30) REVERT: f 63 ASP cc_start: 0.6196 (t0) cc_final: 0.5870 (t0) REVERT: g 22 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6599 (mtm110) REVERT: g 24 MET cc_start: 0.6884 (mmm) cc_final: 0.6648 (tpt) REVERT: g 26 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7285 (tt0) REVERT: g 50 GLN cc_start: 0.7935 (pt0) cc_final: 0.7567 (mm-40) REVERT: g 90 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8052 (mm-30) REVERT: h 17 ARG cc_start: 0.7246 (mmm-85) cc_final: 0.6934 (mtt90) REVERT: h 47 ARG cc_start: 0.6779 (mtm110) cc_final: 0.6483 (ttm110) REVERT: i 5 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7001 (mp10) REVERT: i 21 ARG cc_start: 0.6899 (ttm-80) cc_final: 0.6522 (tpt170) REVERT: i 51 ASP cc_start: 0.7929 (t0) cc_final: 0.7714 (t0) REVERT: i 53 LYS cc_start: 0.7547 (mmtm) cc_final: 0.7306 (mmmt) REVERT: i 134 ILE cc_start: 0.8581 (mm) cc_final: 0.8342 (mm) REVERT: j 37 MET cc_start: 0.6715 (mmt) cc_final: 0.6496 (mmm) REVERT: k 63 THR cc_start: 0.7213 (p) cc_final: 0.6959 (p) REVERT: k 65 ASP cc_start: 0.5667 (p0) cc_final: 0.5302 (p0) REVERT: k 143 PHE cc_start: 0.5286 (m-10) cc_final: 0.4856 (m-10) REVERT: k 214 MET cc_start: 0.6713 (mmm) cc_final: 0.6274 (mmt) REVERT: k 288 GLN cc_start: 0.7332 (tt0) cc_final: 0.6989 (tt0) REVERT: k 298 GLU cc_start: 0.6038 (pt0) cc_final: 0.5666 (mt-10) REVERT: l 12 ASP cc_start: 0.6967 (t0) cc_final: 0.6655 (t0) REVERT: l 79 LYS cc_start: 0.6976 (tttm) cc_final: 0.6698 (ttpt) REVERT: m 17 VAL cc_start: 0.8177 (t) cc_final: 0.7787 (m) REVERT: m 43 MET cc_start: 0.7849 (mtp) cc_final: 0.7645 (mtp) REVERT: n 28 LEU cc_start: 0.5888 (mm) cc_final: 0.5596 (mt) REVERT: n 48 GLU cc_start: 0.6093 (pt0) cc_final: 0.5821 (pt0) REVERT: n 71 LYS cc_start: 0.6290 (ttmt) cc_final: 0.5772 (tptp) REVERT: p 43 LYS cc_start: 0.7086 (tppt) cc_final: 0.6731 (tptt) REVERT: p 46 TYR cc_start: 0.6473 (t80) cc_final: 0.6270 (t80) REVERT: p 82 ASN cc_start: 0.2153 (p0) cc_final: 0.1115 (t0) REVERT: p 92 PHE cc_start: 0.5613 (m-10) cc_final: 0.5366 (m-10) REVERT: p 94 ILE cc_start: 0.5515 (pp) cc_final: 0.5130 (mm) REVERT: q 8 ASP cc_start: 0.7359 (t0) cc_final: 0.6947 (t70) REVERT: q 23 ASN cc_start: 0.7806 (t0) cc_final: 0.7529 (t0) REVERT: q 120 MET cc_start: 0.7587 (tpp) cc_final: 0.7211 (tpp) REVERT: r 66 HIS cc_start: 0.3078 (t70) cc_final: 0.2624 (t-90) REVERT: r 76 ILE cc_start: 0.8076 (mt) cc_final: 0.7861 (mm) REVERT: r 83 TYR cc_start: 0.7664 (t80) cc_final: 0.7125 (t80) REVERT: r 89 VAL cc_start: 0.7364 (t) cc_final: 0.7063 (t) REVERT: s 8 TYR cc_start: 0.5507 (m-10) cc_final: 0.5007 (m-80) REVERT: s 38 MET cc_start: 0.5669 (tpt) cc_final: 0.5187 (tpp) REVERT: s 81 HIS cc_start: 0.5616 (t-90) cc_final: 0.5382 (t-90) REVERT: t 26 LEU cc_start: 0.7826 (tp) cc_final: 0.7595 (mm) REVERT: t 172 ARG cc_start: 0.6136 (ptt-90) cc_final: 0.5524 (ptt180) REVERT: u 45 ASP cc_start: 0.5731 (m-30) cc_final: 0.5494 (m-30) REVERT: u 67 PRO cc_start: 0.3578 (Cg_exo) cc_final: 0.3370 (Cg_endo) REVERT: v 19 GLU cc_start: 0.5555 (tt0) cc_final: 0.4997 (tp30) REVERT: v 33 ASP cc_start: 0.3936 (m-30) cc_final: 0.3638 (t0) REVERT: v 53 ARG cc_start: 0.5922 (mmt90) cc_final: 0.5092 (mtp-110) REVERT: v 59 ASP cc_start: 0.5617 (t0) cc_final: 0.5315 (p0) REVERT: v 141 GLU cc_start: 0.7403 (mp0) cc_final: 0.7016 (mp0) REVERT: v 148 LYS cc_start: 0.7007 (ttmt) cc_final: 0.6749 (ttmm) REVERT: w 27 GLN cc_start: 0.6286 (mp10) cc_final: 0.5857 (mp-120) REVERT: w 43 ASP cc_start: 0.7622 (m-30) cc_final: 0.7377 (m-30) REVERT: w 56 TRP cc_start: 0.7117 (m100) cc_final: 0.6166 (t60) REVERT: w 92 GLU cc_start: 0.7281 (tp30) cc_final: 0.6897 (tp30) REVERT: w 111 ASN cc_start: 0.6668 (m-40) cc_final: 0.6064 (p0) REVERT: x 14 TRP cc_start: 0.6040 (m100) cc_final: 0.5618 (m-10) REVERT: x 16 LYS cc_start: 0.7114 (ttmt) cc_final: 0.6545 (tptt) REVERT: y 8 ARG cc_start: 0.3966 (tpm170) cc_final: 0.3298 (ttt90) REVERT: y 48 LEU cc_start: 0.6264 (mp) cc_final: 0.5980 (mp) REVERT: z 4 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7108 (mt-10) REVERT: z 25 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7257 (ptt90) outliers start: 132 outliers final: 93 residues processed: 1561 average time/residue: 0.6692 time to fit residues: 1753.5675 Evaluate side-chains 1384 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1290 time to evaluate : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 272 ASP Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 692 THR Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 412 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 398 LEU Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 143 ASN Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 153 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain i residue 142 THR Chi-restraints excluded: chain k residue 62 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 71 LEU Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 21 MET Chi-restraints excluded: chain z residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 600 optimal weight: 7.9990 chunk 491 optimal weight: 30.0000 chunk 199 optimal weight: 6.9990 chunk 723 optimal weight: 30.0000 chunk 781 optimal weight: 5.9990 chunk 644 optimal weight: 10.0000 chunk 717 optimal weight: 30.0000 chunk 246 optimal weight: 7.9990 chunk 580 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 237 ASN 3 581 GLN ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 15 ASN 5 211 GLN 9 90 GLN K 50 ASN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN L 518 ASN M 103 GLN M 184 GLN N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN f 82 GLN f 95 GLN i 135 GLN k 120 GLN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 49 GLN q 53 ASN r 12 GLN s 116 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.245 69151 Z= 0.545 Angle : 1.600 50.684 93464 Z= 1.026 Chirality : 0.313 6.476 10120 Planarity : 0.006 0.073 11650 Dihedral : 13.552 172.567 10628 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.45 % Allowed : 9.65 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.68 (0.09), residues: 8043 helix: 0.25 (0.08), residues: 4216 sheet: -1.16 (0.26), residues: 362 loop : -1.18 (0.10), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 407 HIS 0.011 0.002 HIS a 44 PHE 0.031 0.002 PHE X 60 TYR 0.026 0.002 TYR 9 118 ARG 0.007 0.001 ARG 3 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1323 time to evaluate : 5.890 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: 1 109 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7283 (mm-30) REVERT: 1 354 TYR cc_start: 0.8609 (m-80) cc_final: 0.8144 (m-80) REVERT: 1 436 GLN cc_start: 0.7079 (pt0) cc_final: 0.6827 (tm-30) REVERT: 2 134 ASP cc_start: 0.7218 (p0) cc_final: 0.6835 (m-30) REVERT: 3 14 ASP cc_start: 0.7867 (m-30) cc_final: 0.7631 (m-30) REVERT: 3 190 MET cc_start: 0.7707 (ttm) cc_final: 0.7438 (mmm) REVERT: 3 254 MET cc_start: 0.7919 (tmm) cc_final: 0.7357 (tmm) REVERT: 3 288 LYS cc_start: 0.7329 (mtmp) cc_final: 0.6991 (mttm) REVERT: 3 340 SER cc_start: 0.7630 (t) cc_final: 0.6718 (p) REVERT: 3 431 ASP cc_start: 0.7069 (m-30) cc_final: 0.6405 (t70) REVERT: 3 654 GLN cc_start: 0.6144 (tp-100) cc_final: 0.5777 (tt0) REVERT: 4 50 ASN cc_start: 0.7947 (t0) cc_final: 0.7685 (m110) REVERT: 4 59 HIS cc_start: 0.7495 (m-70) cc_final: 0.6742 (m90) REVERT: 4 75 LYS cc_start: 0.8165 (tttm) cc_final: 0.7844 (tptp) REVERT: 4 259 MET cc_start: 0.8792 (mmm) cc_final: 0.8454 (mmm) REVERT: 4 410 MET cc_start: 0.7551 (mtm) cc_final: 0.7323 (mtp) REVERT: 5 121 VAL cc_start: 0.8136 (m) cc_final: 0.7929 (t) REVERT: 6 32 LYS cc_start: 0.8211 (mmpt) cc_final: 0.7922 (mmtt) REVERT: 6 79 SER cc_start: 0.8347 (t) cc_final: 0.7952 (p) REVERT: 6 178 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7300 (mtp180) REVERT: 9 12 MET cc_start: 0.7598 (tpp) cc_final: 0.7304 (tpp) REVERT: 9 13 ASP cc_start: 0.7519 (p0) cc_final: 0.7272 (p0) REVERT: 9 15 LYS cc_start: 0.7413 (tptp) cc_final: 0.7198 (tptp) REVERT: 9 113 MET cc_start: 0.8772 (mmm) cc_final: 0.8362 (mmm) REVERT: A 49 LEU cc_start: 0.5882 (tp) cc_final: 0.5523 (tt) REVERT: H 85 MET cc_start: 0.8278 (mmm) cc_final: 0.7953 (mmm) REVERT: H 105 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7315 (ttp) REVERT: H 213 VAL cc_start: 0.7204 (m) cc_final: 0.6959 (p) REVERT: J 65 MET cc_start: 0.8218 (mmm) cc_final: 0.7904 (mmp) REVERT: K 8 ILE cc_start: 0.8020 (mm) cc_final: 0.7514 (mt) REVERT: K 38 LEU cc_start: 0.8345 (tp) cc_final: 0.8126 (tp) REVERT: K 91 GLN cc_start: 0.7124 (pm20) cc_final: 0.6692 (pp30) REVERT: L 88 MET cc_start: 0.7758 (mmm) cc_final: 0.7508 (mmm) REVERT: L 95 PHE cc_start: 0.7500 (t80) cc_final: 0.7276 (t80) REVERT: L 108 MET cc_start: 0.7287 (mmm) cc_final: 0.6780 (tpp) REVERT: L 150 MET cc_start: 0.7664 (mmm) cc_final: 0.7416 (mmm) REVERT: L 214 MET cc_start: 0.7378 (mmp) cc_final: 0.6726 (ttt) REVERT: L 277 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7051 (mtt) REVERT: L 340 PHE cc_start: 0.7397 (m-80) cc_final: 0.6727 (m-80) REVERT: L 475 MET cc_start: 0.7152 (mmm) cc_final: 0.6387 (mmt) REVERT: L 491 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5560 (tt) REVERT: L 507 THR cc_start: 0.6595 (p) cc_final: 0.6067 (m) REVERT: L 558 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2910 (mm) REVERT: L 571 MET cc_start: 0.4362 (ttp) cc_final: 0.4031 (ptm) REVERT: M 261 PHE cc_start: 0.7455 (m-80) cc_final: 0.7254 (m-80) REVERT: M 269 MET cc_start: 0.7322 (ptt) cc_final: 0.6990 (ptt) REVERT: M 383 MET cc_start: 0.8504 (mmp) cc_final: 0.8233 (mmp) REVERT: M 433 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7484 (mt-10) REVERT: N 11 MET cc_start: 0.7789 (mmp) cc_final: 0.7214 (tmm) REVERT: N 167 TRP cc_start: 0.6975 (m-90) cc_final: 0.6525 (m-10) REVERT: N 282 MET cc_start: 0.6967 (mtp) cc_final: 0.6514 (mtm) REVERT: N 331 VAL cc_start: 0.8247 (t) cc_final: 0.8016 (p) REVERT: V 87 LEU cc_start: 0.3708 (tm) cc_final: 0.2810 (mt) REVERT: V 137 GLU cc_start: 0.6302 (tp30) cc_final: 0.5880 (mp0) REVERT: W 36 VAL cc_start: 0.7817 (t) cc_final: 0.7542 (p) REVERT: W 91 MET cc_start: 0.7164 (mtp) cc_final: 0.6587 (ttm) REVERT: W 114 MET cc_start: 0.7968 (mtt) cc_final: 0.7656 (mtt) REVERT: X 15 VAL cc_start: 0.7039 (m) cc_final: 0.6667 (p) REVERT: X 33 ASN cc_start: 0.6362 (t0) cc_final: 0.5961 (m-40) REVERT: Y 3 ILE cc_start: 0.7016 (mm) cc_final: 0.6585 (pt) REVERT: Z 131 PHE cc_start: 0.7859 (t80) cc_final: 0.7444 (t80) REVERT: Z 134 VAL cc_start: 0.7928 (p) cc_final: 0.7624 (t) REVERT: Z 162 MET cc_start: 0.7127 (mtp) cc_final: 0.6920 (ttt) REVERT: a 45 ASP cc_start: 0.7455 (m-30) cc_final: 0.6965 (p0) REVERT: a 53 ASP cc_start: 0.7449 (m-30) cc_final: 0.7212 (m-30) REVERT: c 18 ASP cc_start: 0.7325 (t70) cc_final: 0.6760 (p0) REVERT: c 28 GLU cc_start: 0.7713 (mp0) cc_final: 0.7498 (pm20) REVERT: c 66 GLU cc_start: 0.8668 (tt0) cc_final: 0.8389 (tm-30) REVERT: c 90 GLU cc_start: 0.8155 (mp0) cc_final: 0.7536 (mm-30) REVERT: d 219 LYS cc_start: 0.7675 (mttt) cc_final: 0.7038 (ttpt) REVERT: d 238 LEU cc_start: 0.8201 (tp) cc_final: 0.7965 (tt) REVERT: d 313 LYS cc_start: 0.7350 (mmtm) cc_final: 0.7136 (mmtt) REVERT: e 88 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6724 (ttm110) REVERT: f 61 GLU cc_start: 0.6812 (tp30) cc_final: 0.6562 (tp30) REVERT: f 63 ASP cc_start: 0.6208 (t0) cc_final: 0.5764 (t70) REVERT: g 24 MET cc_start: 0.6908 (mmm) cc_final: 0.6706 (tpt) REVERT: g 26 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7227 (tt0) REVERT: g 50 GLN cc_start: 0.7896 (pt0) cc_final: 0.7478 (mm-40) REVERT: g 90 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8026 (mm-30) REVERT: h 17 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.6939 (mmt-90) REVERT: h 47 ARG cc_start: 0.6632 (mtm110) cc_final: 0.6423 (ttm110) REVERT: i 5 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7086 (mp10) REVERT: i 21 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6600 (tpt170) REVERT: i 53 LYS cc_start: 0.7549 (mmtm) cc_final: 0.7299 (mmmt) REVERT: i 78 ASP cc_start: 0.7701 (t0) cc_final: 0.7399 (t0) REVERT: i 88 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8207 (mtp180) REVERT: i 134 ILE cc_start: 0.8664 (mm) cc_final: 0.8289 (mm) REVERT: i 135 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7838 (mm-40) REVERT: k 63 THR cc_start: 0.7184 (p) cc_final: 0.6934 (p) REVERT: k 143 PHE cc_start: 0.5175 (m-10) cc_final: 0.4775 (m-10) REVERT: k 153 ASN cc_start: 0.7590 (m-40) cc_final: 0.7092 (m110) REVERT: k 209 THR cc_start: 0.6190 (OUTLIER) cc_final: 0.5687 (p) REVERT: k 214 MET cc_start: 0.6679 (mmm) cc_final: 0.6105 (mmt) REVERT: k 218 CYS cc_start: 0.6277 (p) cc_final: 0.5591 (p) REVERT: k 288 GLN cc_start: 0.7367 (tt0) cc_final: 0.7061 (tt0) REVERT: l 12 ASP cc_start: 0.6907 (t0) cc_final: 0.6630 (t0) REVERT: m 17 VAL cc_start: 0.8144 (t) cc_final: 0.7853 (m) REVERT: m 43 MET cc_start: 0.7866 (mtp) cc_final: 0.7652 (mtp) REVERT: n 28 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5810 (mt) REVERT: n 48 GLU cc_start: 0.6282 (pt0) cc_final: 0.5985 (pt0) REVERT: n 71 LYS cc_start: 0.6244 (ttmt) cc_final: 0.5824 (tptp) REVERT: p 22 TYR cc_start: 0.2569 (m-10) cc_final: 0.2334 (m-10) REVERT: p 43 LYS cc_start: 0.6984 (tppt) cc_final: 0.6659 (tptt) REVERT: p 82 ASN cc_start: 0.2072 (p0) cc_final: 0.1791 (t0) REVERT: p 92 PHE cc_start: 0.5727 (m-10) cc_final: 0.5527 (m-10) REVERT: p 104 PHE cc_start: 0.7085 (m-10) cc_final: 0.6629 (m-10) REVERT: q 8 ASP cc_start: 0.7349 (t0) cc_final: 0.6920 (t70) REVERT: r 89 VAL cc_start: 0.7368 (t) cc_final: 0.7118 (t) REVERT: s 8 TYR cc_start: 0.5364 (m-10) cc_final: 0.4828 (m-80) REVERT: s 38 MET cc_start: 0.5957 (tpt) cc_final: 0.5553 (tpp) REVERT: t 26 LEU cc_start: 0.7801 (tp) cc_final: 0.7514 (mm) REVERT: t 81 PHE cc_start: 0.6627 (m-80) cc_final: 0.6149 (m-80) REVERT: v 33 ASP cc_start: 0.4179 (m-30) cc_final: 0.3880 (t0) REVERT: v 59 ASP cc_start: 0.5593 (t0) cc_final: 0.5233 (p0) REVERT: v 141 GLU cc_start: 0.7377 (mp0) cc_final: 0.7039 (mp0) REVERT: w 28 GLU cc_start: 0.6515 (tp30) cc_final: 0.5465 (pm20) REVERT: w 56 TRP cc_start: 0.7151 (m100) cc_final: 0.6163 (t60) REVERT: w 111 ASN cc_start: 0.6843 (m-40) cc_final: 0.6069 (p0) REVERT: x 14 TRP cc_start: 0.6054 (m100) cc_final: 0.5598 (m-10) REVERT: x 16 LYS cc_start: 0.7037 (ttmt) cc_final: 0.6505 (tptt) REVERT: y 8 ARG cc_start: 0.3911 (tpm170) cc_final: 0.3103 (ttt90) REVERT: y 29 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7072 (mmmm) REVERT: z 1 MET cc_start: 0.7168 (mtt) cc_final: 0.6951 (mtp) REVERT: z 4 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7412 (mt-10) outliers start: 175 outliers final: 126 residues processed: 1440 average time/residue: 0.6662 time to fit residues: 1610.5684 Evaluate side-chains 1362 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1229 time to evaluate : 5.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 268 VAL Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 315 VAL Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 272 ASP Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 340 ARG Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain V residue 100 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Y residue 153 VAL Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain b residue 32 GLN Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain i residue 88 ARG Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain i residue 142 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 209 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 109 VAL Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 9.9990 chunk 543 optimal weight: 9.9990 chunk 375 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 345 optimal weight: 20.0000 chunk 485 optimal weight: 20.0000 chunk 725 optimal weight: 7.9990 chunk 768 optimal weight: 8.9990 chunk 379 optimal weight: 20.0000 chunk 687 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS 2 214 GLN ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN H 235 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 52 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 138 ASN M 415 GLN N 63 GLN N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN c 67 ASN f 82 GLN f 95 GLN g 69 ASN k 200 GLN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 69151 Z= 0.562 Angle : 1.611 50.742 93464 Z= 1.030 Chirality : 0.312 6.451 10120 Planarity : 0.006 0.076 11650 Dihedral : 13.443 171.622 10628 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.97 % Allowed : 11.10 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.50 (0.09), residues: 8043 helix: 0.39 (0.08), residues: 4226 sheet: -1.11 (0.26), residues: 352 loop : -1.08 (0.11), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 144 HIS 0.012 0.002 HIS a 44 PHE 0.031 0.002 PHE M 256 TYR 0.026 0.002 TYR 9 118 ARG 0.010 0.001 ARG v 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1281 time to evaluate : 5.929 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: 1 354 TYR cc_start: 0.8652 (m-80) cc_final: 0.8177 (m-80) REVERT: 1 395 ILE cc_start: 0.8335 (mt) cc_final: 0.8092 (mm) REVERT: 2 134 ASP cc_start: 0.7191 (p0) cc_final: 0.6786 (m-30) REVERT: 3 14 ASP cc_start: 0.7856 (m-30) cc_final: 0.7623 (m-30) REVERT: 3 254 MET cc_start: 0.7882 (tmm) cc_final: 0.7276 (tmm) REVERT: 3 288 LYS cc_start: 0.7369 (mtmp) cc_final: 0.6967 (mttm) REVERT: 3 340 SER cc_start: 0.7611 (t) cc_final: 0.6684 (p) REVERT: 3 431 ASP cc_start: 0.7014 (m-30) cc_final: 0.6321 (t70) REVERT: 3 648 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7326 (mm) REVERT: 3 654 GLN cc_start: 0.6049 (tp-100) cc_final: 0.5664 (tt0) REVERT: 4 50 ASN cc_start: 0.8018 (t0) cc_final: 0.7703 (m110) REVERT: 4 59 HIS cc_start: 0.7514 (m-70) cc_final: 0.6819 (m90) REVERT: 4 75 LYS cc_start: 0.8123 (tttm) cc_final: 0.7819 (tptp) REVERT: 4 259 MET cc_start: 0.8769 (mmm) cc_final: 0.8417 (mmm) REVERT: 4 410 MET cc_start: 0.7492 (mtm) cc_final: 0.7059 (mtp) REVERT: 6 32 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7940 (mmtt) REVERT: 6 79 SER cc_start: 0.8380 (t) cc_final: 0.7966 (p) REVERT: 6 81 ARG cc_start: 0.7873 (mpt180) cc_final: 0.7553 (mpt180) REVERT: 6 178 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7226 (mtp180) REVERT: 9 113 MET cc_start: 0.8760 (mmm) cc_final: 0.7800 (mmm) REVERT: H 121 TRP cc_start: 0.7179 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: H 213 VAL cc_start: 0.7199 (m) cc_final: 0.6973 (p) REVERT: H 223 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7137 (m-10) REVERT: J 65 MET cc_start: 0.8337 (mmm) cc_final: 0.8015 (mmp) REVERT: K 91 GLN cc_start: 0.7197 (pm20) cc_final: 0.6763 (pp30) REVERT: L 42 CYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7189 (t) REVERT: L 88 MET cc_start: 0.7789 (mmm) cc_final: 0.7375 (mmm) REVERT: L 95 PHE cc_start: 0.7503 (t80) cc_final: 0.7245 (t80) REVERT: L 150 MET cc_start: 0.7658 (mmm) cc_final: 0.7369 (mmm) REVERT: L 203 MET cc_start: 0.7792 (tpt) cc_final: 0.7550 (tpt) REVERT: L 214 MET cc_start: 0.7410 (mmp) cc_final: 0.6750 (ttt) REVERT: L 286 LEU cc_start: 0.7129 (tp) cc_final: 0.6658 (tt) REVERT: L 340 PHE cc_start: 0.7415 (m-80) cc_final: 0.6867 (m-80) REVERT: L 375 ILE cc_start: 0.8213 (mt) cc_final: 0.7960 (tt) REVERT: L 491 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5675 (tt) REVERT: L 507 THR cc_start: 0.6588 (p) cc_final: 0.6071 (m) REVERT: L 520 PHE cc_start: 0.5749 (t80) cc_final: 0.5429 (t80) REVERT: L 571 MET cc_start: 0.4297 (ttp) cc_final: 0.4042 (ptm) REVERT: N 11 MET cc_start: 0.7906 (mmp) cc_final: 0.7370 (tmm) REVERT: N 151 LEU cc_start: 0.7516 (tp) cc_final: 0.7134 (tt) REVERT: N 167 TRP cc_start: 0.6976 (m-90) cc_final: 0.6604 (m-10) REVERT: N 282 MET cc_start: 0.6886 (mtp) cc_final: 0.6563 (mtm) REVERT: N 289 ASN cc_start: 0.6392 (OUTLIER) cc_final: 0.6110 (t0) REVERT: N 304 MET cc_start: 0.4949 (ptp) cc_final: 0.4726 (ptp) REVERT: N 331 VAL cc_start: 0.8317 (t) cc_final: 0.8096 (p) REVERT: V 98 LEU cc_start: 0.1744 (OUTLIER) cc_final: 0.1542 (pp) REVERT: V 114 CYS cc_start: 0.1817 (OUTLIER) cc_final: 0.0653 (t) REVERT: V 137 GLU cc_start: 0.6295 (tp30) cc_final: 0.5894 (mp0) REVERT: W 36 VAL cc_start: 0.7857 (t) cc_final: 0.7648 (m) REVERT: W 91 MET cc_start: 0.7181 (mtp) cc_final: 0.6498 (ttm) REVERT: W 114 MET cc_start: 0.7991 (mtt) cc_final: 0.7662 (mtt) REVERT: X 15 VAL cc_start: 0.7280 (m) cc_final: 0.6899 (p) REVERT: X 33 ASN cc_start: 0.6284 (t0) cc_final: 0.5897 (m-40) REVERT: X 37 MET cc_start: 0.5006 (mmp) cc_final: 0.4657 (tpp) REVERT: X 58 PHE cc_start: 0.5717 (m-80) cc_final: 0.5331 (m-80) REVERT: Y 3 ILE cc_start: 0.7042 (mm) cc_final: 0.6611 (pt) REVERT: Z 22 GLN cc_start: 0.5706 (tm-30) cc_final: 0.5433 (tp40) REVERT: Z 134 VAL cc_start: 0.7975 (p) cc_final: 0.7652 (t) REVERT: Z 162 MET cc_start: 0.7122 (mtp) cc_final: 0.6916 (ttt) REVERT: a 53 ASP cc_start: 0.7382 (m-30) cc_final: 0.7124 (m-30) REVERT: c 18 ASP cc_start: 0.7212 (t70) cc_final: 0.6644 (p0) REVERT: c 66 GLU cc_start: 0.8686 (tt0) cc_final: 0.8410 (tm-30) REVERT: c 90 GLU cc_start: 0.8159 (mp0) cc_final: 0.7536 (mm-30) REVERT: d 219 LYS cc_start: 0.7700 (mttt) cc_final: 0.7059 (ttpt) REVERT: e 88 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6751 (ttm110) REVERT: f 61 GLU cc_start: 0.6529 (tp30) cc_final: 0.6265 (tp30) REVERT: f 63 ASP cc_start: 0.6228 (t0) cc_final: 0.5795 (t70) REVERT: g 26 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7247 (tt0) REVERT: g 50 GLN cc_start: 0.7840 (pt0) cc_final: 0.7369 (mm-40) REVERT: g 60 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7228 (t70) REVERT: g 90 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7998 (mm-30) REVERT: h 17 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.6916 (mmt-90) REVERT: i 5 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7016 (mp10) REVERT: i 21 ARG cc_start: 0.7089 (ttm-80) cc_final: 0.6638 (tpt170) REVERT: i 53 LYS cc_start: 0.7670 (mmtm) cc_final: 0.7391 (mmmt) REVERT: i 134 ILE cc_start: 0.8642 (mm) cc_final: 0.8261 (mm) REVERT: k 63 THR cc_start: 0.7193 (p) cc_final: 0.6949 (p) REVERT: k 76 ASN cc_start: 0.7075 (t0) cc_final: 0.6801 (t0) REVERT: k 143 PHE cc_start: 0.5175 (m-10) cc_final: 0.4781 (m-10) REVERT: k 153 ASN cc_start: 0.7642 (m-40) cc_final: 0.7166 (m110) REVERT: k 209 THR cc_start: 0.6218 (OUTLIER) cc_final: 0.5754 (p) REVERT: k 210 PHE cc_start: 0.7079 (t80) cc_final: 0.6828 (t80) REVERT: k 214 MET cc_start: 0.6382 (mmm) cc_final: 0.6057 (mmt) REVERT: k 218 CYS cc_start: 0.6406 (p) cc_final: 0.6177 (p) REVERT: k 288 GLN cc_start: 0.7408 (tt0) cc_final: 0.7201 (tt0) REVERT: l 12 ASP cc_start: 0.7098 (t0) cc_final: 0.6731 (t0) REVERT: m 17 VAL cc_start: 0.8239 (t) cc_final: 0.7978 (m) REVERT: n 28 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.6013 (mt) REVERT: n 48 GLU cc_start: 0.6433 (pt0) cc_final: 0.6081 (pt0) REVERT: n 66 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6918 (tp) REVERT: n 71 LYS cc_start: 0.6214 (ttmt) cc_final: 0.5765 (tptp) REVERT: p 43 LYS cc_start: 0.6996 (tppt) cc_final: 0.6663 (tptt) REVERT: p 46 TYR cc_start: 0.6639 (t80) cc_final: 0.6326 (t80) REVERT: p 60 GLU cc_start: 0.6479 (pt0) cc_final: 0.6166 (pt0) REVERT: q 8 ASP cc_start: 0.7352 (t0) cc_final: 0.6888 (t70) REVERT: s 8 TYR cc_start: 0.5422 (m-10) cc_final: 0.4918 (m-80) REVERT: s 30 PHE cc_start: 0.3062 (m-80) cc_final: 0.2336 (m-80) REVERT: s 38 MET cc_start: 0.6128 (tpt) cc_final: 0.5713 (tpp) REVERT: t 26 LEU cc_start: 0.7814 (tp) cc_final: 0.7608 (mm) REVERT: t 81 PHE cc_start: 0.6723 (m-80) cc_final: 0.6488 (m-80) REVERT: v 59 ASP cc_start: 0.5605 (t0) cc_final: 0.5338 (p0) REVERT: v 108 PHE cc_start: 0.6648 (t80) cc_final: 0.6386 (t80) REVERT: v 148 LYS cc_start: 0.6883 (ttmt) cc_final: 0.6611 (ttmm) REVERT: w 92 GLU cc_start: 0.7556 (tp30) cc_final: 0.7304 (tp30) REVERT: w 111 ASN cc_start: 0.6884 (m-40) cc_final: 0.6082 (p0) REVERT: x 14 TRP cc_start: 0.6189 (m100) cc_final: 0.5103 (m-10) REVERT: x 16 LYS cc_start: 0.6974 (ttmt) cc_final: 0.6537 (tptt) REVERT: y 8 ARG cc_start: 0.3800 (tpm170) cc_final: 0.2876 (ttt90) REVERT: y 29 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7039 (mmmm) REVERT: z 1 MET cc_start: 0.7330 (mtt) cc_final: 0.7052 (mtp) REVERT: z 4 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: z 67 GLU cc_start: 0.6821 (pm20) cc_final: 0.6486 (pm20) outliers start: 212 outliers final: 153 residues processed: 1418 average time/residue: 0.6617 time to fit residues: 1587.5000 Evaluate side-chains 1382 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1216 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 268 VAL Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 307 ILE Chi-restraints excluded: chain 1 residue 323 ILE Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 71 MET Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 340 ARG Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 14 ARG Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 29 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain i residue 142 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 209 THR Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 69 CYS Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 153 LEU Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 109 VAL Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 147 ASN Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 54 VAL Chi-restraints excluded: chain z residue 4 GLU Chi-restraints excluded: chain z residue 5 VAL Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 0.9980 chunk 436 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 572 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 655 optimal weight: 7.9990 chunk 531 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 392 optimal weight: 20.0000 chunk 689 optimal weight: 30.0000 chunk 193 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS 2 214 GLN ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 524 ASN N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN f 82 GLN g 69 ASN h 28 GLN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN v 87 ASN v 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69151 Z= 0.522 Angle : 1.584 50.691 93464 Z= 1.019 Chirality : 0.311 6.425 10120 Planarity : 0.005 0.067 11650 Dihedral : 13.147 170.329 10628 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.88 % Allowed : 11.84 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.22 (0.09), residues: 8043 helix: 0.64 (0.08), residues: 4228 sheet: -0.93 (0.27), residues: 346 loop : -0.98 (0.11), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP t 101 HIS 0.009 0.001 HIS Z 55 PHE 0.025 0.002 PHE M 256 TYR 0.025 0.002 TYR r 84 ARG 0.009 0.001 ARG v 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1282 time to evaluate : 6.052 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: 1 317 MET cc_start: 0.8391 (mmm) cc_final: 0.7734 (mmm) REVERT: 1 354 TYR cc_start: 0.8639 (m-80) cc_final: 0.8155 (m-80) REVERT: 1 395 ILE cc_start: 0.8322 (mt) cc_final: 0.8073 (mm) REVERT: 2 134 ASP cc_start: 0.7186 (p0) cc_final: 0.6790 (m-30) REVERT: 3 71 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8032 (tpp) REVERT: 3 190 MET cc_start: 0.7986 (ttm) cc_final: 0.7520 (mmm) REVERT: 3 254 MET cc_start: 0.7943 (tmm) cc_final: 0.7283 (tmm) REVERT: 3 288 LYS cc_start: 0.7293 (mtmp) cc_final: 0.6890 (mttm) REVERT: 3 340 SER cc_start: 0.7652 (t) cc_final: 0.6713 (p) REVERT: 3 431 ASP cc_start: 0.7189 (m-30) cc_final: 0.6425 (t70) REVERT: 3 648 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7299 (mm) REVERT: 3 654 GLN cc_start: 0.6061 (tp-100) cc_final: 0.5655 (tt0) REVERT: 4 50 ASN cc_start: 0.7933 (t0) cc_final: 0.7700 (m110) REVERT: 4 59 HIS cc_start: 0.7500 (m-70) cc_final: 0.6802 (m90) REVERT: 4 75 LYS cc_start: 0.8141 (tttm) cc_final: 0.7846 (tptp) REVERT: 4 259 MET cc_start: 0.8736 (mmm) cc_final: 0.8369 (mmm) REVERT: 4 410 MET cc_start: 0.7559 (mtm) cc_final: 0.7220 (mtp) REVERT: 6 32 LYS cc_start: 0.8216 (mmpt) cc_final: 0.7914 (mmtt) REVERT: 6 79 SER cc_start: 0.8363 (t) cc_final: 0.7952 (p) REVERT: 6 81 ARG cc_start: 0.7860 (mpt180) cc_final: 0.7555 (mpt180) REVERT: 6 178 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7203 (mtp180) REVERT: 9 113 MET cc_start: 0.8730 (mmm) cc_final: 0.8093 (mmm) REVERT: A 44 MET cc_start: 0.3491 (pmm) cc_final: 0.2836 (mtm) REVERT: H 121 TRP cc_start: 0.7154 (OUTLIER) cc_final: 0.6857 (m-10) REVERT: H 213 VAL cc_start: 0.7185 (m) cc_final: 0.6958 (p) REVERT: H 223 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7155 (m-10) REVERT: K 91 GLN cc_start: 0.7186 (pm20) cc_final: 0.6894 (pt0) REVERT: L 60 GLU cc_start: 0.6082 (mt-10) cc_final: 0.5877 (mt-10) REVERT: L 88 MET cc_start: 0.7855 (mmm) cc_final: 0.7427 (mmm) REVERT: L 95 PHE cc_start: 0.7474 (t80) cc_final: 0.7215 (t80) REVERT: L 150 MET cc_start: 0.7612 (mmm) cc_final: 0.7315 (mmm) REVERT: L 203 MET cc_start: 0.7769 (tpt) cc_final: 0.7532 (tpt) REVERT: L 214 MET cc_start: 0.7352 (mmp) cc_final: 0.6675 (ttt) REVERT: L 249 SER cc_start: 0.7139 (OUTLIER) cc_final: 0.6773 (p) REVERT: L 286 LEU cc_start: 0.7150 (tp) cc_final: 0.6665 (tt) REVERT: L 340 PHE cc_start: 0.7377 (m-80) cc_final: 0.6776 (m-80) REVERT: L 475 MET cc_start: 0.7203 (mmm) cc_final: 0.6496 (mmt) REVERT: L 491 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5736 (tt) REVERT: L 507 THR cc_start: 0.6438 (p) cc_final: 0.5880 (m) REVERT: L 520 PHE cc_start: 0.5811 (t80) cc_final: 0.5497 (t80) REVERT: L 558 LEU cc_start: 0.3100 (OUTLIER) cc_final: 0.2825 (mm) REVERT: L 571 MET cc_start: 0.4249 (ttp) cc_final: 0.3977 (ptm) REVERT: M 130 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7832 (tp) REVERT: M 139 GLN cc_start: 0.5686 (mp10) cc_final: 0.5415 (mp10) REVERT: N 11 MET cc_start: 0.7891 (mmp) cc_final: 0.7352 (tmm) REVERT: N 151 LEU cc_start: 0.7487 (tp) cc_final: 0.7110 (tt) REVERT: N 167 TRP cc_start: 0.6893 (m-90) cc_final: 0.6457 (m-10) REVERT: N 265 MET cc_start: 0.8673 (mmp) cc_final: 0.8449 (mmm) REVERT: N 289 ASN cc_start: 0.6159 (OUTLIER) cc_final: 0.5836 (t0) REVERT: V 137 GLU cc_start: 0.6286 (tp30) cc_final: 0.5900 (mp0) REVERT: W 36 VAL cc_start: 0.7852 (t) cc_final: 0.7587 (p) REVERT: W 91 MET cc_start: 0.7197 (mtp) cc_final: 0.6497 (ttm) REVERT: W 114 MET cc_start: 0.8008 (mtt) cc_final: 0.7604 (mtt) REVERT: X 12 LYS cc_start: 0.7118 (mttt) cc_final: 0.6915 (mptt) REVERT: X 15 VAL cc_start: 0.7194 (m) cc_final: 0.6902 (p) REVERT: X 33 ASN cc_start: 0.6255 (t0) cc_final: 0.5875 (m-40) REVERT: X 58 PHE cc_start: 0.5727 (m-80) cc_final: 0.5242 (m-80) REVERT: Y 3 ILE cc_start: 0.6976 (mm) cc_final: 0.6579 (pt) REVERT: Z 84 MET cc_start: 0.6837 (ttp) cc_final: 0.6605 (ttm) REVERT: Z 134 VAL cc_start: 0.7997 (p) cc_final: 0.7679 (t) REVERT: Z 162 MET cc_start: 0.7151 (mtp) cc_final: 0.6934 (ttt) REVERT: a 53 ASP cc_start: 0.7385 (m-30) cc_final: 0.7161 (m-30) REVERT: c 9 GLN cc_start: 0.5830 (pp30) cc_final: 0.5519 (pt0) REVERT: c 10 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6532 (mp) REVERT: c 18 ASP cc_start: 0.7269 (t70) cc_final: 0.6641 (p0) REVERT: c 66 GLU cc_start: 0.8660 (tt0) cc_final: 0.8399 (tm-30) REVERT: c 90 GLU cc_start: 0.8154 (mp0) cc_final: 0.7535 (mm-30) REVERT: d 219 LYS cc_start: 0.7754 (mttt) cc_final: 0.7107 (ttpt) REVERT: d 238 LEU cc_start: 0.8169 (tp) cc_final: 0.7694 (tt) REVERT: e 88 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6777 (ttm110) REVERT: f 61 GLU cc_start: 0.6496 (tp30) cc_final: 0.6217 (tp30) REVERT: f 63 ASP cc_start: 0.6135 (t0) cc_final: 0.5845 (t0) REVERT: g 26 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7165 (tt0) REVERT: g 60 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7206 (t70) REVERT: g 90 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8023 (mm-30) REVERT: h 17 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.6920 (mmt-90) REVERT: h 109 GLU cc_start: 0.7366 (tt0) cc_final: 0.7141 (tt0) REVERT: i 5 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7158 (mp10) REVERT: i 21 ARG cc_start: 0.7067 (ttm-80) cc_final: 0.6637 (tpt170) REVERT: i 53 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7384 (mmmt) REVERT: i 134 ILE cc_start: 0.8641 (mm) cc_final: 0.8300 (mm) REVERT: j 37 MET cc_start: 0.6546 (mmt) cc_final: 0.6255 (mmt) REVERT: j 58 PHE cc_start: 0.6241 (m-80) cc_final: 0.5983 (m-80) REVERT: k 63 THR cc_start: 0.7171 (p) cc_final: 0.6927 (p) REVERT: k 76 ASN cc_start: 0.7084 (t0) cc_final: 0.6768 (t0) REVERT: k 143 PHE cc_start: 0.5222 (m-10) cc_final: 0.4828 (m-10) REVERT: k 209 THR cc_start: 0.6256 (OUTLIER) cc_final: 0.5801 (p) REVERT: k 210 PHE cc_start: 0.7054 (t80) cc_final: 0.6841 (t80) REVERT: k 214 MET cc_start: 0.6321 (mmm) cc_final: 0.6012 (tpp) REVERT: k 218 CYS cc_start: 0.6348 (p) cc_final: 0.5581 (p) REVERT: l 12 ASP cc_start: 0.7065 (t0) cc_final: 0.6702 (t0) REVERT: m 17 VAL cc_start: 0.8238 (t) cc_final: 0.7973 (m) REVERT: n 48 GLU cc_start: 0.6326 (pt0) cc_final: 0.6024 (pt0) REVERT: n 71 LYS cc_start: 0.6206 (ttmt) cc_final: 0.5750 (tptp) REVERT: o 75 LEU cc_start: 0.8382 (mt) cc_final: 0.8165 (mt) REVERT: p 43 LYS cc_start: 0.7013 (tppt) cc_final: 0.6668 (tptt) REVERT: p 46 TYR cc_start: 0.6651 (t80) cc_final: 0.6290 (t80) REVERT: p 60 GLU cc_start: 0.6482 (pt0) cc_final: 0.6168 (pt0) REVERT: p 104 PHE cc_start: 0.7094 (m-10) cc_final: 0.6893 (m-10) REVERT: q 8 ASP cc_start: 0.7362 (t0) cc_final: 0.6951 (t70) REVERT: s 38 MET cc_start: 0.6004 (tpt) cc_final: 0.5672 (tpp) REVERT: t 26 LEU cc_start: 0.7835 (tp) cc_final: 0.7615 (mm) REVERT: t 81 PHE cc_start: 0.6597 (m-80) cc_final: 0.6302 (m-80) REVERT: v 59 ASP cc_start: 0.5633 (t0) cc_final: 0.5312 (p0) REVERT: v 108 PHE cc_start: 0.6570 (t80) cc_final: 0.6338 (t80) REVERT: v 148 LYS cc_start: 0.6771 (ttmt) cc_final: 0.6514 (ttmm) REVERT: w 111 ASN cc_start: 0.6903 (m-40) cc_final: 0.6119 (p0) REVERT: x 14 TRP cc_start: 0.6125 (m100) cc_final: 0.5635 (m-10) REVERT: x 16 LYS cc_start: 0.6997 (ttmt) cc_final: 0.6553 (tptt) REVERT: y 8 ARG cc_start: 0.3719 (tpm170) cc_final: 0.2786 (ttt90) REVERT: y 29 LYS cc_start: 0.7614 (ttmm) cc_final: 0.7138 (mmmm) REVERT: z 4 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7481 (mt-10) REVERT: z 67 GLU cc_start: 0.6784 (pm20) cc_final: 0.6485 (pm20) outliers start: 205 outliers final: 160 residues processed: 1403 average time/residue: 0.6527 time to fit residues: 1549.2338 Evaluate side-chains 1394 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1222 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 307 ILE Chi-restraints excluded: chain 1 residue 315 VAL Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 71 MET Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 524 ASN Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 14 ARG Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain b residue 32 GLN Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 231 VAL Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain i residue 142 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 209 THR Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain u residue 21 GLN Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 71 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 147 ASN Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 5 VAL Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 7.9990 chunk 692 optimal weight: 50.0000 chunk 151 optimal weight: 9.9990 chunk 451 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 769 optimal weight: 10.0000 chunk 638 optimal weight: 8.9990 chunk 356 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 254 optimal weight: 10.0000 chunk 403 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 ASN f 82 GLN g 69 ASN i 135 GLN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 69151 Z= 0.553 Angle : 1.603 50.760 93464 Z= 1.027 Chirality : 0.312 6.436 10120 Planarity : 0.005 0.070 11650 Dihedral : 13.199 170.138 10628 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.31 % Allowed : 11.99 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.24 (0.09), residues: 8043 helix: 0.61 (0.08), residues: 4230 sheet: -1.00 (0.27), residues: 347 loop : -0.97 (0.11), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP t 101 HIS 0.011 0.002 HIS Z 55 PHE 0.027 0.002 PHE X 60 TYR 0.029 0.002 TYR r 84 ARG 0.007 0.001 ARG 4 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1231 time to evaluate : 6.028 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: 1 354 TYR cc_start: 0.8679 (m-80) cc_final: 0.8128 (m-80) REVERT: 1 395 ILE cc_start: 0.8329 (mt) cc_final: 0.8010 (mm) REVERT: 2 134 ASP cc_start: 0.7291 (p0) cc_final: 0.6853 (m-30) REVERT: 3 190 MET cc_start: 0.7888 (ttm) cc_final: 0.7286 (mmm) REVERT: 3 254 MET cc_start: 0.7993 (tmm) cc_final: 0.7311 (tmm) REVERT: 3 288 LYS cc_start: 0.7260 (mtmp) cc_final: 0.6844 (mttm) REVERT: 3 340 SER cc_start: 0.7632 (t) cc_final: 0.6703 (p) REVERT: 3 431 ASP cc_start: 0.7299 (m-30) cc_final: 0.6436 (t70) REVERT: 3 648 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7306 (mm) REVERT: 3 654 GLN cc_start: 0.6051 (tp-100) cc_final: 0.5617 (tt0) REVERT: 4 50 ASN cc_start: 0.7933 (t0) cc_final: 0.7696 (m110) REVERT: 4 59 HIS cc_start: 0.7510 (m-70) cc_final: 0.6838 (m90) REVERT: 4 75 LYS cc_start: 0.8132 (tttm) cc_final: 0.7844 (tptp) REVERT: 4 259 MET cc_start: 0.8750 (mmm) cc_final: 0.8394 (mmm) REVERT: 5 47 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8071 (mm-30) REVERT: 6 32 LYS cc_start: 0.8229 (mmpt) cc_final: 0.7975 (mmtt) REVERT: 6 79 SER cc_start: 0.8274 (t) cc_final: 0.7886 (p) REVERT: 6 81 ARG cc_start: 0.7870 (mpt180) cc_final: 0.7578 (mpt180) REVERT: 6 178 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7276 (mtp180) REVERT: H 85 MET cc_start: 0.8242 (mmm) cc_final: 0.7810 (mmm) REVERT: H 105 MET cc_start: 0.7713 (mtp) cc_final: 0.7299 (mtp) REVERT: H 213 VAL cc_start: 0.7155 (m) cc_final: 0.6929 (p) REVERT: H 223 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7178 (m-10) REVERT: J 65 MET cc_start: 0.8335 (mmm) cc_final: 0.7937 (mmt) REVERT: K 91 GLN cc_start: 0.7171 (pm20) cc_final: 0.6868 (pt0) REVERT: L 60 GLU cc_start: 0.6040 (mt-10) cc_final: 0.5780 (mt-10) REVERT: L 88 MET cc_start: 0.7819 (mmm) cc_final: 0.7362 (mmm) REVERT: L 95 PHE cc_start: 0.7467 (t80) cc_final: 0.7200 (t80) REVERT: L 150 MET cc_start: 0.7636 (mmm) cc_final: 0.7321 (mmm) REVERT: L 203 MET cc_start: 0.7775 (tpt) cc_final: 0.7528 (tpt) REVERT: L 214 MET cc_start: 0.7375 (mmp) cc_final: 0.6694 (ttt) REVERT: L 249 SER cc_start: 0.7105 (OUTLIER) cc_final: 0.6742 (p) REVERT: L 286 LEU cc_start: 0.7188 (tp) cc_final: 0.6720 (tt) REVERT: L 326 PHE cc_start: 0.6679 (t80) cc_final: 0.6474 (t80) REVERT: L 340 PHE cc_start: 0.7368 (m-80) cc_final: 0.6860 (m-80) REVERT: L 375 ILE cc_start: 0.8222 (mt) cc_final: 0.8004 (tt) REVERT: L 475 MET cc_start: 0.7334 (mmm) cc_final: 0.6247 (mmt) REVERT: L 491 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5744 (tt) REVERT: L 507 THR cc_start: 0.6406 (p) cc_final: 0.5860 (m) REVERT: L 558 LEU cc_start: 0.3089 (OUTLIER) cc_final: 0.2866 (mm) REVERT: L 571 MET cc_start: 0.4325 (ttp) cc_final: 0.4036 (ptm) REVERT: M 115 LEU cc_start: 0.7467 (mt) cc_final: 0.7263 (mp) REVERT: M 130 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7811 (tp) REVERT: N 11 MET cc_start: 0.7964 (mmp) cc_final: 0.7462 (tmm) REVERT: N 151 LEU cc_start: 0.7505 (tp) cc_final: 0.7145 (tt) REVERT: N 167 TRP cc_start: 0.6904 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: N 265 MET cc_start: 0.8669 (mmp) cc_final: 0.8465 (mmm) REVERT: N 304 MET cc_start: 0.4916 (ptp) cc_final: 0.4657 (ptp) REVERT: V 137 GLU cc_start: 0.6398 (tp30) cc_final: 0.5975 (mp0) REVERT: W 36 VAL cc_start: 0.7864 (t) cc_final: 0.7595 (p) REVERT: W 91 MET cc_start: 0.7291 (mtp) cc_final: 0.6540 (ttm) REVERT: W 114 MET cc_start: 0.8049 (mtt) cc_final: 0.7710 (mtt) REVERT: X 15 VAL cc_start: 0.7134 (m) cc_final: 0.6775 (p) REVERT: X 33 ASN cc_start: 0.6260 (t0) cc_final: 0.5875 (m-40) REVERT: X 55 GLU cc_start: 0.6319 (mt-10) cc_final: 0.6119 (mt-10) REVERT: X 58 PHE cc_start: 0.5853 (m-80) cc_final: 0.5356 (m-80) REVERT: X 71 MET cc_start: 0.5091 (mmp) cc_final: 0.4479 (mmt) REVERT: Y 3 ILE cc_start: 0.7020 (mm) cc_final: 0.6645 (pt) REVERT: Z 134 VAL cc_start: 0.8013 (p) cc_final: 0.7694 (t) REVERT: a 53 ASP cc_start: 0.7380 (m-30) cc_final: 0.7122 (m-30) REVERT: c 9 GLN cc_start: 0.5884 (pp30) cc_final: 0.5570 (pt0) REVERT: c 10 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6540 (mp) REVERT: c 18 ASP cc_start: 0.7236 (t70) cc_final: 0.6617 (p0) REVERT: c 66 GLU cc_start: 0.8650 (tt0) cc_final: 0.8391 (tm-30) REVERT: c 90 GLU cc_start: 0.8152 (mp0) cc_final: 0.7537 (mm-30) REVERT: d 238 LEU cc_start: 0.8223 (tp) cc_final: 0.7906 (tt) REVERT: e 88 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6772 (ttm110) REVERT: f 61 GLU cc_start: 0.6484 (tp30) cc_final: 0.6237 (tp30) REVERT: f 63 ASP cc_start: 0.6264 (t0) cc_final: 0.5881 (t0) REVERT: g 26 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7235 (tt0) REVERT: g 60 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7232 (t70) REVERT: g 90 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8020 (mm-30) REVERT: h 17 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.6928 (mmt-90) REVERT: h 109 GLU cc_start: 0.7307 (tt0) cc_final: 0.7066 (tt0) REVERT: i 5 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7062 (mp10) REVERT: i 134 ILE cc_start: 0.8672 (mm) cc_final: 0.8343 (mm) REVERT: i 135 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8078 (mm-40) REVERT: j 37 MET cc_start: 0.6571 (mmt) cc_final: 0.6282 (mmt) REVERT: j 58 PHE cc_start: 0.6248 (m-80) cc_final: 0.5974 (m-80) REVERT: k 63 THR cc_start: 0.7140 (p) cc_final: 0.6910 (p) REVERT: k 76 ASN cc_start: 0.7107 (t0) cc_final: 0.6771 (t0) REVERT: k 143 PHE cc_start: 0.5157 (m-10) cc_final: 0.4810 (m-10) REVERT: k 209 THR cc_start: 0.6193 (OUTLIER) cc_final: 0.5755 (p) REVERT: k 210 PHE cc_start: 0.7064 (t80) cc_final: 0.6827 (t80) REVERT: k 214 MET cc_start: 0.6322 (mmm) cc_final: 0.6001 (tpp) REVERT: k 218 CYS cc_start: 0.6344 (p) cc_final: 0.5559 (p) REVERT: l 12 ASP cc_start: 0.7105 (t0) cc_final: 0.6901 (t0) REVERT: m 17 VAL cc_start: 0.8250 (t) cc_final: 0.7991 (m) REVERT: n 62 PHE cc_start: 0.6641 (t80) cc_final: 0.6408 (t80) REVERT: n 66 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6876 (tp) REVERT: n 71 LYS cc_start: 0.6218 (ttmt) cc_final: 0.5742 (tptp) REVERT: o 1 MET cc_start: 0.5912 (ptt) cc_final: 0.5548 (ttp) REVERT: p 43 LYS cc_start: 0.6997 (tppt) cc_final: 0.6652 (tptt) REVERT: p 60 GLU cc_start: 0.6470 (pt0) cc_final: 0.6069 (pt0) REVERT: q 8 ASP cc_start: 0.7280 (t0) cc_final: 0.6815 (t70) REVERT: r 94 TYR cc_start: 0.7533 (m-10) cc_final: 0.7315 (m-10) REVERT: s 8 TYR cc_start: 0.5392 (m-10) cc_final: 0.4823 (m-80) REVERT: s 30 PHE cc_start: 0.3851 (m-80) cc_final: 0.3512 (m-80) REVERT: s 38 MET cc_start: 0.6220 (tpt) cc_final: 0.5910 (tpp) REVERT: t 26 LEU cc_start: 0.7778 (tp) cc_final: 0.7559 (mm) REVERT: t 81 PHE cc_start: 0.6725 (m-80) cc_final: 0.6498 (m-80) REVERT: v 81 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7461 (tp) REVERT: v 108 PHE cc_start: 0.6732 (t80) cc_final: 0.6482 (t80) REVERT: v 148 LYS cc_start: 0.6765 (ttmt) cc_final: 0.6510 (ttmm) REVERT: w 111 ASN cc_start: 0.6904 (m-40) cc_final: 0.6110 (p0) REVERT: x 14 TRP cc_start: 0.6075 (m100) cc_final: 0.5590 (m-10) REVERT: y 8 ARG cc_start: 0.3747 (tpm170) cc_final: 0.2796 (ttt90) REVERT: y 29 LYS cc_start: 0.7705 (ttmm) cc_final: 0.7264 (mmmm) REVERT: z 67 GLU cc_start: 0.6705 (pm20) cc_final: 0.6421 (pm20) outliers start: 236 outliers final: 186 residues processed: 1379 average time/residue: 0.6486 time to fit residues: 1519.3183 Evaluate side-chains 1393 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1195 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 268 VAL Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 307 ILE Chi-restraints excluded: chain 1 residue 315 VAL Chi-restraints excluded: chain 1 residue 323 ILE Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 66 VAL Chi-restraints excluded: chain 3 residue 71 MET Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 29 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 6 residue 107 MET Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain M residue 423 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 167 TRP Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Y residue 153 VAL Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 14 ARG Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 45 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 104 ASP Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 231 VAL Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain i residue 142 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 209 THR Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 69 CYS Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 153 LEU Chi-restraints excluded: chain u residue 21 GLN Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 71 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 147 ASN Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 54 VAL Chi-restraints excluded: chain z residue 5 VAL Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 6.9990 chunk 86 optimal weight: 30.0000 chunk 438 optimal weight: 30.0000 chunk 561 optimal weight: 9.9990 chunk 435 optimal weight: 40.0000 chunk 647 optimal weight: 0.9980 chunk 429 optimal weight: 20.0000 chunk 766 optimal weight: 0.7980 chunk 479 optimal weight: 40.0000 chunk 467 optimal weight: 30.0000 chunk 353 optimal weight: 9.9990 overall best weight: 5.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 180 ASN d 234 ASN f 82 GLN g 69 ASN i 122 GLN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69151 Z= 0.517 Angle : 1.582 50.687 93464 Z= 1.018 Chirality : 0.311 6.420 10120 Planarity : 0.005 0.066 11650 Dihedral : 12.978 170.460 10628 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.99 % Allowed : 12.83 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.05 (0.09), residues: 8043 helix: 0.77 (0.08), residues: 4235 sheet: -0.87 (0.27), residues: 337 loop : -0.90 (0.11), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP t 101 HIS 0.009 0.001 HIS Z 55 PHE 0.027 0.002 PHE M 122 TYR 0.028 0.002 TYR r 84 ARG 0.008 0.001 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1243 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: 1 317 MET cc_start: 0.8381 (mmm) cc_final: 0.7770 (mmm) REVERT: 1 354 TYR cc_start: 0.8654 (m-80) cc_final: 0.8134 (m-80) REVERT: 1 395 ILE cc_start: 0.8321 (mt) cc_final: 0.8068 (mm) REVERT: 2 134 ASP cc_start: 0.7295 (p0) cc_final: 0.6874 (m-30) REVERT: 3 14 ASP cc_start: 0.7850 (m-30) cc_final: 0.7602 (m-30) REVERT: 3 71 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8024 (tpp) REVERT: 3 190 MET cc_start: 0.7856 (ttm) cc_final: 0.7361 (mmm) REVERT: 3 254 MET cc_start: 0.8040 (tmm) cc_final: 0.7334 (tmm) REVERT: 3 288 LYS cc_start: 0.7305 (mtmp) cc_final: 0.6895 (mttm) REVERT: 3 340 SER cc_start: 0.7649 (t) cc_final: 0.6698 (p) REVERT: 3 431 ASP cc_start: 0.7283 (m-30) cc_final: 0.6405 (t0) REVERT: 3 648 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7289 (mm) REVERT: 3 654 GLN cc_start: 0.6045 (tp-100) cc_final: 0.5611 (tt0) REVERT: 4 50 ASN cc_start: 0.7836 (t0) cc_final: 0.7617 (m110) REVERT: 4 59 HIS cc_start: 0.7460 (m-70) cc_final: 0.6778 (m90) REVERT: 4 75 LYS cc_start: 0.8142 (tttm) cc_final: 0.7852 (tptp) REVERT: 4 259 MET cc_start: 0.8724 (mmm) cc_final: 0.8359 (mmm) REVERT: 4 410 MET cc_start: 0.7515 (mtp) cc_final: 0.7250 (mtp) REVERT: 5 47 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8051 (mm-30) REVERT: 6 32 LYS cc_start: 0.8221 (mmpt) cc_final: 0.7935 (mmtt) REVERT: 6 79 SER cc_start: 0.8264 (t) cc_final: 0.7768 (p) REVERT: 6 81 ARG cc_start: 0.7830 (mpt180) cc_final: 0.7549 (mpt180) REVERT: 6 178 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7252 (mtp180) REVERT: A 113 TRP cc_start: 0.6470 (m-10) cc_final: 0.6058 (m-90) REVERT: H 85 MET cc_start: 0.8237 (mmm) cc_final: 0.7974 (mmm) REVERT: H 223 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7177 (m-10) REVERT: J 2 MET cc_start: 0.6234 (mmm) cc_final: 0.5047 (mmt) REVERT: J 65 MET cc_start: 0.8318 (mmm) cc_final: 0.7964 (mmp) REVERT: K 91 GLN cc_start: 0.6928 (pm20) cc_final: 0.6592 (pt0) REVERT: L 88 MET cc_start: 0.7739 (mmm) cc_final: 0.7253 (mmm) REVERT: L 95 PHE cc_start: 0.7406 (t80) cc_final: 0.7161 (t80) REVERT: L 105 MET cc_start: 0.7419 (mtp) cc_final: 0.7104 (tpp) REVERT: L 150 MET cc_start: 0.7634 (mmm) cc_final: 0.7315 (mmm) REVERT: L 203 MET cc_start: 0.7757 (tpt) cc_final: 0.7506 (tpt) REVERT: L 214 MET cc_start: 0.7372 (mmp) cc_final: 0.6684 (ttt) REVERT: L 249 SER cc_start: 0.7064 (p) cc_final: 0.6716 (p) REVERT: L 286 LEU cc_start: 0.7058 (tp) cc_final: 0.6555 (tt) REVERT: L 340 PHE cc_start: 0.7366 (m-80) cc_final: 0.6829 (m-80) REVERT: L 475 MET cc_start: 0.7365 (mmm) cc_final: 0.6275 (mmt) REVERT: L 507 THR cc_start: 0.6324 (p) cc_final: 0.5751 (m) REVERT: L 558 LEU cc_start: 0.3087 (OUTLIER) cc_final: 0.2852 (mm) REVERT: L 571 MET cc_start: 0.4305 (ttp) cc_final: 0.4022 (ptm) REVERT: M 130 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7816 (tp) REVERT: M 374 ASN cc_start: 0.8052 (m110) cc_final: 0.7850 (m110) REVERT: N 11 MET cc_start: 0.7892 (mmp) cc_final: 0.7361 (tmm) REVERT: N 151 LEU cc_start: 0.7538 (tp) cc_final: 0.7170 (tt) REVERT: N 167 TRP cc_start: 0.6864 (OUTLIER) cc_final: 0.6396 (m-10) REVERT: N 265 MET cc_start: 0.8643 (mmp) cc_final: 0.8436 (mmm) REVERT: N 289 ASN cc_start: 0.6192 (OUTLIER) cc_final: 0.5864 (t0) REVERT: N 304 MET cc_start: 0.4891 (ptp) cc_final: 0.4563 (ptp) REVERT: V 137 GLU cc_start: 0.6299 (tp30) cc_final: 0.5966 (mp0) REVERT: W 36 VAL cc_start: 0.7838 (t) cc_final: 0.7577 (p) REVERT: W 91 MET cc_start: 0.7234 (mtp) cc_final: 0.6610 (ttm) REVERT: W 114 MET cc_start: 0.8052 (mtt) cc_final: 0.7613 (mtt) REVERT: X 15 VAL cc_start: 0.7144 (m) cc_final: 0.6921 (p) REVERT: X 33 ASN cc_start: 0.6322 (t0) cc_final: 0.5859 (m-40) REVERT: X 55 GLU cc_start: 0.6324 (mt-10) cc_final: 0.5786 (mt-10) REVERT: X 56 ASP cc_start: 0.6910 (m-30) cc_final: 0.5948 (t0) REVERT: X 71 MET cc_start: 0.5142 (mmp) cc_final: 0.4508 (mmt) REVERT: Y 3 ILE cc_start: 0.6991 (mm) cc_final: 0.6633 (pt) REVERT: Z 134 VAL cc_start: 0.8007 (p) cc_final: 0.7686 (t) REVERT: a 53 ASP cc_start: 0.7385 (m-30) cc_final: 0.7164 (m-30) REVERT: c 9 GLN cc_start: 0.5878 (pp30) cc_final: 0.5579 (pt0) REVERT: c 10 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6561 (mp) REVERT: c 18 ASP cc_start: 0.7235 (t70) cc_final: 0.6595 (p0) REVERT: c 66 GLU cc_start: 0.8638 (tt0) cc_final: 0.8367 (tm-30) REVERT: c 90 GLU cc_start: 0.8103 (mp0) cc_final: 0.7535 (mm-30) REVERT: d 238 LEU cc_start: 0.8184 (tp) cc_final: 0.7738 (tt) REVERT: e 88 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6788 (ttm110) REVERT: f 61 GLU cc_start: 0.6494 (tp30) cc_final: 0.6293 (tp30) REVERT: f 63 ASP cc_start: 0.6216 (t0) cc_final: 0.5990 (t0) REVERT: g 60 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7213 (t70) REVERT: g 90 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8023 (mm-30) REVERT: h 17 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.6940 (mmt-90) REVERT: h 109 GLU cc_start: 0.7281 (tt0) cc_final: 0.7046 (tt0) REVERT: i 134 ILE cc_start: 0.8682 (mm) cc_final: 0.8355 (mm) REVERT: i 135 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7781 (mm-40) REVERT: j 37 MET cc_start: 0.6589 (mmt) cc_final: 0.6311 (mmt) REVERT: j 58 PHE cc_start: 0.6214 (m-80) cc_final: 0.5949 (m-80) REVERT: k 76 ASN cc_start: 0.7116 (t0) cc_final: 0.6768 (t0) REVERT: k 143 PHE cc_start: 0.5152 (m-10) cc_final: 0.4796 (m-10) REVERT: k 214 MET cc_start: 0.6375 (mmm) cc_final: 0.6076 (tpp) REVERT: k 218 CYS cc_start: 0.6305 (p) cc_final: 0.5583 (p) REVERT: l 12 ASP cc_start: 0.7069 (t0) cc_final: 0.6861 (t0) REVERT: m 17 VAL cc_start: 0.8246 (t) cc_final: 0.7983 (m) REVERT: n 42 ASP cc_start: 0.3150 (OUTLIER) cc_final: 0.2864 (t0) REVERT: n 66 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6789 (tp) REVERT: n 71 LYS cc_start: 0.6208 (ttmt) cc_final: 0.5725 (tptp) REVERT: o 1 MET cc_start: 0.5962 (ptt) cc_final: 0.5513 (ttp) REVERT: p 43 LYS cc_start: 0.7033 (tppt) cc_final: 0.6674 (tptt) REVERT: p 46 TYR cc_start: 0.6575 (t80) cc_final: 0.6216 (t80) REVERT: p 60 GLU cc_start: 0.6495 (pt0) cc_final: 0.6167 (pt0) REVERT: q 8 ASP cc_start: 0.7263 (t0) cc_final: 0.6794 (t70) REVERT: r 94 TYR cc_start: 0.7582 (m-10) cc_final: 0.7311 (m-10) REVERT: s 8 TYR cc_start: 0.5363 (m-10) cc_final: 0.4811 (m-80) REVERT: s 30 PHE cc_start: 0.4077 (m-80) cc_final: 0.3827 (m-80) REVERT: s 38 MET cc_start: 0.6016 (tpt) cc_final: 0.5721 (tpp) REVERT: t 26 LEU cc_start: 0.7734 (tp) cc_final: 0.7524 (mm) REVERT: t 81 PHE cc_start: 0.6748 (m-80) cc_final: 0.6515 (m-80) REVERT: u 11 TYR cc_start: 0.5684 (t80) cc_final: 0.5481 (t80) REVERT: u 32 MET cc_start: 0.6504 (ttp) cc_final: 0.6286 (ttp) REVERT: v 81 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7393 (tp) REVERT: v 108 PHE cc_start: 0.6690 (t80) cc_final: 0.6452 (t80) REVERT: v 148 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6526 (ttmm) REVERT: w 82 ASP cc_start: 0.7931 (t0) cc_final: 0.7509 (t70) REVERT: w 111 ASN cc_start: 0.6921 (m-40) cc_final: 0.6080 (p0) REVERT: x 14 TRP cc_start: 0.6071 (m100) cc_final: 0.5615 (m-10) REVERT: y 8 ARG cc_start: 0.3751 (tpm170) cc_final: 0.2860 (ttt90) REVERT: y 29 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7274 (mmmm) outliers start: 213 outliers final: 176 residues processed: 1374 average time/residue: 0.6674 time to fit residues: 1557.0191 Evaluate side-chains 1386 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1198 time to evaluate : 5.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 307 ILE Chi-restraints excluded: chain 1 residue 315 VAL Chi-restraints excluded: chain 1 residue 323 ILE Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 66 VAL Chi-restraints excluded: chain 3 residue 71 MET Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 29 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 482 MET Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 167 TRP Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 12 LYS Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 231 VAL Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 57 CYS Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain i residue 142 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 69 CYS Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 153 LEU Chi-restraints excluded: chain u residue 21 GLN Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 71 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 87 ASN Chi-restraints excluded: chain v residue 109 VAL Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 147 ASN Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 5 VAL Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 457 optimal weight: 6.9990 chunk 230 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 487 optimal weight: 8.9990 chunk 522 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 602 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN H 235 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** Z 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 ASN f 82 GLN g 69 ASN i 122 GLN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69151 Z= 0.516 Angle : 1.581 50.695 93464 Z= 1.018 Chirality : 0.311 6.418 10120 Planarity : 0.005 0.066 11650 Dihedral : 12.848 173.476 10628 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.92 % Allowed : 13.26 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.03 (0.09), residues: 8043 helix: 0.83 (0.08), residues: 4242 sheet: -0.83 (0.27), residues: 337 loop : -0.85 (0.11), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP t 101 HIS 0.009 0.001 HIS Z 55 PHE 0.034 0.002 PHE s 24 TYR 0.028 0.002 TYR r 84 ARG 0.006 0.001 ARG v 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1226 time to evaluate : 6.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 317 MET cc_start: 0.8378 (mmm) cc_final: 0.7791 (mmm) REVERT: 1 354 TYR cc_start: 0.8643 (m-80) cc_final: 0.8193 (m-80) REVERT: 1 395 ILE cc_start: 0.8323 (mt) cc_final: 0.8069 (mm) REVERT: 1 430 MET cc_start: 0.8202 (mtm) cc_final: 0.7879 (mtt) REVERT: 2 134 ASP cc_start: 0.7298 (p0) cc_final: 0.6876 (m-30) REVERT: 3 71 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8028 (tpp) REVERT: 3 190 MET cc_start: 0.7846 (ttm) cc_final: 0.7345 (mmm) REVERT: 3 254 MET cc_start: 0.8063 (tmm) cc_final: 0.7323 (tmm) REVERT: 3 288 LYS cc_start: 0.7299 (mtmp) cc_final: 0.6876 (mttm) REVERT: 3 340 SER cc_start: 0.7614 (t) cc_final: 0.6685 (p) REVERT: 3 648 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7291 (mm) REVERT: 3 654 GLN cc_start: 0.6038 (tp-100) cc_final: 0.5603 (tt0) REVERT: 4 59 HIS cc_start: 0.7441 (m-70) cc_final: 0.6762 (m90) REVERT: 4 75 LYS cc_start: 0.8180 (tttm) cc_final: 0.7877 (tptp) REVERT: 4 259 MET cc_start: 0.8738 (mmm) cc_final: 0.8381 (mmm) REVERT: 5 47 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8040 (mm-30) REVERT: 6 32 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7943 (mmtt) REVERT: 6 79 SER cc_start: 0.8268 (t) cc_final: 0.7762 (p) REVERT: 6 81 ARG cc_start: 0.7831 (mpt180) cc_final: 0.7562 (mpt180) REVERT: 6 178 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7248 (mtp180) REVERT: H 85 MET cc_start: 0.8240 (mmm) cc_final: 0.7966 (mmm) REVERT: H 105 MET cc_start: 0.7512 (mtp) cc_final: 0.7145 (ttp) REVERT: H 223 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7177 (m-10) REVERT: J 2 MET cc_start: 0.6204 (mmm) cc_final: 0.4941 (mmt) REVERT: J 65 MET cc_start: 0.8327 (mmm) cc_final: 0.7968 (mmp) REVERT: K 91 GLN cc_start: 0.6907 (pm20) cc_final: 0.6591 (pt0) REVERT: L 88 MET cc_start: 0.7739 (mmm) cc_final: 0.7264 (mmm) REVERT: L 95 PHE cc_start: 0.7400 (t80) cc_final: 0.7119 (t80) REVERT: L 150 MET cc_start: 0.7637 (mmm) cc_final: 0.7310 (mmm) REVERT: L 203 MET cc_start: 0.7703 (tpt) cc_final: 0.7469 (tpt) REVERT: L 214 MET cc_start: 0.7407 (mmp) cc_final: 0.6705 (ttt) REVERT: L 249 SER cc_start: 0.7024 (p) cc_final: 0.6665 (p) REVERT: L 286 LEU cc_start: 0.7056 (tp) cc_final: 0.6577 (tt) REVERT: L 340 PHE cc_start: 0.7361 (m-80) cc_final: 0.6798 (m-80) REVERT: L 475 MET cc_start: 0.7429 (mmm) cc_final: 0.6305 (mmt) REVERT: L 507 THR cc_start: 0.6315 (p) cc_final: 0.5725 (m) REVERT: L 558 LEU cc_start: 0.3089 (OUTLIER) cc_final: 0.2864 (mm) REVERT: L 571 MET cc_start: 0.4267 (ttp) cc_final: 0.3967 (ptm) REVERT: M 130 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7824 (tp) REVERT: M 204 MET cc_start: 0.7528 (mmm) cc_final: 0.7132 (mmm) REVERT: M 206 LYS cc_start: 0.8264 (ttmm) cc_final: 0.8061 (ttmm) REVERT: M 374 ASN cc_start: 0.8029 (m110) cc_final: 0.7820 (m110) REVERT: M 396 MET cc_start: 0.8113 (mmt) cc_final: 0.7897 (mmt) REVERT: N 11 MET cc_start: 0.7891 (mmp) cc_final: 0.7356 (tmm) REVERT: N 151 LEU cc_start: 0.7523 (tp) cc_final: 0.7156 (tt) REVERT: N 167 TRP cc_start: 0.6833 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: N 265 MET cc_start: 0.8649 (mmp) cc_final: 0.8437 (mmm) REVERT: N 289 ASN cc_start: 0.6188 (OUTLIER) cc_final: 0.5849 (t0) REVERT: V 137 GLU cc_start: 0.6270 (tp30) cc_final: 0.5860 (mp0) REVERT: W 36 VAL cc_start: 0.7747 (t) cc_final: 0.7508 (p) REVERT: W 91 MET cc_start: 0.7196 (mtp) cc_final: 0.6571 (ttm) REVERT: W 114 MET cc_start: 0.8059 (mtt) cc_final: 0.7639 (mtt) REVERT: X 15 VAL cc_start: 0.7294 (m) cc_final: 0.6988 (p) REVERT: X 33 ASN cc_start: 0.6316 (t0) cc_final: 0.5855 (m-40) REVERT: X 52 MET cc_start: 0.6313 (mmt) cc_final: 0.6113 (mmt) REVERT: X 55 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5662 (mt-10) REVERT: X 71 MET cc_start: 0.5093 (mmp) cc_final: 0.4480 (mmt) REVERT: Y 3 ILE cc_start: 0.6979 (mm) cc_final: 0.6635 (pt) REVERT: Z 22 GLN cc_start: 0.5556 (tm-30) cc_final: 0.5206 (tp40) REVERT: Z 134 VAL cc_start: 0.7941 (p) cc_final: 0.7653 (t) REVERT: a 53 ASP cc_start: 0.7388 (m-30) cc_final: 0.7171 (m-30) REVERT: c 9 GLN cc_start: 0.5878 (pp30) cc_final: 0.5594 (pt0) REVERT: c 10 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6576 (mp) REVERT: c 15 GLU cc_start: 0.5269 (mp0) cc_final: 0.4887 (mt-10) REVERT: c 18 ASP cc_start: 0.7238 (t70) cc_final: 0.6587 (p0) REVERT: c 66 GLU cc_start: 0.8638 (tt0) cc_final: 0.8366 (tm-30) REVERT: d 238 LEU cc_start: 0.8188 (tp) cc_final: 0.7877 (tt) REVERT: e 88 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6790 (ttm110) REVERT: f 63 ASP cc_start: 0.6096 (t0) cc_final: 0.5885 (t0) REVERT: g 24 MET cc_start: 0.6644 (mmm) cc_final: 0.6349 (tpp) REVERT: g 60 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7219 (t70) REVERT: g 90 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8025 (mm-30) REVERT: h 17 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.6939 (mmt-90) REVERT: h 61 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7760 (mt-10) REVERT: i 8 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6600 (tttt) REVERT: i 134 ILE cc_start: 0.8685 (mm) cc_final: 0.8357 (mm) REVERT: i 135 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7812 (mm-40) REVERT: j 37 MET cc_start: 0.6579 (mmt) cc_final: 0.6299 (mmt) REVERT: j 58 PHE cc_start: 0.6157 (m-80) cc_final: 0.5876 (m-80) REVERT: k 76 ASN cc_start: 0.7030 (t0) cc_final: 0.6717 (t0) REVERT: k 143 PHE cc_start: 0.5107 (m-10) cc_final: 0.4756 (m-10) REVERT: k 209 THR cc_start: 0.6069 (OUTLIER) cc_final: 0.5617 (p) REVERT: k 214 MET cc_start: 0.6321 (mmm) cc_final: 0.6079 (tpp) REVERT: k 218 CYS cc_start: 0.6306 (p) cc_final: 0.5662 (p) REVERT: l 12 ASP cc_start: 0.7053 (t0) cc_final: 0.6845 (t0) REVERT: m 10 ASN cc_start: 0.7607 (t0) cc_final: 0.7376 (t0) REVERT: m 17 VAL cc_start: 0.8245 (t) cc_final: 0.7983 (m) REVERT: n 42 ASP cc_start: 0.3115 (OUTLIER) cc_final: 0.2806 (t0) REVERT: n 66 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6769 (tp) REVERT: n 71 LYS cc_start: 0.6171 (ttmt) cc_final: 0.5707 (tptp) REVERT: o 1 MET cc_start: 0.5472 (ptt) cc_final: 0.5015 (ttp) REVERT: p 43 LYS cc_start: 0.7033 (tppt) cc_final: 0.6667 (tptt) REVERT: p 60 GLU cc_start: 0.6495 (pt0) cc_final: 0.6079 (pt0) REVERT: q 8 ASP cc_start: 0.7270 (t0) cc_final: 0.6787 (t70) REVERT: r 94 TYR cc_start: 0.7627 (m-10) cc_final: 0.7356 (m-10) REVERT: s 30 PHE cc_start: 0.4215 (m-80) cc_final: 0.3994 (m-80) REVERT: s 38 MET cc_start: 0.6049 (tpt) cc_final: 0.5774 (tpp) REVERT: t 26 LEU cc_start: 0.7751 (tp) cc_final: 0.7533 (mm) REVERT: t 61 GLN cc_start: 0.6092 (tm-30) cc_final: 0.5777 (tm-30) REVERT: t 70 PHE cc_start: 0.5286 (t80) cc_final: 0.5056 (t80) REVERT: v 81 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7368 (tp) REVERT: v 108 PHE cc_start: 0.6816 (t80) cc_final: 0.6604 (t80) REVERT: v 148 LYS cc_start: 0.6797 (ttmt) cc_final: 0.6524 (ttmm) REVERT: w 82 ASP cc_start: 0.7977 (t0) cc_final: 0.7594 (t70) REVERT: w 111 ASN cc_start: 0.6934 (m-40) cc_final: 0.6083 (p0) REVERT: x 14 TRP cc_start: 0.6123 (m100) cc_final: 0.5678 (m-10) REVERT: y 8 ARG cc_start: 0.3765 (tpm170) cc_final: 0.2852 (ttt90) REVERT: y 29 LYS cc_start: 0.7715 (ttmm) cc_final: 0.7322 (mmmm) outliers start: 208 outliers final: 175 residues processed: 1358 average time/residue: 0.6548 time to fit residues: 1505.0237 Evaluate side-chains 1375 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1186 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 307 ILE Chi-restraints excluded: chain 1 residue 315 VAL Chi-restraints excluded: chain 1 residue 323 ILE Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 66 VAL Chi-restraints excluded: chain 3 residue 71 MET Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 29 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 352 ASP Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 558 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 167 TRP Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 14 ARG Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 231 VAL Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 26 GLU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain i residue 142 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 209 THR Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 86 ILE Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 153 LEU Chi-restraints excluded: chain u residue 21 GLN Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 71 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 87 ASN Chi-restraints excluded: chain v residue 109 VAL Chi-restraints excluded: chain v residue 121 THR Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 147 ASN Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 54 VAL Chi-restraints excluded: chain z residue 5 VAL Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 0.1980 chunk 734 optimal weight: 20.0000 chunk 669 optimal weight: 8.9990 chunk 714 optimal weight: 5.9990 chunk 733 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 560 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 645 optimal weight: 6.9990 chunk 675 optimal weight: 7.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS 3 82 ASN ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 ASN f 82 GLN g 69 ASN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN w 57 ASN y 30 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69151 Z= 0.519 Angle : 1.584 50.703 93464 Z= 1.019 Chirality : 0.311 6.419 10120 Planarity : 0.005 0.067 11650 Dihedral : 12.794 177.392 10628 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.06 % Allowed : 13.24 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.08 (0.09), residues: 8043 helix: 0.86 (0.08), residues: 4241 sheet: -0.79 (0.27), residues: 335 loop : -0.83 (0.11), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP t 101 HIS 0.010 0.001 HIS Z 55 PHE 0.030 0.002 PHE N 292 TYR 0.031 0.002 TYR r 84 ARG 0.011 0.001 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1212 time to evaluate : 6.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 TYR cc_start: 0.8609 (m-80) cc_final: 0.8159 (m-80) REVERT: 1 395 ILE cc_start: 0.8320 (mt) cc_final: 0.8063 (mm) REVERT: 1 430 MET cc_start: 0.8194 (mtm) cc_final: 0.7857 (mtt) REVERT: 2 134 ASP cc_start: 0.7301 (p0) cc_final: 0.6882 (m-30) REVERT: 3 190 MET cc_start: 0.7884 (ttm) cc_final: 0.7274 (mmm) REVERT: 3 254 MET cc_start: 0.8065 (tmm) cc_final: 0.7281 (tmm) REVERT: 3 288 LYS cc_start: 0.7331 (mtmp) cc_final: 0.6864 (mttm) REVERT: 3 340 SER cc_start: 0.7604 (t) cc_final: 0.6657 (p) REVERT: 3 648 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7294 (mm) REVERT: 3 654 GLN cc_start: 0.6032 (tp-100) cc_final: 0.5593 (tt0) REVERT: 4 59 HIS cc_start: 0.7427 (m-70) cc_final: 0.6743 (m90) REVERT: 4 75 LYS cc_start: 0.8182 (tttm) cc_final: 0.7879 (tptp) REVERT: 4 259 MET cc_start: 0.8738 (mmm) cc_final: 0.8382 (mmm) REVERT: 5 47 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8051 (mm-30) REVERT: 6 32 LYS cc_start: 0.8229 (mmpt) cc_final: 0.7947 (mmtt) REVERT: 6 79 SER cc_start: 0.8273 (t) cc_final: 0.7766 (p) REVERT: 6 81 ARG cc_start: 0.7831 (mpt180) cc_final: 0.7563 (mpt180) REVERT: 6 178 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7247 (mtp180) REVERT: H 85 MET cc_start: 0.8237 (mmm) cc_final: 0.7967 (mmm) REVERT: H 105 MET cc_start: 0.7501 (mtp) cc_final: 0.7067 (ttp) REVERT: H 223 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7178 (m-10) REVERT: H 233 MET cc_start: 0.8337 (tmm) cc_final: 0.7988 (tmm) REVERT: J 2 MET cc_start: 0.6207 (mmm) cc_final: 0.4934 (mmt) REVERT: J 65 MET cc_start: 0.8322 (mmm) cc_final: 0.7971 (mmp) REVERT: K 91 GLN cc_start: 0.6908 (pm20) cc_final: 0.6584 (pt0) REVERT: L 88 MET cc_start: 0.7670 (mmm) cc_final: 0.7289 (mmm) REVERT: L 95 PHE cc_start: 0.7398 (t80) cc_final: 0.7135 (t80) REVERT: L 150 MET cc_start: 0.7635 (mmm) cc_final: 0.7294 (mmm) REVERT: L 203 MET cc_start: 0.7726 (tpt) cc_final: 0.7483 (tpt) REVERT: L 214 MET cc_start: 0.7413 (mmp) cc_final: 0.6711 (ttt) REVERT: L 235 SER cc_start: 0.7275 (m) cc_final: 0.6897 (p) REVERT: L 249 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6714 (p) REVERT: L 286 LEU cc_start: 0.7062 (tp) cc_final: 0.6585 (tt) REVERT: L 340 PHE cc_start: 0.7363 (m-80) cc_final: 0.6801 (m-80) REVERT: L 475 MET cc_start: 0.7436 (mmm) cc_final: 0.6321 (mmt) REVERT: L 507 THR cc_start: 0.6472 (p) cc_final: 0.5963 (m) REVERT: L 571 MET cc_start: 0.4269 (ttp) cc_final: 0.3960 (ptm) REVERT: M 130 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7803 (tp) REVERT: M 204 MET cc_start: 0.7490 (mmm) cc_final: 0.7104 (mmm) REVERT: M 206 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7987 (ttmm) REVERT: M 374 ASN cc_start: 0.8038 (m110) cc_final: 0.7827 (m110) REVERT: M 396 MET cc_start: 0.8161 (mmt) cc_final: 0.7911 (mmt) REVERT: N 11 MET cc_start: 0.7894 (mmp) cc_final: 0.7358 (tmm) REVERT: N 151 LEU cc_start: 0.7539 (tp) cc_final: 0.7179 (tt) REVERT: N 167 TRP cc_start: 0.6828 (OUTLIER) cc_final: 0.6501 (m-10) REVERT: N 265 MET cc_start: 0.8660 (mmp) cc_final: 0.8416 (mmm) REVERT: N 304 MET cc_start: 0.4804 (ptp) cc_final: 0.4552 (ptp) REVERT: V 137 GLU cc_start: 0.6361 (tp30) cc_final: 0.5991 (mp0) REVERT: W 36 VAL cc_start: 0.7744 (t) cc_final: 0.7499 (p) REVERT: W 91 MET cc_start: 0.7202 (mtp) cc_final: 0.6559 (ttm) REVERT: W 114 MET cc_start: 0.8062 (mtt) cc_final: 0.7640 (mtt) REVERT: X 15 VAL cc_start: 0.7310 (m) cc_final: 0.7020 (p) REVERT: X 33 ASN cc_start: 0.6319 (t0) cc_final: 0.5860 (m-40) REVERT: X 55 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5843 (mt-10) REVERT: X 56 ASP cc_start: 0.6975 (m-30) cc_final: 0.5961 (t0) REVERT: X 71 MET cc_start: 0.5077 (mmp) cc_final: 0.4466 (mmt) REVERT: Y 3 ILE cc_start: 0.6905 (mm) cc_final: 0.6577 (pt) REVERT: Z 134 VAL cc_start: 0.7944 (p) cc_final: 0.7655 (t) REVERT: a 53 ASP cc_start: 0.7388 (m-30) cc_final: 0.7173 (m-30) REVERT: c 9 GLN cc_start: 0.5784 (pp30) cc_final: 0.5507 (pt0) REVERT: c 10 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6578 (mp) REVERT: c 15 GLU cc_start: 0.5280 (mp0) cc_final: 0.4916 (mt-10) REVERT: c 18 ASP cc_start: 0.7239 (t70) cc_final: 0.6577 (p0) REVERT: c 66 GLU cc_start: 0.8669 (tt0) cc_final: 0.8419 (tm-30) REVERT: d 238 LEU cc_start: 0.8194 (tp) cc_final: 0.7617 (tt) REVERT: e 88 ARG cc_start: 0.7118 (mtm-85) cc_final: 0.6806 (ttm110) REVERT: g 24 MET cc_start: 0.6711 (mmm) cc_final: 0.6335 (tpp) REVERT: g 60 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7223 (t70) REVERT: g 90 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8023 (mm-30) REVERT: h 17 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.6944 (mmt-90) REVERT: i 8 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6600 (tttt) REVERT: i 134 ILE cc_start: 0.8684 (mm) cc_final: 0.8349 (mm) REVERT: i 135 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7801 (mm-40) REVERT: j 37 MET cc_start: 0.6618 (mmt) cc_final: 0.6337 (mmt) REVERT: j 58 PHE cc_start: 0.6200 (m-80) cc_final: 0.5968 (m-80) REVERT: k 76 ASN cc_start: 0.7028 (t0) cc_final: 0.6704 (t0) REVERT: k 143 PHE cc_start: 0.5096 (m-10) cc_final: 0.4742 (m-10) REVERT: k 209 THR cc_start: 0.6048 (OUTLIER) cc_final: 0.5559 (p) REVERT: k 214 MET cc_start: 0.6284 (mmm) cc_final: 0.6071 (tpp) REVERT: k 218 CYS cc_start: 0.6280 (p) cc_final: 0.5646 (p) REVERT: l 12 ASP cc_start: 0.7047 (t0) cc_final: 0.6834 (t0) REVERT: m 10 ASN cc_start: 0.7664 (t0) cc_final: 0.7401 (t0) REVERT: m 17 VAL cc_start: 0.8245 (t) cc_final: 0.7983 (m) REVERT: n 42 ASP cc_start: 0.3124 (OUTLIER) cc_final: 0.2778 (t0) REVERT: n 66 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6764 (tp) REVERT: p 43 LYS cc_start: 0.6971 (tppt) cc_final: 0.6647 (tptt) REVERT: p 46 TYR cc_start: 0.6534 (t80) cc_final: 0.6194 (t80) REVERT: p 60 GLU cc_start: 0.6500 (pt0) cc_final: 0.6082 (pt0) REVERT: q 8 ASP cc_start: 0.7275 (t0) cc_final: 0.6792 (t70) REVERT: r 94 TYR cc_start: 0.7608 (m-10) cc_final: 0.7333 (m-10) REVERT: s 30 PHE cc_start: 0.4204 (m-80) cc_final: 0.3998 (m-80) REVERT: s 38 MET cc_start: 0.6044 (tpt) cc_final: 0.5776 (tpp) REVERT: t 26 LEU cc_start: 0.7770 (tp) cc_final: 0.7560 (mm) REVERT: t 50 HIS cc_start: 0.5933 (OUTLIER) cc_final: 0.5336 (m170) REVERT: t 61 GLN cc_start: 0.6084 (tm-30) cc_final: 0.5760 (tm-30) REVERT: t 70 PHE cc_start: 0.5308 (t80) cc_final: 0.5099 (t80) REVERT: u 69 ASP cc_start: 0.0998 (OUTLIER) cc_final: 0.0219 (t70) REVERT: v 81 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7448 (tp) REVERT: v 108 PHE cc_start: 0.6906 (t80) cc_final: 0.6696 (t80) REVERT: v 148 LYS cc_start: 0.6800 (ttmt) cc_final: 0.6530 (ttmm) REVERT: w 82 ASP cc_start: 0.7948 (t0) cc_final: 0.7660 (t70) REVERT: w 111 ASN cc_start: 0.6941 (m-40) cc_final: 0.6085 (p0) REVERT: x 14 TRP cc_start: 0.6061 (m100) cc_final: 0.5628 (m-10) REVERT: y 8 ARG cc_start: 0.3836 (tpm170) cc_final: 0.2800 (ttt90) REVERT: y 29 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7337 (mmmm) REVERT: y 38 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6945 (ttp-170) outliers start: 218 outliers final: 188 residues processed: 1351 average time/residue: 0.6502 time to fit residues: 1488.7257 Evaluate side-chains 1389 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1187 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 307 ILE Chi-restraints excluded: chain 1 residue 315 VAL Chi-restraints excluded: chain 1 residue 323 ILE Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 66 VAL Chi-restraints excluded: chain 3 residue 71 MET Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 29 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 167 TRP Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 14 ARG Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 231 VAL Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 57 CYS Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 26 GLU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain k residue 32 CYS Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 209 THR Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain o residue 112 VAL Chi-restraints excluded: chain p residue 69 CYS Chi-restraints excluded: chain p residue 115 ILE Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 27 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 50 HIS Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 153 LEU Chi-restraints excluded: chain u residue 21 GLN Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 71 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 87 ASN Chi-restraints excluded: chain v residue 109 VAL Chi-restraints excluded: chain v residue 121 THR Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 147 ASN Chi-restraints excluded: chain v residue 158 ILE Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 54 VAL Chi-restraints excluded: chain z residue 5 VAL Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 30.0000 chunk 468 optimal weight: 30.0000 chunk 755 optimal weight: 8.9990 chunk 460 optimal weight: 30.0000 chunk 358 optimal weight: 0.9990 chunk 524 optimal weight: 1.9990 chunk 792 optimal weight: 3.9990 chunk 728 optimal weight: 20.0000 chunk 630 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 487 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS 3 82 ASN ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 ASN M 279 GLN N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 234 ASN f 82 GLN g 69 ASN ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN ** s 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 69151 Z= 0.508 Angle : 1.579 50.672 93464 Z= 1.017 Chirality : 0.311 6.411 10120 Planarity : 0.005 0.072 11650 Dihedral : 12.639 177.841 10628 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.89 % Allowed : 13.42 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.17 (0.09), residues: 8043 helix: 0.93 (0.08), residues: 4263 sheet: -0.69 (0.27), residues: 341 loop : -0.78 (0.11), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP t 101 HIS 0.010 0.001 HIS Z 55 PHE 0.029 0.002 PHE M 256 TYR 0.032 0.002 TYR r 84 ARG 0.010 0.000 ARG p 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16086 Ramachandran restraints generated. 8043 Oldfield, 0 Emsley, 8043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1238 time to evaluate : 5.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 354 TYR cc_start: 0.8586 (m-80) cc_final: 0.8141 (m-80) REVERT: 1 430 MET cc_start: 0.8217 (mtm) cc_final: 0.7877 (mtt) REVERT: 2 134 ASP cc_start: 0.7296 (p0) cc_final: 0.6887 (m-30) REVERT: 3 71 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8024 (tpp) REVERT: 3 190 MET cc_start: 0.7832 (ttm) cc_final: 0.7298 (mmm) REVERT: 3 254 MET cc_start: 0.8077 (tmm) cc_final: 0.7309 (tmm) REVERT: 3 288 LYS cc_start: 0.7333 (mtmp) cc_final: 0.6867 (mttm) REVERT: 3 340 SER cc_start: 0.7671 (t) cc_final: 0.6716 (p) REVERT: 3 654 GLN cc_start: 0.6025 (tp-100) cc_final: 0.5589 (tt0) REVERT: 4 59 HIS cc_start: 0.7403 (m-70) cc_final: 0.6721 (m90) REVERT: 4 75 LYS cc_start: 0.8192 (tttm) cc_final: 0.7874 (tptp) REVERT: 4 259 MET cc_start: 0.8740 (mmm) cc_final: 0.8387 (mmm) REVERT: 5 47 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8027 (mm-30) REVERT: 6 32 LYS cc_start: 0.8238 (mmpt) cc_final: 0.7943 (mmtt) REVERT: 6 79 SER cc_start: 0.8274 (t) cc_final: 0.7760 (p) REVERT: 6 81 ARG cc_start: 0.7837 (mpt180) cc_final: 0.7572 (mpt180) REVERT: 6 178 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7228 (mtp180) REVERT: A 23 TRP cc_start: 0.5452 (m-90) cc_final: 0.4928 (m-10) REVERT: H 85 MET cc_start: 0.8224 (mmm) cc_final: 0.7968 (mmm) REVERT: H 105 MET cc_start: 0.7541 (mtp) cc_final: 0.7112 (ttp) REVERT: H 223 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7136 (m-10) REVERT: H 233 MET cc_start: 0.8331 (tmm) cc_final: 0.7989 (tmm) REVERT: J 2 MET cc_start: 0.6220 (mmm) cc_final: 0.4969 (mmt) REVERT: J 65 MET cc_start: 0.8310 (mmm) cc_final: 0.7959 (mmp) REVERT: K 91 GLN cc_start: 0.6774 (pm20) cc_final: 0.6446 (pt0) REVERT: L 88 MET cc_start: 0.7533 (mmm) cc_final: 0.7153 (mmm) REVERT: L 95 PHE cc_start: 0.7368 (t80) cc_final: 0.7110 (t80) REVERT: L 150 MET cc_start: 0.7616 (mmm) cc_final: 0.7282 (mmm) REVERT: L 203 MET cc_start: 0.7664 (tpt) cc_final: 0.7429 (tpt) REVERT: L 214 MET cc_start: 0.7378 (mmp) cc_final: 0.6700 (ttt) REVERT: L 235 SER cc_start: 0.7230 (m) cc_final: 0.6846 (p) REVERT: L 249 SER cc_start: 0.7058 (OUTLIER) cc_final: 0.6727 (p) REVERT: L 261 ILE cc_start: 0.7709 (mm) cc_final: 0.7386 (tt) REVERT: L 286 LEU cc_start: 0.6978 (tp) cc_final: 0.6472 (tt) REVERT: L 340 PHE cc_start: 0.7368 (m-80) cc_final: 0.6818 (m-80) REVERT: L 507 THR cc_start: 0.6459 (p) cc_final: 0.5929 (m) REVERT: L 528 TYR cc_start: 0.5296 (m-10) cc_final: 0.5049 (m-10) REVERT: L 571 MET cc_start: 0.4299 (ttp) cc_final: 0.3998 (ptm) REVERT: M 130 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7792 (tp) REVERT: M 195 MET cc_start: 0.7194 (mmm) cc_final: 0.6874 (tpt) REVERT: M 204 MET cc_start: 0.7452 (mmm) cc_final: 0.7072 (mmm) REVERT: M 206 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7609 (ttmm) REVERT: M 374 ASN cc_start: 0.8040 (m110) cc_final: 0.7828 (m110) REVERT: M 396 MET cc_start: 0.8142 (mmt) cc_final: 0.7900 (mmt) REVERT: N 11 MET cc_start: 0.7883 (mmp) cc_final: 0.7343 (tmm) REVERT: N 151 LEU cc_start: 0.7522 (tp) cc_final: 0.7154 (tt) REVERT: N 167 TRP cc_start: 0.6786 (OUTLIER) cc_final: 0.6462 (m-10) REVERT: N 265 MET cc_start: 0.8663 (mmp) cc_final: 0.8392 (mmm) REVERT: N 304 MET cc_start: 0.4815 (ptp) cc_final: 0.4592 (ptp) REVERT: V 137 GLU cc_start: 0.6268 (tp30) cc_final: 0.5967 (mp0) REVERT: W 36 VAL cc_start: 0.7760 (t) cc_final: 0.7510 (p) REVERT: W 91 MET cc_start: 0.7172 (mtp) cc_final: 0.6534 (ttm) REVERT: W 114 MET cc_start: 0.8109 (mtt) cc_final: 0.7673 (mtt) REVERT: X 15 VAL cc_start: 0.7310 (m) cc_final: 0.7038 (p) REVERT: X 33 ASN cc_start: 0.6331 (t0) cc_final: 0.5878 (m-40) REVERT: X 52 MET cc_start: 0.6513 (mmt) cc_final: 0.6216 (mmt) REVERT: X 55 GLU cc_start: 0.6375 (mt-10) cc_final: 0.5875 (mt-10) REVERT: X 56 ASP cc_start: 0.6967 (m-30) cc_final: 0.5955 (t0) REVERT: X 71 MET cc_start: 0.5094 (mmp) cc_final: 0.4477 (mmt) REVERT: Y 3 ILE cc_start: 0.6881 (mm) cc_final: 0.6577 (pt) REVERT: Z 134 VAL cc_start: 0.7938 (p) cc_final: 0.7650 (t) REVERT: a 53 ASP cc_start: 0.7390 (m-30) cc_final: 0.7182 (m-30) REVERT: c 9 GLN cc_start: 0.5623 (pp30) cc_final: 0.5359 (pt0) REVERT: c 10 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6556 (mp) REVERT: c 15 GLU cc_start: 0.5358 (mp0) cc_final: 0.4943 (mt-10) REVERT: c 18 ASP cc_start: 0.7306 (t70) cc_final: 0.6641 (p0) REVERT: c 22 LEU cc_start: 0.8192 (mt) cc_final: 0.7978 (mt) REVERT: c 66 GLU cc_start: 0.8675 (tt0) cc_final: 0.8423 (tm-30) REVERT: d 238 LEU cc_start: 0.8187 (tp) cc_final: 0.7870 (tt) REVERT: e 88 ARG cc_start: 0.7110 (mtm-85) cc_final: 0.6792 (ttm110) REVERT: g 24 MET cc_start: 0.6734 (mmm) cc_final: 0.6357 (tpp) REVERT: g 50 GLN cc_start: 0.8013 (pt0) cc_final: 0.7526 (mm-40) REVERT: g 60 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7267 (t70) REVERT: g 90 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8018 (mm-30) REVERT: h 17 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.6918 (mmt-90) REVERT: h 61 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7704 (mt-10) REVERT: i 8 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6561 (tttt) REVERT: i 134 ILE cc_start: 0.8680 (mm) cc_final: 0.8342 (mm) REVERT: i 135 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7810 (mm-40) REVERT: j 37 MET cc_start: 0.6648 (mmt) cc_final: 0.6362 (mmt) REVERT: j 58 PHE cc_start: 0.6129 (m-80) cc_final: 0.5889 (m-80) REVERT: k 143 PHE cc_start: 0.5068 (m-10) cc_final: 0.4707 (m-10) REVERT: k 209 THR cc_start: 0.6190 (OUTLIER) cc_final: 0.5691 (p) REVERT: k 218 CYS cc_start: 0.6324 (p) cc_final: 0.5403 (p) REVERT: l 12 ASP cc_start: 0.6996 (t0) cc_final: 0.6777 (t0) REVERT: l 81 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7088 (tm-30) REVERT: m 17 VAL cc_start: 0.8241 (t) cc_final: 0.7972 (m) REVERT: n 42 ASP cc_start: 0.3176 (OUTLIER) cc_final: 0.2800 (t0) REVERT: n 56 PHE cc_start: 0.4771 (m-10) cc_final: 0.4545 (m-80) REVERT: n 66 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6771 (tp) REVERT: o 109 TYR cc_start: 0.6139 (m-80) cc_final: 0.5846 (m-80) REVERT: p 43 LYS cc_start: 0.6958 (tppt) cc_final: 0.6630 (tptt) REVERT: p 46 TYR cc_start: 0.6569 (t80) cc_final: 0.6099 (t80) REVERT: p 60 GLU cc_start: 0.6467 (pt0) cc_final: 0.6135 (pt0) REVERT: q 8 ASP cc_start: 0.7273 (t0) cc_final: 0.6791 (t70) REVERT: s 38 MET cc_start: 0.6077 (tpt) cc_final: 0.5810 (tpp) REVERT: s 83 GLN cc_start: 0.7150 (tp40) cc_final: 0.6895 (tp40) REVERT: t 26 LEU cc_start: 0.7766 (tp) cc_final: 0.7564 (mm) REVERT: t 61 GLN cc_start: 0.6080 (tm-30) cc_final: 0.5751 (tm-30) REVERT: u 69 ASP cc_start: 0.0890 (OUTLIER) cc_final: 0.0141 (t70) REVERT: v 81 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7441 (tp) REVERT: v 108 PHE cc_start: 0.6854 (t80) cc_final: 0.6629 (t80) REVERT: v 148 LYS cc_start: 0.6793 (ttmt) cc_final: 0.6527 (ttmm) REVERT: w 82 ASP cc_start: 0.7967 (t0) cc_final: 0.7760 (t70) REVERT: w 111 ASN cc_start: 0.6929 (m-40) cc_final: 0.6086 (p0) REVERT: x 14 TRP cc_start: 0.6064 (m100) cc_final: 0.5637 (m-10) REVERT: y 8 ARG cc_start: 0.3842 (tpm170) cc_final: 0.2872 (ttt90) REVERT: y 29 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7347 (mmmm) outliers start: 206 outliers final: 179 residues processed: 1366 average time/residue: 0.6517 time to fit residues: 1517.5287 Evaluate side-chains 1387 residues out of total 7129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1195 time to evaluate : 5.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 87 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 272 MET Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 302 SER Chi-restraints excluded: chain 1 residue 307 ILE Chi-restraints excluded: chain 1 residue 315 VAL Chi-restraints excluded: chain 1 residue 323 ILE Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 2 residue 114 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 66 VAL Chi-restraints excluded: chain 3 residue 71 MET Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 148 THR Chi-restraints excluded: chain 3 residue 227 SER Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 428 ILE Chi-restraints excluded: chain 3 residue 456 SER Chi-restraints excluded: chain 3 residue 588 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 184 VAL Chi-restraints excluded: chain 4 residue 225 LEU Chi-restraints excluded: chain 4 residue 418 ILE Chi-restraints excluded: chain 4 residue 429 ASP Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 103 VAL Chi-restraints excluded: chain 9 residue 1 THR Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 169 LEU Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 394 LEU Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 409 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 540 MET Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 283 LYS Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 167 TRP Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain X residue 6 LEU Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 14 ARG Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 231 VAL Chi-restraints excluded: chain d residue 315 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 57 CYS Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 26 GLU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain i residue 2 GLU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain k residue 32 CYS Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 209 THR Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 96 HIS Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 101 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 78 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 69 CYS Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 95 THR Chi-restraints excluded: chain r residue 6 ASP Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain s residue 79 CYS Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 136 VAL Chi-restraints excluded: chain t residue 153 LEU Chi-restraints excluded: chain u residue 21 GLN Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain v residue 5 THR Chi-restraints excluded: chain v residue 71 LEU Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 82 ASP Chi-restraints excluded: chain v residue 121 THR Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 147 ASN Chi-restraints excluded: chain v residue 158 ILE Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain x residue 48 LEU Chi-restraints excluded: chain y residue 9 ASP Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 54 VAL Chi-restraints excluded: chain z residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 9.9990 chunk 500 optimal weight: 5.9990 chunk 671 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 581 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 631 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 437 HIS 3 82 ASN 3 475 GLN ** 4 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN L 192 ASN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 ASN N 289 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN f 82 GLN g 69 ASN i 122 GLN k 76 ASN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 116 GLN ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.085494 restraints weight = 145273.993| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.89 r_work: 0.3138 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 69151 Z= 0.539 Angle : 1.597 50.744 93464 Z= 1.024 Chirality : 0.312 6.429 10120 Planarity : 0.005 0.072 11650 Dihedral : 12.766 177.106 10628 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.96 % Allowed : 13.63 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.08 (0.09), residues: 8043 helix: 0.87 (0.08), residues: 4245 sheet: -0.80 (0.27), residues: 337 loop : -0.83 (0.11), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP t 101 HIS 0.009 0.001 HIS Z 55 PHE 0.036 0.002 PHE N 292 TYR 0.034 0.002 TYR t 90 ARG 0.008 0.001 ARG p 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23738.06 seconds wall clock time: 414 minutes 5.40 seconds (24845.40 seconds total)