Starting phenix.real_space_refine on Fri Feb 16 10:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkp_11257/02_2024/6zkp_11257_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 44 5.49 5 S 466 5.16 5 C 43597 2.51 5 N 11138 2.21 5 O 12078 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 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "9 TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "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 "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 72": "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 "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67353 Number of models: 1 Model: "" Number of chains: 70 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: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3390 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 393} Chain breaks: 2 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: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2489 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 290} Chain breaks: 1 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1273 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" 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: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 290 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 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: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 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: "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: "h" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "i" 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: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "o" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 90 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: "y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 103.147 53.444 241.541 1.00 15.26 S ATOM 2676 SG CYS 1 359 110.053 53.888 242.337 1.00 32.49 S ATOM 3039 SG CYS 1 405 106.840 47.771 240.768 1.00 26.97 S ATOM 4116 SG CYS 2 103 100.864 48.822 260.584 1.00 66.83 S ATOM 4150 SG CYS 2 108 98.544 46.536 262.664 1.00 39.67 S ATOM 4430 SG CYS 2 144 102.325 45.199 257.046 1.00 51.64 S ATOM 4453 SG CYS 2 148 100.456 42.459 258.440 1.00 45.39 S ATOM 5793 SG CYS 3 114 105.655 71.822 226.814 1.00 22.07 S ATOM 5732 SG CYS 3 105 100.332 75.151 228.713 1.00 25.85 S ATOM 5753 SG CYS 3 108 106.383 76.851 230.573 1.00 20.78 S ATOM 6125 SG CYS 3 156 112.840 64.314 231.606 1.00 17.44 S ATOM 6102 SG CYS 3 153 110.583 67.333 237.129 1.00 18.64 S ATOM 6149 SG CYS 3 159 116.773 68.066 235.440 1.00 52.15 S ATOM 6479 SG CYS 3 203 112.587 70.585 231.796 1.00 50.36 S ATOM 5238 SG CYS 3 41 111.862 57.879 229.670 1.00 43.30 S ATOM 5324 SG CYS 3 52 108.171 58.885 229.042 1.00 21.78 S ATOM 5349 SG CYS 3 55 108.660 53.937 225.311 1.00 17.24 S ATOM 5450 SG CYS 3 69 112.231 53.988 226.741 1.00 33.24 S ATOM 16341 SG CYS 6 149 87.392 95.264 208.946 1.00 58.53 S ATOM 15607 SG CYS 6 54 84.084 94.972 203.074 1.00 71.85 S ATOM 17533 SG CYS 9 116 91.605 96.133 215.587 1.00 34.14 S ATOM 17580 SG CYS 9 122 92.079 91.630 220.251 1.00 17.04 S ATOM 17307 SG CYS 9 87 95.983 91.344 214.947 1.00 11.66 S ATOM 17609 SG CYS 9 126 94.222 88.313 227.584 1.00 15.93 S ATOM 17280 SG CYS 9 83 97.869 89.989 222.474 1.00 19.00 S ATOM 17238 SG CYS 9 77 99.930 91.615 228.289 1.00 11.87 S ATOM 17257 SG CYS 9 80 99.213 85.091 226.452 1.00 42.39 S ATOM 41151 SG CYS b 59 95.613 84.111 242.851 1.00 28.56 S ATOM 41329 SG CYS b 84 98.784 83.941 240.695 1.00 19.38 S ATOM 41351 SG CYS b 87 97.072 86.958 241.472 1.00 24.71 S Time building chain proxies: 27.38, per 1000 atoms: 0.41 Number of scatterers: 67353 At special positions: 0 Unit cell: (176.79, 198.37, 292.16, 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 44 15.00 O 12078 8.00 N 11138 7.00 C 43597 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=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 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: 21.57 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " 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="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 500 " pdb="FE1 SF4 1 500 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 500 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 500 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 500 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="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 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " 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 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 340 helices and 29 sheets defined 51.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.71 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 39 removed outlier: 3.698A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 62 removed outlier: 4.129A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.782A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.695A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 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 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 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 309 through 312 No H-bonds generated for 'chain '1' and resid 309 through 312' Processing helix chain '1' and resid 319 through 323 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.379A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 4.177A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.808A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.398A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 4.140A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.763A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 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: 4.119A 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 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' 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 201 removed outlier: 3.956A pdb=" N ILE 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) Processing helix chain '3' and resid 265 through 272 removed outlier: 5.094A pdb=" N TYR 3 271 " --> pdb=" O THR 3 267 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP 3 272 " --> pdb=" O ARG 3 268 " (cutoff:3.500A) Processing helix chain '3' and resid 296 through 307 removed outlier: 3.979A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 336 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 3.954A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA 3 433 " --> pdb=" O GLN 3 430 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER 3 434 " --> pdb=" O ASP 3 431 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 removed outlier: 3.941A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 463 through 480 removed outlier: 3.589A pdb=" N SER 3 480 " --> pdb=" O LYS 3 476 " (cutoff:3.500A) Processing helix chain '3' and resid 499 through 504 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 649 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 4.437A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.651A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 105 Proline residue: 4 101 - end of helix removed outlier: 4.012A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG 4 105 " --> pdb=" O PRO 4 101 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 125 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.503A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 185 removed outlier: 4.068A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 3.976A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) 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 316 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 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.743A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 3.970A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.098A 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 57 through 66 Processing helix chain '5' and resid 120 through 122 No H-bonds generated for 'chain '5' and resid 120 through 122' Processing helix chain '5' and resid 125 through 137 removed outlier: 3.903A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 44 Processing helix chain '6' and resid 54 through 63 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 106 Processing helix chain '6' and resid 117 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 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 86 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 172 removed outlier: 5.722A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (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: 5.576A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.585A 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: 3.667A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 removed outlier: 3.627A pdb=" N ILE H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.598A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 3.932A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.955A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 217 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: 5.359A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.815A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 65 through 73 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.300A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.295A 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: 3.683A 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 84 removed outlier: 3.667A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.811A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) 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: 3.852A 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: 4.316A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 4.083A 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: 4.068A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.026A 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 238 removed outlier: 4.108A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.715A pdb=" N HIS L 248 " --> pdb=" O SER L 244 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.183A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.614A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.829A 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 349 removed outlier: 4.361A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.011A 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 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 389 No H-bonds generated for 'chain 'L' and resid 387 through 389' Processing helix chain 'L' and resid 392 through 400 Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.600A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.969A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.618A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 532 Proline residue: L 530 - end of helix Processing helix chain 'L' and resid 537 through 546 removed outlier: 3.962A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.072A 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 23 through 42 removed outlier: 3.984A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 81 removed outlier: 3.710A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.766A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.547A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.619A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.765A 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: 3.797A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.451A 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: 4.868A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 246 Processing helix chain 'M' and resid 253 through 278 removed outlier: 5.169A pdb=" N ALA M 258 " --> pdb=" O ASP M 255 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR M 259 " --> pdb=" O PHE M 256 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 4.262A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER M 273 " --> pdb=" O ILE M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.320A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.202A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 removed outlier: 3.678A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.070A 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 106 Processing helix chain 'N' and resid 115 through 121 removed outlier: 3.547A pdb=" N GLN N 120 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.050A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.988A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.583A 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 236 removed outlier: 3.853A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.552A pdb=" N THR N 247 " --> pdb=" O VAL N 244 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU N 249 " --> pdb=" O ILE N 246 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET N 251 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.740A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.666A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.778A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.535A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.684A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 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: 4.678A 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 56 through 76 removed outlier: 4.236A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU Y 68 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.800A 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 123 removed outlier: 4.282A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 172 removed outlier: 3.583A pdb=" N ALA Z 172 " --> pdb=" O ALA Z 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.657A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.762A 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 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.314A 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 3 through 5 No H-bonds generated for 'chain 'd' and resid 3 through 5' Processing helix chain 'd' and resid 30 through 41 removed outlier: 3.909A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 62 removed outlier: 5.077A 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 183 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 321 removed outlier: 6.212A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 39 removed outlier: 3.733A pdb=" N LYS e 38 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 44 No H-bonds generated for 'chain 'e' and resid 41 through 44' 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: 4.295A 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: 4.055A 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 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.755A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) 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 3 through 17 removed outlier: 3.708A 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: 3.896A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.676A 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 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 73 through 82 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 44 removed outlier: 4.583A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (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 141 removed outlier: 3.773A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN k 141 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.681A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 184 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 217 removed outlier: 4.021A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.274A 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 271 Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 306 through 308 No H-bonds generated for 'chain 'k' and resid 306 through 308' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.191A 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 33 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 36 through 45 removed outlier: 4.046A pdb=" N LYS m 39 " --> pdb=" O PRO m 36 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 18 through 20 No H-bonds generated for 'chain 'n' and resid 18 through 20' Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 48 through 52 removed outlier: 3.726A pdb=" N ARG n 51 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 17 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.956A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 22 Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.988A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 71 Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 91 Processing helix chain 'p' and resid 95 through 117 removed outlier: 3.569A pdb=" N GLU p 117 " --> pdb=" O LYS p 113 " (cutoff:3.500A) 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 'q' and resid 138 through 141 No H-bonds generated for 'chain 'q' and resid 138 through 141' Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 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 52 through 54 No H-bonds generated for 'chain 's' and resid 52 through 54' Processing helix chain 's' and resid 60 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 95 No H-bonds generated for 'chain 't' and resid 93 through 95' Processing helix chain 't' and resid 100 through 105 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 139 removed outlier: 4.124A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'u' and resid 61 through 64 No H-bonds generated for 'chain 'u' and resid 61 through 64' 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 65 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 3.967A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (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 14 removed outlier: 3.656A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 11 through 14' Processing helix chain 'y' and resid 16 through 33 removed outlier: 3.507A pdb=" N GLY y 23 " --> pdb=" O GLY y 19 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.809A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 3.784A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 54 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.959A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 266 through 271 Processing sheet with id= C, first strand: chain '2' and resid 137 through 142 removed outlier: 6.598A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 283 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.477A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.448A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 572 through 574 Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.703A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 47 through 51 removed outlier: 6.623A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 65 through 67 Processing sheet with id= R, first strand: chain '9' and resid 92 through 98 removed outlier: 6.201A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.336A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.570A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.847A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.448A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.234A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2781 hydrogen bonds defined for protein. 7722 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: 21.42 Time building geometry restraints manager: 23.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.43: 28372 1.43 - 1.66: 39786 1.66 - 1.89: 758 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 68996 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.591 0.242 3.80e-02 6.93e+02 4.06e+01 bond pdb=" OA3 CDL h 201 " pdb=" PA1 CDL h 201 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.00e-02 1.00e+04 3.76e+01 bond pdb=" OA3 CDL L1004 " pdb=" PA1 CDL L1004 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.00e-02 1.00e+04 3.64e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.332 0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 68991 not shown) Histogram of bond angle deviations from ideal: 61.78 - 77.02: 72 77.02 - 92.27: 8 92.27 - 107.51: 3849 107.51 - 122.75: 83450 122.75 - 138.00: 5853 Bond angle restraints: 93232 Sorted by residual: angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 133.21 -25.47 1.95e+00 2.62e-01 1.70e+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 90.63 13.70 1.14e+00 7.69e-01 1.44e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.57 13.76 1.20e+00 6.94e-01 1.32e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 92.04 12.29 1.14e+00 7.69e-01 1.16e+02 angle pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " pdb="FE2 FES 3 803 " ideal model delta sigma weight residual 75.66 87.56 -11.90 1.14e+00 7.69e-01 1.09e+02 ... (remaining 93227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 41143 34.24 - 68.47: 768 68.47 - 102.71: 43 102.71 - 136.95: 4 136.95 - 171.18: 6 Dihedral angle restraints: 41964 sinusoidal: 18204 harmonic: 23760 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 -127.92 -52.08 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -133.76 -46.24 0 5.00e+00 4.00e-02 8.55e+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 -139.43 -40.57 0 5.00e+00 4.00e-02 6.58e+01 ... (remaining 41961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.220: 10072 4.220 - 8.439: 5 8.439 - 12.659: 0 12.659 - 16.879: 0 16.879 - 21.098: 24 Chirality restraints: 10101 Sorted by residual: chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.54 21.10 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.53 -21.09 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S3 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False -10.55 10.53 -21.09 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10098 not shown) Planarity restraints: 11630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.027 2.00e-02 2.50e+03 3.22e-02 2.08e+01 pdb=" CG TYR 9 40 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 1 371 " 0.027 2.00e-02 2.50e+03 2.62e-02 1.72e+01 pdb=" CG TRP 1 371 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP 1 371 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP 1 371 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP 1 371 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP 1 371 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP 1 371 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP 1 371 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP 1 371 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 125 " 0.031 2.00e-02 2.50e+03 2.93e-02 1.71e+01 pdb=" CG TYR 6 125 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 125 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 125 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 125 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 125 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 6 125 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 6 125 " 0.003 2.00e-02 2.50e+03 ... (remaining 11627 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 20118 2.82 - 3.40: 71702 3.40 - 3.98: 136233 3.98 - 4.56: 195484 4.56 - 5.14: 283296 Nonbonded interactions: 706833 Sorted by model distance: nonbonded pdb=" OG1 THR 4 145 " pdb=" OH TYR 4 181 " model vdw 2.241 2.440 nonbonded pdb=" O GLU c 28 " pdb=" OG1 THR c 32 " model vdw 2.242 2.440 nonbonded pdb=" OE2 GLU 4 224 " pdb=" OH TYR 9 40 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR d 22 " pdb=" OG SER d 88 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR l 91 " pdb=" OE1 GLU q 92 " model vdw 2.253 2.440 ... (remaining 706828 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 6.900 Check model and map are aligned: 0.760 Set scattering table: 0.490 Process input model: 161.200 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.260 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.010 0.242 68996 Z= 0.637 Angle : 1.042 25.467 93232 Z= 0.557 Chirality : 1.025 21.098 10101 Planarity : 0.008 0.071 11630 Dihedral : 12.740 171.182 26619 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.81 % Favored : 96.18 % Rotamer: Outliers : 0.13 % Allowed : 2.44 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: -3.03 (0.08), residues: 8036 helix: -2.02 (0.06), residues: 4240 sheet: -1.53 (0.23), residues: 394 loop : -1.88 (0.09), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP 1 371 HIS 0.018 0.003 HIS Z 55 PHE 0.059 0.004 PHE 4 171 TYR 0.073 0.004 TYR 9 40 ARG 0.026 0.002 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1962 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1953 time to evaluate : 5.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8830 (t80) cc_final: 0.7905 (m-10) REVERT: 1 105 CYS cc_start: 0.8451 (p) cc_final: 0.7927 (p) REVERT: 1 248 GLU cc_start: 0.8640 (tt0) cc_final: 0.8316 (mp0) REVERT: 1 356 HIS cc_start: 0.8682 (m-70) cc_final: 0.8382 (m-70) REVERT: 1 400 GLU cc_start: 0.8631 (tt0) cc_final: 0.8350 (tt0) REVERT: 1 431 GLN cc_start: 0.8574 (pt0) cc_final: 0.7855 (pp30) REVERT: 2 127 LYS cc_start: 0.8476 (ptpt) cc_final: 0.8238 (mtpp) REVERT: 2 134 ASP cc_start: 0.8879 (p0) cc_final: 0.7848 (t0) REVERT: 3 21 GLU cc_start: 0.8512 (tt0) cc_final: 0.8301 (mt-10) REVERT: 3 164 SER cc_start: 0.9116 (t) cc_final: 0.8911 (m) REVERT: 3 243 ARG cc_start: 0.9311 (tmm-80) cc_final: 0.8987 (ttp-170) REVERT: 3 246 GLU cc_start: 0.8964 (tt0) cc_final: 0.8739 (pt0) REVERT: 3 427 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7770 (pttm) REVERT: 3 656 LEU cc_start: 0.8280 (mt) cc_final: 0.7866 (mp) REVERT: 4 75 LYS cc_start: 0.8676 (tttm) cc_final: 0.8395 (tptt) REVERT: 4 108 TYR cc_start: 0.8798 (p90) cc_final: 0.8507 (p90) REVERT: 4 109 VAL cc_start: 0.9193 (m) cc_final: 0.8963 (p) REVERT: 4 182 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9055 (tm-30) REVERT: 4 342 MET cc_start: 0.9308 (tpt) cc_final: 0.8877 (tpt) REVERT: 5 49 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8386 (mp0) REVERT: 5 147 ASP cc_start: 0.8525 (t0) cc_final: 0.8015 (p0) REVERT: 6 58 GLU cc_start: 0.8989 (tp30) cc_final: 0.8742 (mm-30) REVERT: 6 102 LYS cc_start: 0.8908 (tttt) cc_final: 0.8598 (ttpp) REVERT: 6 177 TYR cc_start: 0.8582 (t80) cc_final: 0.8359 (t80) REVERT: 9 40 TYR cc_start: 0.9109 (m-80) cc_final: 0.8819 (m-80) REVERT: 9 78 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.8753 (pp) REVERT: 9 172 ASP cc_start: 0.8928 (t70) cc_final: 0.8476 (t70) REVERT: H 81 LEU cc_start: 0.9088 (mt) cc_final: 0.8701 (mm) REVERT: K 73 LEU cc_start: 0.9251 (tm) cc_final: 0.8996 (tp) REVERT: K 91 GLN cc_start: 0.8057 (pm20) cc_final: 0.7746 (tp40) REVERT: L 8 THR cc_start: 0.8381 (m) cc_final: 0.8108 (m) REVERT: L 159 TYR cc_start: 0.9188 (p90) cc_final: 0.8907 (p90) REVERT: L 412 THR cc_start: 0.7955 (m) cc_final: 0.7722 (m) REVERT: L 441 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8101 (mp) REVERT: L 540 MET cc_start: 0.7830 (mtm) cc_final: 0.7501 (mmp) REVERT: L 544 MET cc_start: 0.7112 (tmm) cc_final: 0.6872 (ttt) REVERT: L 547 LYS cc_start: 0.8067 (mttm) cc_final: 0.7647 (mttp) REVERT: L 606 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6536 (mt-10) REVERT: N 346 LEU cc_start: 0.9099 (mt) cc_final: 0.8864 (mt) REVERT: W 77 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.8087 (ttt180) REVERT: W 111 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8559 (mtp85) REVERT: X 26 ASP cc_start: 0.7686 (p0) cc_final: 0.7477 (p0) REVERT: Y 108 LYS cc_start: 0.8537 (tptt) cc_final: 0.7936 (ttpt) REVERT: Z 42 ARG cc_start: 0.7664 (mtp-110) cc_final: 0.7359 (mmt90) REVERT: Z 121 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7889 (ttm-80) REVERT: Z 144 ASP cc_start: 0.8901 (m-30) cc_final: 0.8700 (m-30) REVERT: Z 169 THR cc_start: 0.7961 (m) cc_final: 0.7723 (p) REVERT: a 58 LEU cc_start: 0.9087 (mt) cc_final: 0.8512 (mp) REVERT: b 14 THR cc_start: 0.8921 (m) cc_final: 0.8662 (p) REVERT: b 37 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8659 (pm20) REVERT: b 80 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8430 (ttpp) REVERT: c 115 SER cc_start: 0.9284 (t) cc_final: 0.9067 (p) REVERT: d 60 ARG cc_start: 0.8863 (mtt-85) cc_final: 0.8637 (mtt-85) REVERT: d 162 GLU cc_start: 0.8940 (mp0) cc_final: 0.8532 (mm-30) REVERT: d 175 GLU cc_start: 0.8634 (mp0) cc_final: 0.8363 (mp0) REVERT: d 224 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8438 (mmt180) REVERT: d 293 THR cc_start: 0.7760 (m) cc_final: 0.7456 (p) REVERT: d 338 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8054 (mptt) REVERT: e 45 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8453 (mtpt) REVERT: f 105 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7797 (mm-30) REVERT: g 47 HIS cc_start: 0.8630 (t70) cc_final: 0.8070 (t-170) REVERT: g 50 GLN cc_start: 0.8357 (pt0) cc_final: 0.7914 (mm-40) REVERT: g 56 LYS cc_start: 0.8497 (tmmt) cc_final: 0.7641 (tptm) REVERT: g 67 LYS cc_start: 0.8894 (mttt) cc_final: 0.8676 (tttt) REVERT: g 110 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7835 (mp0) REVERT: h 71 SER cc_start: 0.8761 (m) cc_final: 0.8458 (p) REVERT: i 1 MET cc_start: 0.6796 (tpt) cc_final: 0.6360 (mtm) REVERT: i 25 ARG cc_start: 0.8717 (ttt90) cc_final: 0.8148 (ttp-110) REVERT: i 122 GLN cc_start: 0.8632 (mp10) cc_final: 0.8396 (pt0) REVERT: j 16 LEU cc_start: 0.8130 (mt) cc_final: 0.7717 (mt) REVERT: j 17 TYR cc_start: 0.7801 (t80) cc_final: 0.7396 (t80) REVERT: j 24 LYS cc_start: 0.8185 (ttmp) cc_final: 0.7764 (mmmt) REVERT: j 46 ASP cc_start: 0.8286 (m-30) cc_final: 0.7991 (m-30) REVERT: j 57 GLU cc_start: 0.6690 (tp30) cc_final: 0.6320 (mm-30) REVERT: k 153 ASN cc_start: 0.8670 (m-40) cc_final: 0.8433 (m-40) REVERT: k 265 ASP cc_start: 0.8321 (t0) cc_final: 0.7895 (m-30) REVERT: l 81 GLN cc_start: 0.8864 (tp40) cc_final: 0.8656 (tp-100) REVERT: l 84 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7773 (tttt) REVERT: m 14 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8091 (mmmt) REVERT: n 42 ASP cc_start: 0.6857 (t70) cc_final: 0.5817 (p0) REVERT: o 1 MET cc_start: 0.8068 (ttp) cc_final: 0.7070 (ttp) REVERT: o 25 LYS cc_start: 0.8723 (mttt) cc_final: 0.8268 (mtpt) REVERT: p 78 ASN cc_start: 0.8416 (m-40) cc_final: 0.7826 (m110) REVERT: r 14 LEU cc_start: 0.8227 (mm) cc_final: 0.7993 (mt) REVERT: r 121 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6935 (mp0) REVERT: s 23 THR cc_start: 0.8234 (p) cc_final: 0.7957 (m) REVERT: s 34 LYS cc_start: 0.7184 (ptpt) cc_final: 0.6903 (pttt) REVERT: s 71 ASP cc_start: 0.7193 (m-30) cc_final: 0.6702 (m-30) REVERT: s 81 HIS cc_start: 0.7480 (t-90) cc_final: 0.7082 (t-170) REVERT: t 50 HIS cc_start: 0.8044 (m-70) cc_final: 0.7260 (m-70) REVERT: t 52 ASN cc_start: 0.6928 (m-40) cc_final: 0.6304 (p0) REVERT: w 26 TRP cc_start: 0.7021 (p90) cc_final: 0.6313 (p90) REVERT: w 117 LYS cc_start: 0.7961 (ptpt) cc_final: 0.7745 (pttp) REVERT: x 36 ASN cc_start: 0.8321 (m-40) cc_final: 0.7948 (m-40) REVERT: x 37 GLU cc_start: 0.8286 (tt0) cc_final: 0.7964 (tm-30) REVERT: x 42 TYR cc_start: 0.8385 (t80) cc_final: 0.7940 (t80) REVERT: z 25 ARG cc_start: 0.8624 (mtp85) cc_final: 0.7916 (ttp80) REVERT: z 64 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8317 (mmmt) outliers start: 9 outliers final: 3 residues processed: 1958 average time/residue: 0.7365 time to fit residues: 2358.6763 Evaluate side-chains 1301 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1296 time to evaluate : 5.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain r residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 5.9990 chunk 602 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 406 optimal weight: 5.9990 chunk 321 optimal weight: 5.9990 chunk 623 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 378 optimal weight: 7.9990 chunk 463 optimal weight: 6.9990 chunk 721 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN 1 250 ASN ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 356 HIS 1 373 ASN 1 437 HIS ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 101 GLN 2 121 GLN 3 179 ASN 3 277 GLN 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN 5 95 ASN 5 160 HIS 9 65 HIS H 247 HIS H 292 ASN J 46 ASN K 7 ASN K 92 ASN L 175 ASN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 HIS L 434 GLN L 442 ASN L 446 ASN L 509 HIS M 81 GLN M 103 GLN M 399 ASN N 174 GLN ** Y 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 142 HIS Z 54 GLN Z 143 HIS b 36 ASN c 46 GLN d 36 ASN d 87 HIS d 119 GLN d 136 ASN f 49 GLN f 95 GLN g 125 HIS h 35 GLN i 69 ASN i 123 GLN j 74 GLN k 92 ASN k 180 GLN k 204 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 44 HIS l 81 GLN ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 6 GLN o 61 GLN p 47 GLN p 116 GLN q 60 GLN s 46 ASN t 17 GLN u 16 GLN v 28 ASN v 66 HIS v 136 ASN w 57 ASN x 13 ASN y 13 HIS ** z 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 58 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.263 68996 Z= 0.544 Angle : 1.579 50.975 93232 Z= 1.018 Chirality : 0.315 6.718 10101 Planarity : 0.005 0.051 11630 Dihedral : 12.912 168.971 10501 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.71 % Allowed : 6.99 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -1.21 (0.09), residues: 8036 helix: -0.27 (0.07), residues: 4265 sheet: -1.33 (0.24), residues: 391 loop : -1.31 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 1 371 HIS 0.015 0.001 HIS t 50 PHE 0.035 0.002 PHE N 292 TYR 0.033 0.002 TYR M 406 ARG 0.009 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1397 time to evaluate : 6.242 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 73 PHE cc_start: 0.8776 (t80) cc_final: 0.7900 (m-80) REVERT: 1 105 CYS cc_start: 0.7876 (p) cc_final: 0.7595 (p) REVERT: 1 248 GLU cc_start: 0.8670 (tt0) cc_final: 0.8251 (mp0) REVERT: 1 425 GLU cc_start: 0.7783 (tp30) cc_final: 0.7440 (tp30) REVERT: 1 431 GLN cc_start: 0.8426 (pt0) cc_final: 0.8128 (pp30) REVERT: 2 127 LYS cc_start: 0.8431 (ptpt) cc_final: 0.8169 (mtpp) REVERT: 2 134 ASP cc_start: 0.8774 (p0) cc_final: 0.7887 (t0) REVERT: 3 243 ARG cc_start: 0.9314 (tmm-80) cc_final: 0.8954 (ttp-170) REVERT: 3 246 GLU cc_start: 0.8997 (tt0) cc_final: 0.8734 (pt0) REVERT: 3 427 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7810 (pttt) REVERT: 3 656 LEU cc_start: 0.8223 (mt) cc_final: 0.7951 (mp) REVERT: 4 75 LYS cc_start: 0.8618 (tttm) cc_final: 0.8308 (tptp) REVERT: 4 109 VAL cc_start: 0.9180 (m) cc_final: 0.8933 (p) REVERT: 4 152 MET cc_start: 0.9074 (tpt) cc_final: 0.8739 (tpt) REVERT: 4 182 GLU cc_start: 0.9385 (tm-30) cc_final: 0.9172 (tm-30) REVERT: 4 236 ARG cc_start: 0.9040 (mtp85) cc_final: 0.8809 (mtp-110) REVERT: 5 147 ASP cc_start: 0.8526 (t0) cc_final: 0.8009 (p0) REVERT: 6 58 GLU cc_start: 0.9103 (tp30) cc_final: 0.8877 (mm-30) REVERT: 6 102 LYS cc_start: 0.8984 (tttt) cc_final: 0.8715 (ttpp) REVERT: 6 105 ASP cc_start: 0.8819 (m-30) cc_final: 0.8585 (m-30) REVERT: 9 40 TYR cc_start: 0.9051 (m-80) cc_final: 0.8787 (m-80) REVERT: 9 78 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8625 (pp) REVERT: 9 172 ASP cc_start: 0.8949 (t70) cc_final: 0.8473 (t70) REVERT: H 259 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8215 (p90) REVERT: J 122 MET cc_start: 0.6603 (mtm) cc_final: 0.6227 (mtp) REVERT: K 91 GLN cc_start: 0.8065 (pm20) cc_final: 0.7810 (tp40) REVERT: L 159 TYR cc_start: 0.9220 (p90) cc_final: 0.8938 (p90) REVERT: L 412 THR cc_start: 0.7983 (m) cc_final: 0.7763 (m) REVERT: L 540 MET cc_start: 0.7898 (mtm) cc_final: 0.7584 (mmp) REVERT: L 544 MET cc_start: 0.7470 (tmm) cc_final: 0.7073 (ttt) REVERT: L 547 LYS cc_start: 0.8136 (mttm) cc_final: 0.7723 (mttp) REVERT: L 572 LYS cc_start: 0.7540 (tptt) cc_final: 0.7284 (tptt) REVERT: L 606 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6596 (mt-10) REVERT: W 77 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.8168 (ttt180) REVERT: Y 101 LYS cc_start: 0.8547 (ptmm) cc_final: 0.8201 (tttm) REVERT: Z 42 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7451 (mmt90) REVERT: Z 54 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7542 (mm-40) REVERT: Z 121 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7832 (ttm-80) REVERT: a 58 LEU cc_start: 0.9018 (mt) cc_final: 0.8481 (mp) REVERT: b 37 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8638 (pm20) REVERT: d 162 GLU cc_start: 0.8905 (mp0) cc_final: 0.8552 (mm-30) REVERT: d 175 GLU cc_start: 0.8656 (mp0) cc_final: 0.8449 (mp0) REVERT: d 224 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8423 (mmt180) REVERT: d 293 THR cc_start: 0.7648 (m) cc_final: 0.7336 (p) REVERT: d 338 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8056 (mptt) REVERT: e 17 GLU cc_start: 0.8698 (pt0) cc_final: 0.8374 (pt0) REVERT: e 45 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8464 (mtpt) REVERT: g 47 HIS cc_start: 0.8607 (t70) cc_final: 0.8038 (t-170) REVERT: g 50 GLN cc_start: 0.8527 (pt0) cc_final: 0.7829 (mm-40) REVERT: g 56 LYS cc_start: 0.8669 (tmmt) cc_final: 0.8468 (ttpt) REVERT: g 67 LYS cc_start: 0.8943 (mttt) cc_final: 0.8695 (tttt) REVERT: g 110 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7809 (mp0) REVERT: i 1 MET cc_start: 0.6738 (tpt) cc_final: 0.6319 (mtm) REVERT: i 25 ARG cc_start: 0.8729 (ttt90) cc_final: 0.8242 (ttp-110) REVERT: i 122 GLN cc_start: 0.8721 (mp10) cc_final: 0.8483 (pt0) REVERT: j 16 LEU cc_start: 0.7993 (mt) cc_final: 0.7634 (mt) REVERT: j 17 TYR cc_start: 0.7608 (t80) cc_final: 0.7373 (t80) REVERT: j 22 TYR cc_start: 0.7329 (t80) cc_final: 0.6970 (t80) REVERT: j 24 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7766 (mmmt) REVERT: j 46 ASP cc_start: 0.8338 (m-30) cc_final: 0.7985 (m-30) REVERT: j 57 GLU cc_start: 0.6571 (tp30) cc_final: 0.6280 (mm-30) REVERT: j 66 ASP cc_start: 0.8097 (p0) cc_final: 0.7877 (p0) REVERT: k 153 ASN cc_start: 0.8716 (m-40) cc_final: 0.8491 (m-40) REVERT: k 265 ASP cc_start: 0.8313 (t0) cc_final: 0.7827 (m-30) REVERT: n 42 ASP cc_start: 0.7047 (t70) cc_final: 0.6266 (p0) REVERT: o 5 ARG cc_start: 0.6684 (mtp-110) cc_final: 0.6408 (mtp-110) REVERT: o 25 LYS cc_start: 0.8594 (mttt) cc_final: 0.8122 (mtpt) REVERT: p 78 ASN cc_start: 0.8396 (m-40) cc_final: 0.7773 (m110) REVERT: r 14 LEU cc_start: 0.8326 (mm) cc_final: 0.8062 (mt) REVERT: s 23 THR cc_start: 0.8188 (p) cc_final: 0.7901 (m) REVERT: s 34 LYS cc_start: 0.7192 (ptpt) cc_final: 0.6902 (pttt) REVERT: s 71 ASP cc_start: 0.7088 (m-30) cc_final: 0.6718 (m-30) REVERT: s 80 LYS cc_start: 0.8615 (mmtm) cc_final: 0.7864 (pttp) REVERT: t 50 HIS cc_start: 0.7804 (m-70) cc_final: 0.7425 (m-70) REVERT: t 52 ASN cc_start: 0.7027 (m-40) cc_final: 0.6397 (p0) REVERT: t 93 TYR cc_start: 0.8500 (m-80) cc_final: 0.8285 (m-80) REVERT: w 26 TRP cc_start: 0.7202 (p90) cc_final: 0.6426 (p90) REVERT: z 25 ARG cc_start: 0.8500 (mtp85) cc_final: 0.8094 (mmt180) REVERT: z 64 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8254 (mmmt) outliers start: 122 outliers final: 75 residues processed: 1460 average time/residue: 0.6792 time to fit residues: 1653.5316 Evaluate side-chains 1346 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1268 time to evaluate : 5.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 71 GLU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 140 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 119 GLN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 234 ASN Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 180 GLN Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain t residue 161 ASP Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 110 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: 9.9990 chunk 600 optimal weight: 7.9990 chunk 491 optimal weight: 30.0000 chunk 199 optimal weight: 5.9990 chunk 723 optimal weight: 30.0000 chunk 781 optimal weight: 10.0000 chunk 644 optimal weight: 0.6980 chunk 717 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 580 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN K 25 HIS K 52 HIS L 27 HIS ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 470 ASN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 ASN Y 63 ASN Y 142 HIS Z 106 GLN f 95 GLN i 69 ASN j 74 GLN k 180 GLN k 204 ASN l 15 HIS ** l 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 59 HIS p 32 GLN p 47 GLN p 116 GLN s 81 HIS u 16 GLN v 28 ASN v 136 ASN x 36 ASN ** z 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 58 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 68996 Z= 0.554 Angle : 1.572 50.594 93232 Z= 1.016 Chirality : 0.311 6.419 10101 Planarity : 0.005 0.047 11630 Dihedral : 12.297 168.824 10497 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.06 % Allowed : 8.53 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 8036 helix: 0.43 (0.08), residues: 4269 sheet: -1.30 (0.23), residues: 415 loop : -0.99 (0.10), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 272 HIS 0.007 0.001 HIS t 50 PHE 0.034 0.002 PHE N 292 TYR 0.027 0.002 TYR M 406 ARG 0.005 0.000 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1322 time to evaluate : 7.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8779 (t80) cc_final: 0.7884 (m-80) REVERT: 1 105 CYS cc_start: 0.7747 (p) cc_final: 0.7483 (p) REVERT: 1 248 GLU cc_start: 0.8697 (tt0) cc_final: 0.8273 (mp0) REVERT: 1 354 TYR cc_start: 0.9149 (m-80) cc_final: 0.8948 (m-80) REVERT: 1 400 GLU cc_start: 0.8529 (tt0) cc_final: 0.8271 (tt0) REVERT: 1 425 GLU cc_start: 0.7817 (tp30) cc_final: 0.7466 (tp30) REVERT: 1 431 GLN cc_start: 0.8450 (pt0) cc_final: 0.8179 (pp30) REVERT: 1 435 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: 2 127 LYS cc_start: 0.8476 (ptpt) cc_final: 0.8181 (mtpp) REVERT: 2 134 ASP cc_start: 0.8936 (p0) cc_final: 0.8025 (t0) REVERT: 3 246 GLU cc_start: 0.9020 (tt0) cc_final: 0.8739 (pt0) REVERT: 3 656 LEU cc_start: 0.8210 (mt) cc_final: 0.7877 (mp) REVERT: 4 75 LYS cc_start: 0.8549 (tttm) cc_final: 0.8239 (tptp) REVERT: 4 108 TYR cc_start: 0.8917 (p90) cc_final: 0.8563 (p90) REVERT: 4 152 MET cc_start: 0.9060 (tpt) cc_final: 0.8847 (tpt) REVERT: 4 182 GLU cc_start: 0.9401 (tm-30) cc_final: 0.9171 (tm-30) REVERT: 4 411 LEU cc_start: 0.9057 (tp) cc_final: 0.8738 (tp) REVERT: 5 147 ASP cc_start: 0.8448 (t0) cc_final: 0.7959 (p0) REVERT: 6 58 GLU cc_start: 0.9195 (tp30) cc_final: 0.8964 (mm-30) REVERT: 6 102 LYS cc_start: 0.8945 (tttt) cc_final: 0.8680 (ttpp) REVERT: 6 105 ASP cc_start: 0.8862 (m-30) cc_final: 0.8636 (m-30) REVERT: 9 78 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8565 (pp) REVERT: 9 172 ASP cc_start: 0.8971 (t70) cc_final: 0.8505 (t70) REVERT: A 105 GLU cc_start: 0.8916 (tp30) cc_final: 0.8683 (tt0) REVERT: H 81 LEU cc_start: 0.9127 (mt) cc_final: 0.8744 (mm) REVERT: H 259 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8203 (p90) REVERT: J 97 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6319 (mp) REVERT: J 122 MET cc_start: 0.6633 (mtm) cc_final: 0.6284 (mtp) REVERT: K 91 GLN cc_start: 0.8133 (pm20) cc_final: 0.7389 (tm-30) REVERT: L 159 TYR cc_start: 0.9241 (p90) cc_final: 0.8971 (p90) REVERT: L 441 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8337 (mp) REVERT: L 540 MET cc_start: 0.8021 (mtm) cc_final: 0.7589 (mmp) REVERT: L 544 MET cc_start: 0.7579 (tmm) cc_final: 0.7176 (ttt) REVERT: L 547 LYS cc_start: 0.8083 (mttm) cc_final: 0.7670 (mttp) REVERT: L 572 LYS cc_start: 0.7453 (tptt) cc_final: 0.7168 (tptt) REVERT: L 606 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6586 (mt-10) REVERT: W 77 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8189 (ttt180) REVERT: X 19 LEU cc_start: 0.7675 (mt) cc_final: 0.7466 (mp) REVERT: Y 101 LYS cc_start: 0.8557 (ptmm) cc_final: 0.8287 (tttm) REVERT: Z 42 ARG cc_start: 0.7755 (mtp-110) cc_final: 0.7485 (mmt90) REVERT: Z 58 ASN cc_start: 0.7517 (p0) cc_final: 0.7275 (p0) REVERT: Z 121 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7815 (ttm-80) REVERT: a 58 LEU cc_start: 0.8999 (mt) cc_final: 0.8605 (mp) REVERT: b 37 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8650 (pm20) REVERT: d 162 GLU cc_start: 0.8926 (mp0) cc_final: 0.8587 (mm-30) REVERT: d 224 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8412 (mmt180) REVERT: d 293 THR cc_start: 0.7644 (m) cc_final: 0.7356 (p) REVERT: d 338 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8062 (mptt) REVERT: e 17 GLU cc_start: 0.8698 (pt0) cc_final: 0.8495 (pt0) REVERT: e 45 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8473 (mtpt) REVERT: g 33 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8483 (mm-30) REVERT: g 47 HIS cc_start: 0.8626 (t70) cc_final: 0.8127 (t-170) REVERT: g 50 GLN cc_start: 0.8569 (pt0) cc_final: 0.7902 (mm-40) REVERT: g 67 LYS cc_start: 0.8950 (mttt) cc_final: 0.8736 (tttt) REVERT: i 1 MET cc_start: 0.6731 (tpt) cc_final: 0.6310 (mtm) REVERT: i 25 ARG cc_start: 0.8739 (ttt90) cc_final: 0.8252 (ttp-110) REVERT: i 122 GLN cc_start: 0.8738 (mp10) cc_final: 0.8506 (pt0) REVERT: j 16 LEU cc_start: 0.7994 (mt) cc_final: 0.7630 (mt) REVERT: j 17 TYR cc_start: 0.7656 (t80) cc_final: 0.7429 (t80) REVERT: j 22 TYR cc_start: 0.7429 (t80) cc_final: 0.6855 (t80) REVERT: j 24 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7755 (mmmt) REVERT: j 46 ASP cc_start: 0.8290 (m-30) cc_final: 0.7983 (m-30) REVERT: j 57 GLU cc_start: 0.6580 (tp30) cc_final: 0.6284 (mm-30) REVERT: k 153 ASN cc_start: 0.8760 (m-40) cc_final: 0.8552 (m-40) REVERT: k 265 ASP cc_start: 0.8342 (t0) cc_final: 0.7836 (m-30) REVERT: l 32 CYS cc_start: 0.8574 (m) cc_final: 0.8322 (m) REVERT: n 42 ASP cc_start: 0.7110 (t70) cc_final: 0.6253 (p0) REVERT: o 25 LYS cc_start: 0.8591 (mttt) cc_final: 0.8384 (mtpp) REVERT: r 8 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8295 (tttt) REVERT: r 14 LEU cc_start: 0.8332 (mm) cc_final: 0.8066 (mt) REVERT: s 23 THR cc_start: 0.8149 (p) cc_final: 0.7944 (m) REVERT: s 34 LYS cc_start: 0.7247 (ptpt) cc_final: 0.6905 (pttt) REVERT: s 71 ASP cc_start: 0.7260 (m-30) cc_final: 0.6663 (m-30) REVERT: s 80 LYS cc_start: 0.8667 (mmtm) cc_final: 0.7911 (pttp) REVERT: t 50 HIS cc_start: 0.7875 (m-70) cc_final: 0.7597 (m-70) REVERT: t 52 ASN cc_start: 0.7049 (m-40) cc_final: 0.6449 (p0) REVERT: u 45 ASP cc_start: 0.7607 (m-30) cc_final: 0.7395 (t0) REVERT: w 26 TRP cc_start: 0.7239 (p90) cc_final: 0.6432 (p90) REVERT: y 9 ASP cc_start: 0.4774 (p0) cc_final: 0.4561 (p0) REVERT: z 25 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8084 (mmt180) REVERT: z 58 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.8022 (t0) REVERT: z 64 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8327 (mmmt) outliers start: 147 outliers final: 91 residues processed: 1396 average time/residue: 0.6781 time to fit residues: 1580.9945 Evaluate side-chains 1348 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1250 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 71 GLU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain e residue 37 GLU Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 180 GLN Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 27 THR Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 95 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 7 ILE Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain x residue 32 ILE Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain z residue 58 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 7.9990 chunk 543 optimal weight: 10.0000 chunk 375 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 485 optimal weight: 7.9990 chunk 725 optimal weight: 20.0000 chunk 768 optimal weight: 30.0000 chunk 379 optimal weight: 5.9990 chunk 687 optimal weight: 40.0000 chunk 207 optimal weight: 9.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 436 GLN 2 55 GLN 3 441 GLN ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 79 HIS 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 142 HIS ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 ASN f 95 GLN i 69 ASN k 141 GLN k 180 GLN k 204 ASN l 96 HIS l 97 HIS n 58 ASN p 116 GLN q 89 ASN s 81 HIS u 13 GLN v 28 ASN v 87 ASN v 136 ASN v 137 ASN x 36 ASN z 31 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.239 68996 Z= 0.634 Angle : 1.596 50.701 93232 Z= 1.025 Chirality : 0.311 6.407 10101 Planarity : 0.005 0.078 11630 Dihedral : 12.169 170.062 10497 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.54 % Allowed : 9.71 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.23 (0.09), residues: 8036 helix: 0.57 (0.08), residues: 4299 sheet: -1.17 (0.24), residues: 412 loop : -0.89 (0.11), residues: 3325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 272 HIS 0.014 0.002 HIS s 81 PHE 0.033 0.002 PHE N 292 TYR 0.025 0.002 TYR M 406 ARG 0.013 0.001 ARG p 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1265 time to evaluate : 5.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8819 (t80) cc_final: 0.7928 (m-80) REVERT: 1 105 CYS cc_start: 0.8018 (p) cc_final: 0.7719 (p) REVERT: 1 248 GLU cc_start: 0.8717 (tt0) cc_final: 0.8246 (mp0) REVERT: 1 350 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8703 (mp) REVERT: 1 400 GLU cc_start: 0.8619 (tt0) cc_final: 0.8362 (tt0) REVERT: 1 425 GLU cc_start: 0.7831 (tp30) cc_final: 0.7462 (tp30) REVERT: 1 431 GLN cc_start: 0.8484 (pt0) cc_final: 0.8177 (pp30) REVERT: 1 435 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: 2 134 ASP cc_start: 0.8974 (p0) cc_final: 0.8080 (t0) REVERT: 3 427 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7686 (pttt) REVERT: 3 531 CYS cc_start: 0.8505 (m) cc_final: 0.8284 (m) REVERT: 3 656 LEU cc_start: 0.8174 (mt) cc_final: 0.7973 (mp) REVERT: 4 75 LYS cc_start: 0.8640 (tttm) cc_final: 0.8308 (tptp) REVERT: 4 108 TYR cc_start: 0.9014 (p90) cc_final: 0.8766 (p90) REVERT: 4 182 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9205 (tm-30) REVERT: 5 147 ASP cc_start: 0.8438 (t0) cc_final: 0.7976 (p0) REVERT: 6 102 LYS cc_start: 0.9000 (tttt) cc_final: 0.8723 (ttpp) REVERT: 9 78 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8632 (pp) REVERT: 9 172 ASP cc_start: 0.9028 (t70) cc_final: 0.8526 (t70) REVERT: A 98 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8921 (tp) REVERT: A 105 GLU cc_start: 0.8978 (tp30) cc_final: 0.8766 (tt0) REVERT: H 81 LEU cc_start: 0.9182 (mt) cc_final: 0.8782 (mm) REVERT: H 259 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8383 (p90) REVERT: J 97 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6352 (mp) REVERT: K 91 GLN cc_start: 0.8216 (pm20) cc_final: 0.7417 (tm-30) REVERT: L 441 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8342 (mp) REVERT: L 540 MET cc_start: 0.8192 (mtm) cc_final: 0.7726 (mmp) REVERT: L 544 MET cc_start: 0.7602 (tmm) cc_final: 0.7225 (ttt) REVERT: L 547 LYS cc_start: 0.8199 (mttm) cc_final: 0.7746 (mttp) REVERT: L 606 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6682 (mt-10) REVERT: M 366 ASN cc_start: 0.8605 (t0) cc_final: 0.8255 (t0) REVERT: V 42 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8587 (mm) REVERT: W 77 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8196 (ttt180) REVERT: X 19 LEU cc_start: 0.7806 (mt) cc_final: 0.7550 (mp) REVERT: Y 101 LYS cc_start: 0.8617 (ptmm) cc_final: 0.8324 (tttm) REVERT: Z 42 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7598 (mmt180) REVERT: Z 58 ASN cc_start: 0.7612 (p0) cc_final: 0.7329 (p0) REVERT: Z 121 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7965 (ttm-80) REVERT: a 58 LEU cc_start: 0.9036 (mt) cc_final: 0.8474 (mp) REVERT: b 37 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8660 (pm20) REVERT: d 57 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8953 (mmt) REVERT: d 224 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8322 (mmp80) REVERT: d 281 ARG cc_start: 0.7811 (tpp-160) cc_final: 0.7464 (mmp80) REVERT: d 338 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8058 (mptt) REVERT: e 17 GLU cc_start: 0.8735 (pt0) cc_final: 0.8505 (pt0) REVERT: f 115 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7822 (pp) REVERT: g 33 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8511 (mm-30) REVERT: g 47 HIS cc_start: 0.8707 (t70) cc_final: 0.8224 (t-170) REVERT: g 50 GLN cc_start: 0.8597 (pt0) cc_final: 0.7822 (mm-40) REVERT: g 67 LYS cc_start: 0.8962 (mttt) cc_final: 0.8750 (tttt) REVERT: i 1 MET cc_start: 0.6917 (tpt) cc_final: 0.6377 (mtm) REVERT: i 25 ARG cc_start: 0.8783 (ttt90) cc_final: 0.8280 (ttp-110) REVERT: i 122 GLN cc_start: 0.8780 (mp10) cc_final: 0.8520 (pt0) REVERT: j 16 LEU cc_start: 0.7985 (mt) cc_final: 0.7603 (mt) REVERT: j 24 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7751 (mmmt) REVERT: j 46 ASP cc_start: 0.8298 (m-30) cc_final: 0.7977 (m-30) REVERT: k 153 ASN cc_start: 0.8808 (m-40) cc_final: 0.8605 (m-40) REVERT: k 265 ASP cc_start: 0.8411 (t0) cc_final: 0.7953 (m-30) REVERT: l 32 CYS cc_start: 0.8610 (m) cc_final: 0.8403 (m) REVERT: n 42 ASP cc_start: 0.7164 (t70) cc_final: 0.6407 (p0) REVERT: o 25 LYS cc_start: 0.8615 (mttt) cc_final: 0.8387 (mtpp) REVERT: q 22 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7839 (mtm-85) REVERT: r 14 LEU cc_start: 0.8356 (mm) cc_final: 0.8110 (mt) REVERT: s 34 LYS cc_start: 0.7260 (ptpt) cc_final: 0.6915 (pttt) REVERT: s 71 ASP cc_start: 0.7229 (m-30) cc_final: 0.6893 (m-30) REVERT: s 80 LYS cc_start: 0.8637 (mmtm) cc_final: 0.7993 (pttt) REVERT: t 50 HIS cc_start: 0.8006 (m-70) cc_final: 0.7739 (m-70) REVERT: t 52 ASN cc_start: 0.7186 (m-40) cc_final: 0.6528 (p0) REVERT: w 26 TRP cc_start: 0.7329 (p90) cc_final: 0.6437 (p90) REVERT: x 19 LEU cc_start: 0.8927 (mt) cc_final: 0.8713 (mt) REVERT: z 25 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8134 (mmt180) REVERT: z 64 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8383 (mmmt) outliers start: 181 outliers final: 118 residues processed: 1364 average time/residue: 0.6835 time to fit residues: 1560.8299 Evaluate side-chains 1347 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1217 time to evaluate : 5.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 350 LEU Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 139 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 4 residue 72 MET Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 444 ASN Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 234 ASN Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 180 GLN Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 242 LYS Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 22 ARG Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 95 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain s residue 63 ILE Chi-restraints excluded: chain t residue 88 THR Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 7 ILE Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 53 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 6.9990 chunk 436 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 572 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 655 optimal weight: 3.9990 chunk 531 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 392 optimal weight: 9.9990 chunk 689 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 150 GLN ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 142 HIS Z 90 GLN d 234 ASN f 82 GLN f 95 GLN ** g 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 GLN i 5 GLN i 69 ASN k 180 GLN k 294 GLN n 58 ASN p 47 GLN p 116 GLN s 81 HIS v 28 ASN v 136 ASN x 36 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 68996 Z= 0.540 Angle : 1.563 50.642 93232 Z= 1.012 Chirality : 0.310 6.376 10101 Planarity : 0.004 0.048 11630 Dihedral : 11.806 168.638 10497 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.22 % Allowed : 10.96 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.15 (0.09), residues: 8036 helix: 0.88 (0.08), residues: 4288 sheet: -1.12 (0.24), residues: 410 loop : -0.69 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 272 HIS 0.006 0.001 HIS t 75 PHE 0.033 0.001 PHE N 292 TYR 0.023 0.001 TYR M 406 ARG 0.006 0.000 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1291 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8791 (t80) cc_final: 0.7924 (m-80) REVERT: 1 105 CYS cc_start: 0.7904 (p) cc_final: 0.7582 (p) REVERT: 1 248 GLU cc_start: 0.8705 (tt0) cc_final: 0.8244 (mp0) REVERT: 1 400 GLU cc_start: 0.8555 (tt0) cc_final: 0.8292 (tt0) REVERT: 1 425 GLU cc_start: 0.7847 (tp30) cc_final: 0.7481 (tp30) REVERT: 1 431 GLN cc_start: 0.8412 (pt0) cc_final: 0.8108 (pp30) REVERT: 1 435 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: 2 134 ASP cc_start: 0.8972 (p0) cc_final: 0.8052 (t0) REVERT: 3 427 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7719 (pttt) REVERT: 3 531 CYS cc_start: 0.8491 (m) cc_final: 0.8256 (m) REVERT: 3 656 LEU cc_start: 0.8110 (mt) cc_final: 0.7909 (mp) REVERT: 4 75 LYS cc_start: 0.8615 (tttm) cc_final: 0.8275 (tptp) REVERT: 4 108 TYR cc_start: 0.8988 (p90) cc_final: 0.8753 (p90) REVERT: 4 182 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9210 (tm-30) REVERT: 5 147 ASP cc_start: 0.8423 (t0) cc_final: 0.7959 (p0) REVERT: 6 102 LYS cc_start: 0.8961 (tttt) cc_final: 0.8693 (ttpp) REVERT: 6 105 ASP cc_start: 0.8785 (m-30) cc_final: 0.8519 (m-30) REVERT: 6 115 SER cc_start: 0.9024 (t) cc_final: 0.8741 (m) REVERT: 9 78 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8598 (pp) REVERT: 9 172 ASP cc_start: 0.9006 (t70) cc_final: 0.8539 (t70) REVERT: H 81 LEU cc_start: 0.9150 (mt) cc_final: 0.8762 (mm) REVERT: H 214 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: H 259 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8245 (p90) REVERT: J 97 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6358 (mp) REVERT: K 91 GLN cc_start: 0.8225 (pm20) cc_final: 0.7456 (tm-30) REVERT: L 441 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8281 (mp) REVERT: L 540 MET cc_start: 0.8249 (mtm) cc_final: 0.7758 (mmp) REVERT: L 544 MET cc_start: 0.7560 (tmm) cc_final: 0.7148 (ttt) REVERT: L 547 LYS cc_start: 0.8186 (mttm) cc_final: 0.7704 (mtmm) REVERT: L 606 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6626 (mt-10) REVERT: M 366 ASN cc_start: 0.8560 (t0) cc_final: 0.8233 (t0) REVERT: V 42 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8309 (mt) REVERT: V 89 TYR cc_start: 0.8268 (m-80) cc_final: 0.8036 (m-80) REVERT: W 77 ARG cc_start: 0.8508 (ttp-110) cc_final: 0.8187 (ttt180) REVERT: Y 101 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8361 (tttm) REVERT: Z 42 ARG cc_start: 0.7846 (mtp-110) cc_final: 0.7608 (mmt180) REVERT: Z 58 ASN cc_start: 0.7582 (p0) cc_final: 0.7274 (p0) REVERT: Z 121 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7864 (ttm-80) REVERT: a 58 LEU cc_start: 0.8989 (mt) cc_final: 0.8583 (mp) REVERT: b 37 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8662 (pm20) REVERT: d 57 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8882 (mmt) REVERT: d 224 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8299 (mmt180) REVERT: d 281 ARG cc_start: 0.7748 (tpp-160) cc_final: 0.7383 (mmp80) REVERT: d 293 THR cc_start: 0.7702 (m) cc_final: 0.7397 (p) REVERT: d 338 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8036 (mptt) REVERT: f 115 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7885 (pp) REVERT: g 47 HIS cc_start: 0.8714 (t70) cc_final: 0.8272 (t70) REVERT: g 50 GLN cc_start: 0.8569 (pt0) cc_final: 0.7786 (mm-40) REVERT: g 67 LYS cc_start: 0.8954 (mttt) cc_final: 0.8746 (tttt) REVERT: g 79 ASP cc_start: 0.8910 (m-30) cc_final: 0.8580 (m-30) REVERT: i 1 MET cc_start: 0.6900 (tpt) cc_final: 0.6376 (mtm) REVERT: i 25 ARG cc_start: 0.8775 (ttt90) cc_final: 0.8269 (ttp-110) REVERT: i 122 GLN cc_start: 0.8746 (mp10) cc_final: 0.8507 (pt0) REVERT: j 16 LEU cc_start: 0.7994 (mt) cc_final: 0.7641 (mt) REVERT: j 17 TYR cc_start: 0.7640 (t80) cc_final: 0.7394 (t80) REVERT: j 22 TYR cc_start: 0.7307 (t80) cc_final: 0.6872 (t80) REVERT: j 24 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7782 (mmmt) REVERT: j 46 ASP cc_start: 0.8302 (m-30) cc_final: 0.7993 (m-30) REVERT: k 153 ASN cc_start: 0.8769 (m-40) cc_final: 0.8467 (m110) REVERT: k 265 ASP cc_start: 0.8381 (t0) cc_final: 0.7884 (m-30) REVERT: m 50 TYR cc_start: 0.8894 (m-80) cc_final: 0.8641 (m-80) REVERT: n 42 ASP cc_start: 0.7162 (t70) cc_final: 0.6255 (p0) REVERT: n 85 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.6025 (t80) REVERT: o 25 LYS cc_start: 0.8577 (mttt) cc_final: 0.8342 (mtpp) REVERT: q 22 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7797 (mtm-85) REVERT: r 14 LEU cc_start: 0.8294 (mm) cc_final: 0.8044 (mt) REVERT: r 76 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9092 (mp) REVERT: s 34 LYS cc_start: 0.7300 (ptpt) cc_final: 0.6966 (pttt) REVERT: s 71 ASP cc_start: 0.7242 (m-30) cc_final: 0.6961 (m-30) REVERT: s 80 LYS cc_start: 0.8493 (mmtm) cc_final: 0.7955 (pttt) REVERT: t 50 HIS cc_start: 0.8058 (m-70) cc_final: 0.7782 (m-70) REVERT: t 52 ASN cc_start: 0.7129 (m-40) cc_final: 0.6508 (p0) REVERT: w 26 TRP cc_start: 0.7273 (p90) cc_final: 0.6408 (p90) REVERT: x 38 ASP cc_start: 0.8815 (m-30) cc_final: 0.8386 (m-30) REVERT: z 25 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8113 (mmt180) REVERT: z 64 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8358 (mmmt) outliers start: 158 outliers final: 103 residues processed: 1381 average time/residue: 0.6707 time to fit residues: 1549.9856 Evaluate side-chains 1348 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1232 time to evaluate : 5.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 221 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 139 ASP Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 521 MET Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 136 ASN Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 57 MET Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 78 GLU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 180 GLN Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 27 THR Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 22 ARG Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 99 LYS Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 7 ILE Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain y residue 53 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 9.9990 chunk 692 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 451 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 769 optimal weight: 20.0000 chunk 638 optimal weight: 6.9990 chunk 356 optimal weight: 20.0000 chunk 63 optimal weight: 0.0770 chunk 254 optimal weight: 6.9990 chunk 403 optimal weight: 9.9990 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 HIS Z 54 GLN d 119 GLN f 95 GLN ** g 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 GLN i 5 GLN i 69 ASN k 180 GLN n 58 ASN p 116 GLN q 53 ASN s 81 HIS v 28 ASN v 136 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 68996 Z= 0.570 Angle : 1.572 50.679 93232 Z= 1.015 Chirality : 0.310 6.377 10101 Planarity : 0.004 0.050 11630 Dihedral : 11.683 168.892 10497 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.62 % Allowed : 11.28 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.26 (0.09), residues: 8036 helix: 0.96 (0.08), residues: 4282 sheet: -0.90 (0.25), residues: 400 loop : -0.65 (0.11), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP r 79 HIS 0.029 0.001 HIS s 81 PHE 0.032 0.002 PHE N 292 TYR 0.022 0.002 TYR M 406 ARG 0.006 0.000 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1257 time to evaluate : 6.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8797 (t80) cc_final: 0.7930 (m-80) REVERT: 1 105 CYS cc_start: 0.7954 (p) cc_final: 0.7629 (p) REVERT: 1 248 GLU cc_start: 0.8721 (tt0) cc_final: 0.8244 (mp0) REVERT: 1 400 GLU cc_start: 0.8581 (tt0) cc_final: 0.8329 (tt0) REVERT: 1 425 GLU cc_start: 0.7879 (tp30) cc_final: 0.7537 (tp30) REVERT: 1 431 GLN cc_start: 0.8385 (pt0) cc_final: 0.8065 (pp30) REVERT: 1 435 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: 2 134 ASP cc_start: 0.8973 (p0) cc_final: 0.8080 (t0) REVERT: 3 427 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7738 (pttt) REVERT: 3 531 CYS cc_start: 0.8521 (m) cc_final: 0.8293 (m) REVERT: 3 656 LEU cc_start: 0.8115 (mt) cc_final: 0.7908 (mp) REVERT: 4 75 LYS cc_start: 0.8627 (tttm) cc_final: 0.8282 (tptp) REVERT: 4 152 MET cc_start: 0.9196 (tpp) cc_final: 0.8886 (tpt) REVERT: 5 147 ASP cc_start: 0.8424 (t0) cc_final: 0.7981 (p0) REVERT: 6 102 LYS cc_start: 0.8965 (tttt) cc_final: 0.8690 (ttpp) REVERT: 9 40 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.7409 (t80) REVERT: 9 78 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8600 (pp) REVERT: 9 172 ASP cc_start: 0.9028 (t70) cc_final: 0.8558 (t70) REVERT: H 81 LEU cc_start: 0.9185 (mt) cc_final: 0.8784 (mm) REVERT: H 214 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: H 259 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8279 (p90) REVERT: J 97 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6358 (mp) REVERT: K 91 GLN cc_start: 0.8242 (pm20) cc_final: 0.7503 (tm-30) REVERT: L 283 MET cc_start: 0.8341 (tpt) cc_final: 0.8098 (ttp) REVERT: L 441 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8251 (mp) REVERT: L 540 MET cc_start: 0.8272 (mtm) cc_final: 0.7786 (mmp) REVERT: L 544 MET cc_start: 0.7536 (tmm) cc_final: 0.7144 (ttt) REVERT: L 547 LYS cc_start: 0.8187 (mttm) cc_final: 0.7697 (mtmm) REVERT: L 606 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6683 (mt-10) REVERT: M 195 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7838 (tpt) REVERT: M 366 ASN cc_start: 0.8589 (t0) cc_final: 0.8234 (t0) REVERT: V 42 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8372 (mt) REVERT: W 77 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8189 (ttt180) REVERT: Y 101 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8364 (tttm) REVERT: Z 17 PRO cc_start: 0.8570 (Cg_endo) cc_final: 0.8327 (Cg_exo) REVERT: Z 42 ARG cc_start: 0.7867 (mtp-110) cc_final: 0.7625 (mmt180) REVERT: Z 58 ASN cc_start: 0.7604 (p0) cc_final: 0.7291 (p0) REVERT: Z 121 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7925 (ttm-80) REVERT: a 58 LEU cc_start: 0.9010 (mt) cc_final: 0.8603 (mp) REVERT: b 3 ARG cc_start: 0.7991 (ptt90) cc_final: 0.7719 (ptt-90) REVERT: b 37 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8666 (pm20) REVERT: d 219 LYS cc_start: 0.8659 (mttt) cc_final: 0.8450 (mttt) REVERT: d 224 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8294 (mmt180) REVERT: d 281 ARG cc_start: 0.7762 (tpp-160) cc_final: 0.7377 (mmp80) REVERT: d 338 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8016 (mptt) REVERT: f 93 MET cc_start: 0.8282 (mmt) cc_final: 0.8046 (mmp) REVERT: f 115 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7872 (pp) REVERT: g 47 HIS cc_start: 0.8703 (t70) cc_final: 0.8302 (t70) REVERT: g 50 GLN cc_start: 0.8605 (pt0) cc_final: 0.7823 (mm-40) REVERT: g 79 ASP cc_start: 0.8918 (m-30) cc_final: 0.8603 (m-30) REVERT: i 1 MET cc_start: 0.6895 (tpt) cc_final: 0.6385 (mtm) REVERT: i 25 ARG cc_start: 0.8770 (ttt90) cc_final: 0.8251 (ttp-110) REVERT: i 122 GLN cc_start: 0.8771 (mp10) cc_final: 0.8522 (pt0) REVERT: j 17 TYR cc_start: 0.7618 (t80) cc_final: 0.7385 (t80) REVERT: j 22 TYR cc_start: 0.7334 (t80) cc_final: 0.6934 (t80) REVERT: j 24 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7793 (mmmt) REVERT: j 46 ASP cc_start: 0.8300 (m-30) cc_final: 0.7994 (m-30) REVERT: k 153 ASN cc_start: 0.8817 (m-40) cc_final: 0.8599 (m-40) REVERT: k 265 ASP cc_start: 0.8353 (t0) cc_final: 0.7866 (m-30) REVERT: l 82 ARG cc_start: 0.8321 (tmm-80) cc_final: 0.7916 (ttm-80) REVERT: m 50 TYR cc_start: 0.8888 (m-80) cc_final: 0.8651 (m-80) REVERT: n 42 ASP cc_start: 0.7172 (t70) cc_final: 0.6263 (p0) REVERT: o 25 LYS cc_start: 0.8585 (mttt) cc_final: 0.8348 (mtpp) REVERT: q 22 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7774 (mtm-85) REVERT: r 14 LEU cc_start: 0.8321 (mm) cc_final: 0.8069 (mt) REVERT: r 75 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8544 (tp) REVERT: r 76 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9115 (mp) REVERT: s 34 LYS cc_start: 0.7329 (ptpt) cc_final: 0.7048 (pttt) REVERT: s 71 ASP cc_start: 0.7324 (m-30) cc_final: 0.6959 (m-30) REVERT: s 80 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7813 (pttt) REVERT: t 50 HIS cc_start: 0.8047 (m-70) cc_final: 0.7774 (m-70) REVERT: t 52 ASN cc_start: 0.7198 (m-40) cc_final: 0.6549 (p0) REVERT: v 18 GLU cc_start: 0.8260 (mp0) cc_final: 0.7957 (pm20) REVERT: w 26 TRP cc_start: 0.7271 (p90) cc_final: 0.6393 (p90) REVERT: z 25 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8110 (mmt180) REVERT: z 58 ASN cc_start: 0.8250 (t0) cc_final: 0.8046 (t0) REVERT: z 64 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8361 (mmmt) outliers start: 187 outliers final: 130 residues processed: 1359 average time/residue: 0.6865 time to fit residues: 1563.9006 Evaluate side-chains 1362 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1218 time to evaluate : 6.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 139 ASP Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 508 LYS Chi-restraints excluded: chain 3 residue 521 MET Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 72 MET Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 69 MET Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 40 TYR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 444 ASN Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 119 GLN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 78 GLU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 53 MET Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 22 ARG Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 95 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 99 LYS Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 7 ILE Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 438 optimal weight: 30.0000 chunk 561 optimal weight: 8.9990 chunk 435 optimal weight: 20.0000 chunk 647 optimal weight: 20.0000 chunk 429 optimal weight: 5.9990 chunk 766 optimal weight: 9.9990 chunk 479 optimal weight: 8.9990 chunk 467 optimal weight: 20.0000 chunk 353 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 ASN M 304 GLN N 144 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 GLN Y 142 HIS ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 148 HIS d 119 GLN f 82 GLN f 95 GLN ** g 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 GLN i 69 ASN n 58 ASN p 116 GLN s 81 HIS v 28 ASN v 136 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 68996 Z= 0.573 Angle : 1.573 50.672 93232 Z= 1.016 Chirality : 0.310 6.374 10101 Planarity : 0.004 0.050 11630 Dihedral : 11.616 168.990 10497 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.64 % Allowed : 11.51 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 8036 helix: 0.99 (0.08), residues: 4287 sheet: -0.86 (0.25), residues: 403 loop : -0.61 (0.11), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 272 HIS 0.008 0.001 HIS s 81 PHE 0.032 0.002 PHE N 292 TYR 0.032 0.002 TYR V 89 ARG 0.006 0.000 ARG t 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1431 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1243 time to evaluate : 7.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8789 (t80) cc_final: 0.7935 (m-80) REVERT: 1 105 CYS cc_start: 0.8018 (p) cc_final: 0.7694 (p) REVERT: 1 248 GLU cc_start: 0.8722 (tt0) cc_final: 0.8238 (mp0) REVERT: 1 400 GLU cc_start: 0.8587 (tt0) cc_final: 0.8334 (tt0) REVERT: 1 425 GLU cc_start: 0.7882 (tp30) cc_final: 0.7518 (tp30) REVERT: 1 431 GLN cc_start: 0.8386 (pt0) cc_final: 0.8049 (pp30) REVERT: 1 435 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: 2 134 ASP cc_start: 0.8975 (p0) cc_final: 0.8082 (t0) REVERT: 3 427 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7747 (pttt) REVERT: 3 531 CYS cc_start: 0.8531 (m) cc_final: 0.8307 (m) REVERT: 3 656 LEU cc_start: 0.8109 (mt) cc_final: 0.7893 (mp) REVERT: 4 75 LYS cc_start: 0.8645 (tttm) cc_final: 0.8294 (tptp) REVERT: 4 152 MET cc_start: 0.9193 (tpp) cc_final: 0.8831 (tpt) REVERT: 5 147 ASP cc_start: 0.8455 (t0) cc_final: 0.8002 (p0) REVERT: 6 102 LYS cc_start: 0.9002 (tttt) cc_final: 0.8741 (ttpp) REVERT: 9 40 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.7405 (t80) REVERT: 9 78 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8611 (pp) REVERT: 9 172 ASP cc_start: 0.9033 (t70) cc_final: 0.8563 (t70) REVERT: H 81 LEU cc_start: 0.9183 (mt) cc_final: 0.8789 (mm) REVERT: H 214 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6854 (mm-30) REVERT: H 259 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8291 (p90) REVERT: J 97 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6365 (mp) REVERT: K 91 GLN cc_start: 0.8256 (pm20) cc_final: 0.7533 (tm-30) REVERT: L 441 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8267 (mp) REVERT: L 540 MET cc_start: 0.8299 (mtm) cc_final: 0.7789 (mmp) REVERT: L 544 MET cc_start: 0.7535 (tmm) cc_final: 0.7151 (ttt) REVERT: L 547 LYS cc_start: 0.8192 (mttm) cc_final: 0.7716 (mtmm) REVERT: L 606 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6785 (mt-10) REVERT: M 195 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7821 (tpp) REVERT: M 366 ASN cc_start: 0.8584 (t0) cc_final: 0.8210 (t0) REVERT: N 117 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: V 42 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8370 (mt) REVERT: W 77 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.8184 (ttt180) REVERT: Y 101 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8399 (tttm) REVERT: Z 17 PRO cc_start: 0.8549 (Cg_endo) cc_final: 0.8313 (Cg_exo) REVERT: Z 42 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7624 (mmt180) REVERT: Z 58 ASN cc_start: 0.7602 (p0) cc_final: 0.7279 (p0) REVERT: Z 121 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7931 (ttm-80) REVERT: a 58 LEU cc_start: 0.9036 (mt) cc_final: 0.8631 (mp) REVERT: b 3 ARG cc_start: 0.7978 (ptt90) cc_final: 0.7714 (ptt-90) REVERT: b 37 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8668 (pm20) REVERT: d 224 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8266 (mmt180) REVERT: d 281 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7360 (mmp80) REVERT: d 338 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8031 (mptt) REVERT: f 93 MET cc_start: 0.8281 (mmt) cc_final: 0.8035 (mmp) REVERT: f 115 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7843 (pp) REVERT: g 47 HIS cc_start: 0.8719 (t70) cc_final: 0.8394 (t70) REVERT: g 50 GLN cc_start: 0.8586 (pt0) cc_final: 0.8086 (mm-40) REVERT: g 79 ASP cc_start: 0.8920 (m-30) cc_final: 0.8616 (m-30) REVERT: i 1 MET cc_start: 0.6887 (tpt) cc_final: 0.6389 (mtm) REVERT: i 25 ARG cc_start: 0.8763 (ttt90) cc_final: 0.8247 (ttp-110) REVERT: i 122 GLN cc_start: 0.8782 (mp10) cc_final: 0.8533 (pt0) REVERT: j 17 TYR cc_start: 0.7667 (t80) cc_final: 0.7412 (t80) REVERT: j 24 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (mmmt) REVERT: j 46 ASP cc_start: 0.8320 (m-30) cc_final: 0.8009 (m-30) REVERT: k 153 ASN cc_start: 0.8824 (m-40) cc_final: 0.8611 (m-40) REVERT: k 173 ASP cc_start: 0.6733 (t0) cc_final: 0.5968 (p0) REVERT: k 265 ASP cc_start: 0.8346 (t0) cc_final: 0.7856 (m-30) REVERT: l 82 ARG cc_start: 0.8322 (tmm-80) cc_final: 0.7944 (ttm-80) REVERT: m 50 TYR cc_start: 0.8888 (m-80) cc_final: 0.8660 (m-80) REVERT: n 42 ASP cc_start: 0.7176 (t70) cc_final: 0.6251 (p0) REVERT: n 85 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.6080 (t80) REVERT: o 25 LYS cc_start: 0.8590 (mttt) cc_final: 0.8350 (mtpp) REVERT: q 22 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: r 14 LEU cc_start: 0.8305 (mm) cc_final: 0.8051 (mt) REVERT: r 75 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8525 (tp) REVERT: r 76 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9100 (mp) REVERT: s 34 LYS cc_start: 0.7371 (ptpt) cc_final: 0.7045 (pttt) REVERT: s 71 ASP cc_start: 0.7481 (m-30) cc_final: 0.7144 (m-30) REVERT: s 80 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7864 (pttt) REVERT: t 50 HIS cc_start: 0.8071 (m-70) cc_final: 0.7787 (m-70) REVERT: t 52 ASN cc_start: 0.7205 (m-40) cc_final: 0.6573 (p0) REVERT: v 18 GLU cc_start: 0.8265 (mp0) cc_final: 0.7948 (pm20) REVERT: w 31 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8043 (tm-30) REVERT: w 92 GLU cc_start: 0.8381 (tp30) cc_final: 0.8068 (tp30) REVERT: x 38 ASP cc_start: 0.8801 (m-30) cc_final: 0.8343 (m-30) REVERT: z 25 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8133 (mmt180) REVERT: z 64 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8450 (mmmt) outliers start: 188 outliers final: 145 residues processed: 1345 average time/residue: 0.7379 time to fit residues: 1678.0319 Evaluate side-chains 1383 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1222 time to evaluate : 6.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 221 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 139 ASP Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 367 THR Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 508 LYS Chi-restraints excluded: chain 3 residue 521 MET Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 4 residue 72 MET Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 69 MET Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 40 TYR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 133 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 391 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 444 ASN Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 140 VAL Chi-restraints excluded: chain W residue 26 ARG Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 119 GLN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 78 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 22 ARG Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 95 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 99 LYS Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain t residue 88 THR Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 7 ILE Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 457 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 487 optimal weight: 8.9990 chunk 522 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 602 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN N 144 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 HIS ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 GLN f 95 GLN ** g 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 GLN i 5 GLN i 69 ASN k 204 ASN p 116 GLN s 81 HIS v 28 ASN v 136 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 68996 Z= 0.561 Angle : 1.570 50.658 93232 Z= 1.015 Chirality : 0.310 6.369 10101 Planarity : 0.004 0.051 11630 Dihedral : 11.493 168.874 10497 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.51 % Allowed : 11.91 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.38 (0.10), residues: 8036 helix: 1.04 (0.08), residues: 4289 sheet: -0.78 (0.25), residues: 408 loop : -0.57 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Y 85 HIS 0.006 0.001 HIS 3 101 PHE 0.032 0.001 PHE N 292 TYR 0.025 0.002 TYR V 89 ARG 0.007 0.000 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1255 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8781 (t80) cc_final: 0.7936 (m-80) REVERT: 1 105 CYS cc_start: 0.8005 (p) cc_final: 0.7680 (p) REVERT: 1 248 GLU cc_start: 0.8713 (tt0) cc_final: 0.8224 (mp0) REVERT: 1 400 GLU cc_start: 0.8585 (tt0) cc_final: 0.8334 (tt0) REVERT: 1 425 GLU cc_start: 0.7889 (tp30) cc_final: 0.7543 (tp30) REVERT: 1 431 GLN cc_start: 0.8376 (pt0) cc_final: 0.8067 (pp30) REVERT: 1 435 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: 2 134 ASP cc_start: 0.8975 (p0) cc_final: 0.8074 (t0) REVERT: 3 427 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7746 (pttt) REVERT: 3 656 LEU cc_start: 0.8098 (mt) cc_final: 0.7879 (mp) REVERT: 4 75 LYS cc_start: 0.8636 (tttm) cc_final: 0.8279 (tptp) REVERT: 5 147 ASP cc_start: 0.8417 (t0) cc_final: 0.7986 (p0) REVERT: 6 102 LYS cc_start: 0.8980 (tttt) cc_final: 0.8716 (ttpp) REVERT: 6 115 SER cc_start: 0.9043 (t) cc_final: 0.8760 (m) REVERT: 9 40 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7413 (t80) REVERT: 9 78 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8604 (pp) REVERT: 9 172 ASP cc_start: 0.9028 (t70) cc_final: 0.8560 (t70) REVERT: H 81 LEU cc_start: 0.9178 (mt) cc_final: 0.8791 (mm) REVERT: H 214 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6849 (mm-30) REVERT: H 259 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8290 (p90) REVERT: J 97 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6363 (mp) REVERT: K 91 GLN cc_start: 0.8268 (pm20) cc_final: 0.7555 (tm-30) REVERT: L 540 MET cc_start: 0.8320 (mtm) cc_final: 0.7758 (mmp) REVERT: L 544 MET cc_start: 0.7520 (tmm) cc_final: 0.7154 (ttt) REVERT: L 547 LYS cc_start: 0.8182 (mttm) cc_final: 0.7691 (mtmm) REVERT: L 606 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6749 (mt-10) REVERT: M 195 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7870 (tpt) REVERT: M 366 ASN cc_start: 0.8572 (t0) cc_final: 0.8223 (t0) REVERT: N 117 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: V 42 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8352 (mt) REVERT: W 77 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.8167 (ttt180) REVERT: X 19 LEU cc_start: 0.7684 (mt) cc_final: 0.7454 (mp) REVERT: X 66 ASP cc_start: 0.8022 (m-30) cc_final: 0.7513 (m-30) REVERT: Y 101 LYS cc_start: 0.8640 (ptmm) cc_final: 0.8411 (tttm) REVERT: Z 17 PRO cc_start: 0.8518 (Cg_endo) cc_final: 0.8287 (Cg_exo) REVERT: Z 42 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7619 (mmt180) REVERT: Z 58 ASN cc_start: 0.7606 (p0) cc_final: 0.7279 (p0) REVERT: Z 121 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7917 (ttm-80) REVERT: b 3 ARG cc_start: 0.7970 (ptt90) cc_final: 0.7706 (ptt-90) REVERT: b 37 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8677 (pm20) REVERT: d 219 LYS cc_start: 0.8612 (mttt) cc_final: 0.8379 (mttp) REVERT: d 224 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8276 (mmt-90) REVERT: d 281 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7329 (mmp80) REVERT: d 338 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8025 (mptt) REVERT: f 115 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7877 (pp) REVERT: g 47 HIS cc_start: 0.8764 (t70) cc_final: 0.8415 (t70) REVERT: g 50 GLN cc_start: 0.8579 (pt0) cc_final: 0.7808 (mm-40) REVERT: g 79 ASP cc_start: 0.8941 (m-30) cc_final: 0.8658 (m-30) REVERT: i 1 MET cc_start: 0.6879 (tpt) cc_final: 0.6386 (mtm) REVERT: i 25 ARG cc_start: 0.8753 (ttt90) cc_final: 0.8251 (ttp-110) REVERT: i 122 GLN cc_start: 0.8767 (mp10) cc_final: 0.8515 (pt0) REVERT: j 16 LEU cc_start: 0.8314 (mm) cc_final: 0.8043 (mm) REVERT: j 17 TYR cc_start: 0.7633 (t80) cc_final: 0.7357 (t80) REVERT: j 22 TYR cc_start: 0.7303 (t80) cc_final: 0.6994 (t80) REVERT: j 24 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7840 (mmmt) REVERT: j 46 ASP cc_start: 0.8334 (m-30) cc_final: 0.8046 (m-30) REVERT: k 153 ASN cc_start: 0.8820 (m-40) cc_final: 0.8610 (m-40) REVERT: k 173 ASP cc_start: 0.6775 (t0) cc_final: 0.6010 (p0) REVERT: k 265 ASP cc_start: 0.8338 (t0) cc_final: 0.7833 (m-30) REVERT: l 82 ARG cc_start: 0.8301 (tmm-80) cc_final: 0.7946 (ttm-80) REVERT: m 50 TYR cc_start: 0.8887 (m-80) cc_final: 0.8675 (m-80) REVERT: n 29 GLU cc_start: 0.6669 (pt0) cc_final: 0.6189 (mt-10) REVERT: n 42 ASP cc_start: 0.7148 (t0) cc_final: 0.6209 (p0) REVERT: o 25 LYS cc_start: 0.8575 (mttt) cc_final: 0.8331 (mtpp) REVERT: q 22 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7721 (mtm-85) REVERT: r 14 LEU cc_start: 0.8302 (mm) cc_final: 0.8043 (mt) REVERT: r 75 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8487 (tp) REVERT: r 76 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9094 (mp) REVERT: s 34 LYS cc_start: 0.7366 (ptpt) cc_final: 0.7032 (pttt) REVERT: s 43 GLN cc_start: 0.8496 (pp30) cc_final: 0.8101 (tp-100) REVERT: s 44 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7251 (mm-30) REVERT: s 71 ASP cc_start: 0.7492 (m-30) cc_final: 0.7104 (m-30) REVERT: s 80 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7834 (pttt) REVERT: t 50 HIS cc_start: 0.8066 (m-70) cc_final: 0.7788 (m-70) REVERT: t 52 ASN cc_start: 0.7227 (m-40) cc_final: 0.6582 (p0) REVERT: v 18 GLU cc_start: 0.8269 (mp0) cc_final: 0.7956 (pm20) REVERT: w 26 TRP cc_start: 0.7289 (p90) cc_final: 0.6463 (p90) REVERT: w 31 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8046 (tm-30) REVERT: w 92 GLU cc_start: 0.8380 (tp30) cc_final: 0.8075 (tp30) REVERT: z 25 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8141 (mmt180) REVERT: z 64 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8455 (mmmt) outliers start: 179 outliers final: 148 residues processed: 1352 average time/residue: 0.6771 time to fit residues: 1530.4033 Evaluate side-chains 1386 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1224 time to evaluate : 5.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 221 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 139 ASP Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 508 LYS Chi-restraints excluded: chain 3 residue 521 MET Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 72 MET Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 69 MET Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 40 TYR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 133 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 145 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 419 THR Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 444 ASN Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 140 VAL Chi-restraints excluded: chain W residue 26 ARG Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 119 GLN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 234 ASN Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 78 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 95 ASP Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 108 THR Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 22 ARG Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 95 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain s residue 81 HIS Chi-restraints excluded: chain t residue 88 THR Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 53 GLU Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 3.9990 chunk 734 optimal weight: 20.0000 chunk 669 optimal weight: 20.0000 chunk 714 optimal weight: 6.9990 chunk 733 optimal weight: 5.9990 chunk 429 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 560 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 645 optimal weight: 3.9990 chunk 675 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 361 GLN ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN H 317 GLN K 7 ASN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN Y 142 HIS d 119 GLN ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN ** g 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 24 GLN i 69 ASN m 51 ASN n 58 ASN p 116 GLN s 81 HIS v 28 ASN v 136 ASN x 36 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 68996 Z= 0.529 Angle : 1.560 50.626 93232 Z= 1.011 Chirality : 0.310 6.354 10101 Planarity : 0.004 0.048 11630 Dihedral : 11.233 168.152 10497 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.16 % Allowed : 12.56 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.53 (0.10), residues: 8036 helix: 1.17 (0.08), residues: 4281 sheet: -0.70 (0.25), residues: 402 loop : -0.51 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 272 HIS 0.042 0.001 HIS s 81 PHE 0.032 0.001 PHE N 292 TYR 0.024 0.001 TYR 4 108 ARG 0.008 0.000 ARG t 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1285 time to evaluate : 6.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8759 (t80) cc_final: 0.7914 (m-80) REVERT: 1 105 CYS cc_start: 0.7830 (p) cc_final: 0.7499 (p) REVERT: 1 248 GLU cc_start: 0.8696 (tt0) cc_final: 0.8220 (mp0) REVERT: 1 400 GLU cc_start: 0.8568 (tt0) cc_final: 0.8315 (tt0) REVERT: 1 425 GLU cc_start: 0.7866 (tp30) cc_final: 0.7523 (tp30) REVERT: 1 431 GLN cc_start: 0.8433 (pt0) cc_final: 0.8055 (pp30) REVERT: 1 435 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: 2 134 ASP cc_start: 0.8991 (p0) cc_final: 0.8087 (t0) REVERT: 3 243 ARG cc_start: 0.9383 (ttp-110) cc_final: 0.9156 (ttp-170) REVERT: 3 427 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7726 (pttt) REVERT: 3 656 LEU cc_start: 0.8071 (mt) cc_final: 0.7852 (mp) REVERT: 4 75 LYS cc_start: 0.8623 (tttm) cc_final: 0.8276 (tptp) REVERT: 4 152 MET cc_start: 0.9183 (tpp) cc_final: 0.8900 (tpt) REVERT: 5 147 ASP cc_start: 0.8397 (t0) cc_final: 0.7982 (p0) REVERT: 6 102 LYS cc_start: 0.8931 (tttt) cc_final: 0.8642 (ttpp) REVERT: 6 105 ASP cc_start: 0.8702 (m-30) cc_final: 0.8480 (m-30) REVERT: 6 115 SER cc_start: 0.9008 (t) cc_final: 0.8776 (m) REVERT: 9 40 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.7474 (t80) REVERT: 9 78 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8597 (pp) REVERT: 9 172 ASP cc_start: 0.9001 (t70) cc_final: 0.8554 (t70) REVERT: H 81 LEU cc_start: 0.9144 (mt) cc_final: 0.8775 (mm) REVERT: H 214 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: H 235 ASN cc_start: 0.8461 (m110) cc_final: 0.8257 (m110) REVERT: H 259 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8206 (p90) REVERT: K 91 GLN cc_start: 0.8254 (pm20) cc_final: 0.7546 (tm-30) REVERT: L 159 TYR cc_start: 0.9227 (p90) cc_final: 0.8981 (p90) REVERT: L 540 MET cc_start: 0.8307 (mtm) cc_final: 0.7738 (mmp) REVERT: L 544 MET cc_start: 0.7495 (tmm) cc_final: 0.7130 (ttt) REVERT: L 547 LYS cc_start: 0.8168 (mttm) cc_final: 0.7690 (mtmm) REVERT: L 606 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6745 (mt-10) REVERT: M 366 ASN cc_start: 0.8541 (t0) cc_final: 0.8187 (t0) REVERT: N 117 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: V 42 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8305 (mt) REVERT: W 77 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.8155 (ttt180) REVERT: X 66 ASP cc_start: 0.7978 (m-30) cc_final: 0.7491 (m-30) REVERT: Y 101 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8357 (tttm) REVERT: Z 17 PRO cc_start: 0.8528 (Cg_endo) cc_final: 0.8301 (Cg_exo) REVERT: Z 42 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7624 (mmt180) REVERT: Z 58 ASN cc_start: 0.7560 (p0) cc_final: 0.7215 (p0) REVERT: Z 121 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7877 (ttm-80) REVERT: b 3 ARG cc_start: 0.7949 (ptt90) cc_final: 0.7694 (ptt-90) REVERT: b 37 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8669 (pm20) REVERT: d 224 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8264 (mmt-90) REVERT: d 281 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7331 (mmp80) REVERT: d 293 THR cc_start: 0.7674 (m) cc_final: 0.7354 (p) REVERT: d 338 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7975 (mptt) REVERT: e 45 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8447 (mtpt) REVERT: f 115 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7938 (pp) REVERT: g 47 HIS cc_start: 0.8730 (t70) cc_final: 0.8392 (t70) REVERT: g 50 GLN cc_start: 0.8543 (pt0) cc_final: 0.7778 (mm-40) REVERT: g 79 ASP cc_start: 0.8931 (m-30) cc_final: 0.8652 (m-30) REVERT: h 5 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7577 (ttp-170) REVERT: i 1 MET cc_start: 0.6842 (tpt) cc_final: 0.6375 (mtm) REVERT: i 25 ARG cc_start: 0.8733 (ttt90) cc_final: 0.8211 (ttp-110) REVERT: i 122 GLN cc_start: 0.8732 (mp10) cc_final: 0.8504 (pt0) REVERT: j 16 LEU cc_start: 0.8344 (mm) cc_final: 0.8012 (mm) REVERT: j 17 TYR cc_start: 0.7598 (t80) cc_final: 0.7337 (t80) REVERT: j 22 TYR cc_start: 0.7286 (t80) cc_final: 0.6946 (t80) REVERT: j 24 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7823 (mmmt) REVERT: j 46 ASP cc_start: 0.8323 (m-30) cc_final: 0.8015 (m-30) REVERT: k 153 ASN cc_start: 0.8813 (m-40) cc_final: 0.8596 (m-40) REVERT: k 173 ASP cc_start: 0.6905 (t0) cc_final: 0.6080 (p0) REVERT: k 265 ASP cc_start: 0.8335 (t0) cc_final: 0.7815 (m-30) REVERT: l 82 ARG cc_start: 0.8260 (tmm-80) cc_final: 0.7909 (ttm-80) REVERT: m 50 TYR cc_start: 0.8863 (m-80) cc_final: 0.8476 (m-80) REVERT: n 29 GLU cc_start: 0.6633 (pt0) cc_final: 0.6146 (mt-10) REVERT: n 42 ASP cc_start: 0.7102 (t0) cc_final: 0.6160 (p0) REVERT: o 25 LYS cc_start: 0.8594 (mttt) cc_final: 0.8340 (mtpp) REVERT: q 22 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7707 (mtm-85) REVERT: r 14 LEU cc_start: 0.8229 (mm) cc_final: 0.7940 (mt) REVERT: r 75 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8397 (tp) REVERT: r 76 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9093 (mp) REVERT: s 34 LYS cc_start: 0.7338 (ptpt) cc_final: 0.7038 (pttt) REVERT: s 43 GLN cc_start: 0.8427 (pp30) cc_final: 0.8029 (tp40) REVERT: s 44 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7234 (mm-30) REVERT: s 71 ASP cc_start: 0.7566 (m-30) cc_final: 0.7273 (m-30) REVERT: s 80 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7876 (tptt) REVERT: t 52 ASN cc_start: 0.7209 (m-40) cc_final: 0.6582 (p0) REVERT: v 18 GLU cc_start: 0.8248 (mp0) cc_final: 0.7933 (pm20) REVERT: w 26 TRP cc_start: 0.7208 (p90) cc_final: 0.6373 (p90) REVERT: w 31 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8064 (tm-30) REVERT: w 92 GLU cc_start: 0.8347 (tp30) cc_final: 0.8110 (tp30) REVERT: x 6 GLU cc_start: 0.7678 (tp30) cc_final: 0.7439 (tm-30) REVERT: x 38 ASP cc_start: 0.8627 (m-30) cc_final: 0.8237 (m-30) REVERT: z 25 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8108 (mmt180) REVERT: z 64 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8464 (mmmt) outliers start: 154 outliers final: 117 residues processed: 1372 average time/residue: 0.6946 time to fit residues: 1597.6313 Evaluate side-chains 1371 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1242 time to evaluate : 6.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 221 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 139 ASP Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 25 THR Chi-restraints excluded: chain 4 residue 72 MET Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 69 MET Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 40 TYR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 133 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 444 ASN Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 119 GLN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 234 ASN Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 78 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 22 ARG Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 95 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain s residue 68 CYS Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain y residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 20.0000 chunk 468 optimal weight: 0.2980 chunk 755 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 chunk 358 optimal weight: 7.9990 chunk 524 optimal weight: 0.9980 chunk 792 optimal weight: 9.9990 chunk 728 optimal weight: 9.9990 chunk 630 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 487 optimal weight: 9.9990 overall best weight: 5.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN H 317 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN M 399 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 HIS d 119 GLN ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN ** g 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN k 204 ASN p 116 GLN s 81 HIS v 28 ASN v 136 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 68996 Z= 0.572 Angle : 1.575 50.685 93232 Z= 1.017 Chirality : 0.310 6.383 10101 Planarity : 0.004 0.056 11630 Dihedral : 11.252 169.203 10497 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.01 % Allowed : 12.91 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.47 (0.10), residues: 8036 helix: 1.10 (0.08), residues: 4294 sheet: -0.77 (0.25), residues: 412 loop : -0.51 (0.11), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 85 HIS 0.011 0.001 HIS s 81 PHE 0.032 0.002 PHE N 292 TYR 0.026 0.002 TYR 4 108 ARG 0.011 0.000 ARG o 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1244 time to evaluate : 6.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 73 PHE cc_start: 0.8775 (t80) cc_final: 0.7925 (m-80) REVERT: 1 105 CYS cc_start: 0.7896 (p) cc_final: 0.7521 (p) REVERT: 1 248 GLU cc_start: 0.8721 (tt0) cc_final: 0.8227 (mp0) REVERT: 1 400 GLU cc_start: 0.8593 (tt0) cc_final: 0.8346 (tt0) REVERT: 1 425 GLU cc_start: 0.7880 (tp30) cc_final: 0.7539 (tp30) REVERT: 1 431 GLN cc_start: 0.8445 (pt0) cc_final: 0.8006 (pp30) REVERT: 1 435 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: 2 134 ASP cc_start: 0.8994 (p0) cc_final: 0.8103 (t0) REVERT: 3 427 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7747 (pttt) REVERT: 3 656 LEU cc_start: 0.8084 (mt) cc_final: 0.7860 (mp) REVERT: 4 75 LYS cc_start: 0.8624 (tttm) cc_final: 0.8289 (tptp) REVERT: 4 152 MET cc_start: 0.9184 (tpp) cc_final: 0.8918 (tpt) REVERT: 5 147 ASP cc_start: 0.8415 (t0) cc_final: 0.8023 (p0) REVERT: 6 102 LYS cc_start: 0.8956 (tttt) cc_final: 0.8662 (ttpp) REVERT: 6 105 ASP cc_start: 0.8748 (m-30) cc_final: 0.8507 (m-30) REVERT: 6 115 SER cc_start: 0.9051 (t) cc_final: 0.8774 (m) REVERT: 9 40 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7474 (t80) REVERT: 9 78 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8599 (pp) REVERT: 9 172 ASP cc_start: 0.9027 (t70) cc_final: 0.8548 (t70) REVERT: H 81 LEU cc_start: 0.9167 (mt) cc_final: 0.8771 (mm) REVERT: H 214 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6769 (mm-30) REVERT: H 235 ASN cc_start: 0.8477 (m110) cc_final: 0.8208 (m110) REVERT: H 259 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8272 (p90) REVERT: K 91 GLN cc_start: 0.8285 (pm20) cc_final: 0.7586 (tm-30) REVERT: L 540 MET cc_start: 0.8367 (mtm) cc_final: 0.7766 (mmp) REVERT: L 544 MET cc_start: 0.7493 (tmm) cc_final: 0.7152 (ttt) REVERT: L 547 LYS cc_start: 0.8175 (mttm) cc_final: 0.7750 (mttp) REVERT: L 606 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6756 (mt-10) REVERT: M 195 MET cc_start: 0.8336 (ttt) cc_final: 0.8103 (ttt) REVERT: M 366 ASN cc_start: 0.8565 (t0) cc_final: 0.8191 (t0) REVERT: N 117 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: V 42 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8569 (mm) REVERT: W 77 ARG cc_start: 0.8521 (ttp-110) cc_final: 0.8164 (ttt180) REVERT: X 19 LEU cc_start: 0.7700 (mt) cc_final: 0.7479 (mp) REVERT: X 66 ASP cc_start: 0.8008 (m-30) cc_final: 0.7509 (m-30) REVERT: Y 101 LYS cc_start: 0.8583 (ptmm) cc_final: 0.8343 (tttm) REVERT: Z 17 PRO cc_start: 0.8552 (Cg_endo) cc_final: 0.8338 (Cg_exo) REVERT: Z 42 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7641 (mmt180) REVERT: Z 58 ASN cc_start: 0.7596 (p0) cc_final: 0.7235 (p0) REVERT: b 3 ARG cc_start: 0.7956 (ptt90) cc_final: 0.7705 (ptt-90) REVERT: b 37 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8681 (pm20) REVERT: d 224 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8288 (mmt-90) REVERT: d 281 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.7337 (mmp80) REVERT: d 293 THR cc_start: 0.7710 (m) cc_final: 0.7357 (p) REVERT: d 338 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7986 (mptt) REVERT: f 115 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8037 (pp) REVERT: g 47 HIS cc_start: 0.8753 (t70) cc_final: 0.8433 (t70) REVERT: g 50 GLN cc_start: 0.8582 (pt0) cc_final: 0.7822 (mm-40) REVERT: g 79 ASP cc_start: 0.8940 (m-30) cc_final: 0.8646 (m-30) REVERT: i 1 MET cc_start: 0.6883 (tpt) cc_final: 0.6371 (mtm) REVERT: i 25 ARG cc_start: 0.8762 (ttt90) cc_final: 0.8219 (ttp-110) REVERT: i 122 GLN cc_start: 0.8747 (mp10) cc_final: 0.8516 (pt0) REVERT: j 16 LEU cc_start: 0.8360 (mm) cc_final: 0.8013 (mm) REVERT: j 17 TYR cc_start: 0.7619 (t80) cc_final: 0.7363 (t80) REVERT: j 24 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7828 (mmmt) REVERT: j 46 ASP cc_start: 0.8341 (m-30) cc_final: 0.8071 (m-30) REVERT: k 153 ASN cc_start: 0.8840 (m-40) cc_final: 0.8634 (m-40) REVERT: k 173 ASP cc_start: 0.7033 (t0) cc_final: 0.6190 (p0) REVERT: k 265 ASP cc_start: 0.8344 (t0) cc_final: 0.7833 (m-30) REVERT: l 82 ARG cc_start: 0.8293 (tmm-80) cc_final: 0.7940 (ttm-80) REVERT: n 29 GLU cc_start: 0.6649 (pt0) cc_final: 0.6147 (mt-10) REVERT: n 42 ASP cc_start: 0.7122 (t0) cc_final: 0.6204 (p0) REVERT: o 25 LYS cc_start: 0.8587 (mttt) cc_final: 0.8332 (mtpp) REVERT: q 22 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7715 (mtm-85) REVERT: r 14 LEU cc_start: 0.8283 (mm) cc_final: 0.8023 (mt) REVERT: r 76 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9104 (mp) REVERT: s 34 LYS cc_start: 0.7366 (ptpt) cc_final: 0.7032 (pttt) REVERT: s 71 ASP cc_start: 0.7526 (m-30) cc_final: 0.7197 (m-30) REVERT: s 80 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8019 (tptt) REVERT: s 93 ASP cc_start: 0.8413 (t0) cc_final: 0.8187 (t0) REVERT: v 18 GLU cc_start: 0.8241 (mp0) cc_final: 0.7905 (pm20) REVERT: w 26 TRP cc_start: 0.7244 (p90) cc_final: 0.6413 (p90) REVERT: w 31 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8062 (tm-30) REVERT: w 92 GLU cc_start: 0.8381 (tp30) cc_final: 0.8063 (tp30) REVERT: x 6 GLU cc_start: 0.7645 (tp30) cc_final: 0.7442 (tm-30) REVERT: x 38 ASP cc_start: 0.8645 (m-30) cc_final: 0.8248 (m-30) REVERT: z 25 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8133 (mmt180) REVERT: z 64 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8360 (mmmt) outliers start: 143 outliers final: 125 residues processed: 1323 average time/residue: 0.6809 time to fit residues: 1514.0471 Evaluate side-chains 1364 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1228 time to evaluate : 6.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 221 THR Chi-restraints excluded: chain 1 residue 362 CYS Chi-restraints excluded: chain 1 residue 409 ASP Chi-restraints excluded: chain 1 residue 435 GLN Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 139 ASP Chi-restraints excluded: chain 3 residue 159 CYS Chi-restraints excluded: chain 3 residue 180 ASP Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 398 SER Chi-restraints excluded: chain 3 residue 533 THR Chi-restraints excluded: chain 3 residue 551 ASP Chi-restraints excluded: chain 3 residue 613 TYR Chi-restraints excluded: chain 3 residue 636 VAL Chi-restraints excluded: chain 3 residue 659 ASP Chi-restraints excluded: chain 4 residue 25 THR Chi-restraints excluded: chain 4 residue 72 MET Chi-restraints excluded: chain 4 residue 109 VAL Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 6 residue 69 MET Chi-restraints excluded: chain 6 residue 137 ASP Chi-restraints excluded: chain 9 residue 40 TYR Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 133 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 444 ASN Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 230 VAL Chi-restraints excluded: chain M residue 265 SER Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain M residue 403 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 73 SER Chi-restraints excluded: chain V residue 94 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 164 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain b residue 57 ILE Chi-restraints excluded: chain b residue 79 THR Chi-restraints excluded: chain c residue 74 SER Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 131 SER Chi-restraints excluded: chain d residue 119 GLN Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 234 ASN Chi-restraints excluded: chain d residue 237 LEU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 78 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain g residue 88 GLU Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 24 LYS Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain k residue 21 ASN Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 224 SER Chi-restraints excluded: chain k residue 297 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 22 ARG Chi-restraints excluded: chain q residue 105 VAL Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 76 ILE Chi-restraints excluded: chain r residue 95 THR Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 45 MET Chi-restraints excluded: chain s residue 68 CYS Chi-restraints excluded: chain t residue 109 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain y residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 10.0000 chunk 500 optimal weight: 8.9990 chunk 671 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 581 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 631 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 648 optimal weight: 0.0040 chunk 79 optimal weight: 6.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 ASN ** 1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 HIS Z 120 HIS Z 148 HIS f 82 GLN f 95 GLN ** g 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 69 ASN ** k 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 58 ASN p 116 GLN s 81 HIS v 28 ASN v 136 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098859 restraints weight = 97990.188| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.39 r_work: 0.3002 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 68996 Z= 0.552 Angle : 1.569 50.653 93232 Z= 1.014 Chirality : 0.310 6.364 10101 Planarity : 0.004 0.056 11630 Dihedral : 11.160 170.301 10497 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.06 % Allowed : 13.04 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.52 (0.10), residues: 8036 helix: 1.13 (0.08), residues: 4301 sheet: -0.70 (0.25), residues: 406 loop : -0.48 (0.11), residues: 3329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 272 HIS 0.011 0.001 HIS t 50 PHE 0.031 0.001 PHE N 292 TYR 0.024 0.001 TYR x 42 ARG 0.009 0.000 ARG 1 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23514.72 seconds wall clock time: 410 minutes 0.37 seconds (24600.37 seconds total)