Starting phenix.real_space_refine on Sat Feb 24 23:07:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/02_2024/5w65_8775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/02_2024/5w65_8775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/02_2024/5w65_8775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/02_2024/5w65_8775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/02_2024/5w65_8775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w65_8775/02_2024/5w65_8775.pdb" } resolution = 4.3 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= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 102 5.49 5 S 210 5.16 5 C 29683 2.51 5 N 8189 2.21 5 O 9117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 280": "NH1" <-> "NH2" Residue "O ARG 407": "NH1" <-> "NH2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O ARG 472": "NH1" <-> "NH2" Residue "O ARG 484": "NH1" <-> "NH2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O GLU 664": "OE1" <-> "OE2" Residue "P ARG 305": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 371": "OE1" <-> "OE2" Residue "P GLU 496": "OE1" <-> "OE2" Residue "Q PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q ARG 17": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q ARG 302": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47308 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1461, 11542 Classifications: {'peptide': 1461} Link IDs: {'PTRANS': 59, 'TRANS': 1401} Chain breaks: 7 Chain: "B" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9351 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 58, 'TRANS': 1119} Chain breaks: 2 Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2431 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1070 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 841 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "N" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "O" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5063 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 620} Chain breaks: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "P" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3978 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2923 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 935 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1082 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 170.512 82.522 85.801 1.00 0.00 S ATOM 806 SG CYS A 105 170.989 79.750 85.913 1.00 0.00 S ATOM 1605 SG CYS A 233 172.206 82.303 88.151 1.00 0.00 S ATOM 1627 SG CYS A 236 172.663 82.108 85.728 1.00 0.00 S ATOM 461 SG CYS A 62 123.339 63.294 87.358 1.00 0.00 S ATOM 480 SG CYS A 65 122.175 60.653 89.288 1.00 0.00 S ATOM 535 SG CYS A 72 122.504 62.741 89.844 1.00 0.00 S ATOM 20196 SG CYS B1104 137.759 55.666 95.347 1.00 0.00 S ATOM 20222 SG CYS B1107 138.386 58.705 95.395 1.00 0.00 S ATOM 20369 SG CYS B1128 136.523 57.073 93.358 1.00 0.00 S ATOM 20397 SG CYS B1131 139.378 55.281 93.520 1.00 0.00 S ATOM 28945 SG CYS I 10 154.612 149.515 92.973 1.00 0.00 S ATOM 28967 SG CYS I 13 152.207 147.753 92.091 1.00 0.00 S ATOM 29087 SG CYS I 30 155.042 147.176 91.289 1.00 0.00 S ATOM 29108 SG CYS I 33 155.476 149.886 91.294 1.00 0.00 S ATOM 29415 SG CYS J 7 84.663 98.083 137.483 1.00 0.00 S ATOM 29438 SG CYS J 10 82.295 96.912 139.106 1.00 0.00 S ATOM 29718 SG CYS J 45 84.845 98.722 140.496 1.00 0.00 S ATOM 29724 SG CYS J 46 81.371 99.662 139.686 1.00 0.00 S ATOM 30790 SG CYS L 31 81.686 103.787 93.493 1.00 0.00 S ATOM 30810 SG CYS L 34 78.814 104.355 93.272 1.00 0.00 S ATOM 30914 SG CYS L 48 80.307 103.469 91.088 1.00 0.00 S ATOM 30937 SG CYS L 51 81.767 105.502 91.057 1.00 0.00 S ATOM 38332 SG CYS P 10 104.321 53.867 99.656 1.00 0.00 S ATOM 38365 SG CYS P 15 100.113 53.658 99.493 1.00 0.00 S ATOM 38485 SG CYS P 29 100.749 55.952 100.683 1.00 0.00 S Time building chain proxies: 25.43, per 1000 atoms: 0.54 Number of scatterers: 47308 At special positions: 0 Unit cell: (206.7, 191.1, 204.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 210 16.00 P 102 15.00 O 9117 8.00 N 8189 7.00 C 29683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 20.51 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN P 601 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 15 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 29 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 10 " Number of angles added : 33 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10714 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 61 sheets defined 42.7% alpha, 16.6% beta 36 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 16.77 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.533A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.513A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.679A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.464A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.948A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 407 Processing helix chain 'A' and resid 416 through 439 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.825A pdb=" N ARG A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.654A pdb=" N ILE A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 802 through 825 Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.667A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.675A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 885 through 916 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1028 removed outlier: 3.837A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.312A pdb=" N SER A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N HIS A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1081 through 1085 removed outlier: 3.763A pdb=" N ALA A1084 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.770A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1177 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1298 through 1306 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1320 through 1337 Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.563A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.692A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.683A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 4.392A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.573A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.914A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.907A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.577A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.186A pdb=" N LYS B 174 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 175 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.811A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.718A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 339 removed outlier: 5.220A pdb=" N VAL B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.561A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.691A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.993A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.514A pdb=" N SER B 524 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 559 No H-bonds generated for 'chain 'B' and resid 557 through 559' Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.822A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.610A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.035A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 815 through 819 removed outlier: 4.282A pdb=" N ASP B 819 " --> pdb=" O ASN B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.500A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.783A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1173 through 1185 Proline residue: B1179 - end of helix Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.634A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.592A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.631A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.291A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.739A pdb=" N ASN D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.586A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.527A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.594A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.548A pdb=" N TYR G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'I' and resid 37 through 41 removed outlier: 4.171A pdb=" N SER I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.839A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.504A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.576A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 4.236A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 98 Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 104 through 107 removed outlier: 3.742A pdb=" N ASN M 107 " --> pdb=" O SER M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 107' Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 93 through 97 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 Processing helix chain 'O' and resid 294 through 298 removed outlier: 3.783A pdb=" N ILE O 297 " --> pdb=" O PHE O 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 577 Processing helix chain 'O' and resid 582 through 614 Processing helix chain 'O' and resid 618 through 644 removed outlier: 3.601A pdb=" N TRP O 641 " --> pdb=" O LEU O 637 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 686 Processing helix chain 'O' and resid 695 through 704 removed outlier: 4.047A pdb=" N LEU O 699 " --> pdb=" O GLY O 695 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU O 700 " --> pdb=" O PHE O 696 " (cutoff:3.500A) Processing helix chain 'O' and resid 712 through 724 removed outlier: 3.574A pdb=" N ASN O 716 " --> pdb=" O ASP O 712 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN O 720 " --> pdb=" O ASN O 716 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP O 722 " --> pdb=" O LEU O 718 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU O 724 " --> pdb=" O GLN O 720 " (cutoff:3.500A) Processing helix chain 'O' and resid 732 through 744 removed outlier: 3.650A pdb=" N VAL O 737 " --> pdb=" O THR O 733 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE O 740 " --> pdb=" O ILE O 736 " (cutoff:3.500A) Processing helix chain 'O' and resid 752 through 764 Processing helix chain 'O' and resid 765 through 777 Processing helix chain 'P' and resid 80 through 89 Processing helix chain 'P' and resid 97 through 124 removed outlier: 3.524A pdb=" N LEU P 103 " --> pdb=" O GLU P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 147 removed outlier: 3.693A pdb=" N GLU P 130 " --> pdb=" O PRO P 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR P 143 " --> pdb=" O LYS P 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 173 removed outlier: 4.069A pdb=" N THR P 161 " --> pdb=" O HIS P 157 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE P 162 " --> pdb=" O MET P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 Processing helix chain 'P' and resid 201 through 206 Processing helix chain 'P' and resid 211 through 215 Processing helix chain 'P' and resid 225 through 238 removed outlier: 3.847A pdb=" N LYS P 229 " --> pdb=" O GLN P 225 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 Processing helix chain 'P' and resid 249 through 260 removed outlier: 4.151A pdb=" N LEU P 253 " --> pdb=" O CYS P 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 278 Processing helix chain 'P' and resid 301 through 319 Processing helix chain 'P' and resid 327 through 339 removed outlier: 4.146A pdb=" N LEU P 332 " --> pdb=" O LEU P 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER P 333 " --> pdb=" O LYS P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 355 Processing helix chain 'P' and resid 362 through 369 Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 402 through 417 removed outlier: 4.160A pdb=" N GLN P 406 " --> pdb=" O MET P 402 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS P 407 " --> pdb=" O THR P 403 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE P 408 " --> pdb=" O ILE P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 437 through 449 Processing helix chain 'P' and resid 470 through 491 Processing helix chain 'P' and resid 496 through 510 removed outlier: 3.593A pdb=" N LEU P 510 " --> pdb=" O LYS P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 34 Processing helix chain 'Q' and resid 122 through 132 Processing helix chain 'Q' and resid 159 through 167 Processing helix chain 'Q' and resid 168 through 179 removed outlier: 3.906A pdb=" N ILE Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Proline residue: Q 176 - end of helix removed outlier: 3.894A pdb=" N HIS Q 179 " --> pdb=" O ILE Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 192 Processing helix chain 'Q' and resid 207 through 225 removed outlier: 3.713A pdb=" N HIS Q 212 " --> pdb=" O TYR Q 208 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE Q 213 " --> pdb=" O ARG Q 209 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL Q 214 " --> pdb=" O THR Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 242 removed outlier: 4.340A pdb=" N LYS Q 234 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 261 removed outlier: 3.625A pdb=" N GLY Q 254 " --> pdb=" O LEU Q 250 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU Q 256 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU Q 258 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 278 Processing helix chain 'Q' and resid 306 through 322 removed outlier: 3.640A pdb=" N ILE Q 310 " --> pdb=" O ALA Q 306 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS Q 322 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 351 Processing helix chain 'Q' and resid 362 through 382 removed outlier: 3.539A pdb=" N TYR Q 368 " --> pdb=" O VAL Q 364 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU Q 379 " --> pdb=" O LYS Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 421 Processing helix chain 'Q' and resid 427 through 443 removed outlier: 3.800A pdb=" N ILE Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG Q 441 " --> pdb=" O SER Q 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.616A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA7, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA8, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.517A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.977A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 removed outlier: 6.129A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.706A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.568A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB6, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 6.653A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 4.074A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.476A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AC1, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.758A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 15.453A pdb=" N HIS G 119 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 16.851A pdb=" N GLU G 102 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.758A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.289A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 145 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN B 151 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC5, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC6, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.582A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.524A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD1, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.456A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.558A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.558A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD5, first strand: chain 'B' and resid 857 through 863 removed outlier: 3.727A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD7, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD8, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD9, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AE1, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.251A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.258A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.325A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE5, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.348A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE9, first strand: chain 'G' and resid 132 through 141 removed outlier: 3.891A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.357A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF4, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF5, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'M' and resid 14 through 16 removed outlier: 3.754A pdb=" N LYS M 92 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 30 through 31 removed outlier: 4.065A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR M 65 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 57 through 60 removed outlier: 3.550A pdb=" N TYR O 548 " --> pdb=" O VAL O 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP O 536 " --> pdb=" O THR O 510 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR O 510 " --> pdb=" O ASP O 536 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU O 538 " --> pdb=" O ILE O 508 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE O 508 " --> pdb=" O LEU O 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS O 540 " --> pdb=" O THR O 506 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 201 through 205 removed outlier: 4.268A pdb=" N GLU O 201 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.629A pdb=" N ILE O 264 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AG3, first strand: chain 'O' and resid 361 through 365 removed outlier: 3.731A pdb=" N GLU O 382 " --> pdb=" O THR O 391 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 402 through 405 removed outlier: 6.879A pdb=" N THR O 417 " --> pdb=" O ARG O 403 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG6, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG7, first strand: chain 'P' and resid 18 through 21 2006 hydrogen bonds defined for protein. 5490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 23.69 Time building geometry restraints manager: 21.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8738 1.32 - 1.45: 13720 1.45 - 1.58: 25422 1.58 - 1.71: 247 1.71 - 1.84: 333 Bond restraints: 48460 Sorted by residual: bond pdb=" CA LEU P 199 " pdb=" C LEU P 199 " ideal model delta sigma weight residual 1.524 1.675 -0.151 1.26e-02 6.30e+03 1.44e+02 bond pdb=" N PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.473 1.608 -0.135 1.40e-02 5.10e+03 9.28e+01 bond pdb=" CA ASP O 353 " pdb=" C ASP O 353 " ideal model delta sigma weight residual 1.524 1.639 -0.115 1.26e-02 6.30e+03 8.40e+01 bond pdb=" CA ILE O 736 " pdb=" C ILE O 736 " ideal model delta sigma weight residual 1.523 1.638 -0.115 1.27e-02 6.20e+03 8.17e+01 bond pdb=" CA SER P 319 " pdb=" C SER P 319 " ideal model delta sigma weight residual 1.526 1.636 -0.110 1.23e-02 6.61e+03 8.04e+01 ... (remaining 48455 not shown) Histogram of bond angle deviations from ideal: 76.90 - 93.39: 11 93.39 - 109.88: 10299 109.88 - 126.37: 54667 126.37 - 142.86: 959 142.86 - 159.35: 1 Bond angle restraints: 65937 Sorted by residual: angle pdb=" C LYS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta sigma weight residual 120.66 89.99 30.67 1.09e+00 8.42e-01 7.92e+02 angle pdb=" N ASN P 49 " pdb=" CA ASN P 49 " pdb=" C ASN P 49 " ideal model delta sigma weight residual 110.50 76.90 33.60 1.41e+00 5.03e-01 5.68e+02 angle pdb=" N VAL P 356 " pdb=" CA VAL P 356 " pdb=" C VAL P 356 " ideal model delta sigma weight residual 112.17 91.83 20.34 9.50e-01 1.11e+00 4.58e+02 angle pdb=" N HIS O 705 " pdb=" CA HIS O 705 " pdb=" C HIS O 705 " ideal model delta sigma weight residual 113.21 91.01 22.20 1.15e+00 7.56e-01 3.73e+02 angle pdb=" N ASN O 346 " pdb=" CA ASN O 346 " pdb=" CB ASN O 346 " ideal model delta sigma weight residual 110.49 83.11 27.38 1.69e+00 3.50e-01 2.62e+02 ... (remaining 65932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 28454 35.21 - 70.41: 731 70.41 - 105.62: 38 105.62 - 140.82: 1 140.82 - 176.03: 1 Dihedral angle restraints: 29225 sinusoidal: 12702 harmonic: 16523 Sorted by residual: dihedral pdb=" C ILE P 56 " pdb=" N ILE P 56 " pdb=" CA ILE P 56 " pdb=" CB ILE P 56 " ideal model delta harmonic sigma weight residual -122.00 -163.66 41.66 0 2.50e+00 1.60e-01 2.78e+02 dihedral pdb=" N ILE P 56 " pdb=" C ILE P 56 " pdb=" CA ILE P 56 " pdb=" CB ILE P 56 " ideal model delta harmonic sigma weight residual 123.40 159.46 -36.06 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" C GLN Q 147 " pdb=" N GLN Q 147 " pdb=" CA GLN Q 147 " pdb=" CB GLN Q 147 " ideal model delta harmonic sigma weight residual -122.60 -153.16 30.56 0 2.50e+00 1.60e-01 1.49e+02 ... (remaining 29222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.325: 7241 0.325 - 0.650: 118 0.650 - 0.974: 11 0.974 - 1.299: 1 1.299 - 1.624: 2 Chirality restraints: 7373 Sorted by residual: chirality pdb=" CA ILE P 56 " pdb=" N ILE P 56 " pdb=" C ILE P 56 " pdb=" CB ILE P 56 " both_signs ideal model delta sigma weight residual False 2.43 0.81 1.62 2.00e-01 2.50e+01 6.59e+01 chirality pdb=" CA GLN Q 147 " pdb=" N GLN Q 147 " pdb=" C GLN Q 147 " pdb=" CB GLN Q 147 " both_signs ideal model delta sigma weight residual False 2.51 1.13 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" CA SER Q 145 " pdb=" N SER Q 145 " pdb=" C SER Q 145 " pdb=" CB SER Q 145 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.82e+01 ... (remaining 7370 not shown) Planarity restraints: 8112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG T 2 " 0.437 2.00e-02 2.50e+03 2.01e-01 1.21e+03 pdb=" N9 DG T 2 " -0.061 2.00e-02 2.50e+03 pdb=" C8 DG T 2 " -0.268 2.00e-02 2.50e+03 pdb=" N7 DG T 2 " -0.208 2.00e-02 2.50e+03 pdb=" C5 DG T 2 " -0.077 2.00e-02 2.50e+03 pdb=" C6 DG T 2 " 0.067 2.00e-02 2.50e+03 pdb=" O6 DG T 2 " 0.328 2.00e-02 2.50e+03 pdb=" N1 DG T 2 " 0.033 2.00e-02 2.50e+03 pdb=" C2 DG T 2 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG T 2 " -0.229 2.00e-02 2.50e+03 pdb=" N3 DG T 2 " 0.038 2.00e-02 2.50e+03 pdb=" C4 DG T 2 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 3 " 0.358 2.00e-02 2.50e+03 1.86e-01 8.64e+02 pdb=" N1 DT T 3 " -0.107 2.00e-02 2.50e+03 pdb=" C2 DT T 3 " -0.196 2.00e-02 2.50e+03 pdb=" O2 DT T 3 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT T 3 " -0.170 2.00e-02 2.50e+03 pdb=" C4 DT T 3 " -0.015 2.00e-02 2.50e+03 pdb=" O4 DT T 3 " 0.339 2.00e-02 2.50e+03 pdb=" C5 DT T 3 " -0.070 2.00e-02 2.50e+03 pdb=" C7 DT T 3 " -0.033 2.00e-02 2.50e+03 pdb=" C6 DT T 3 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 1 " -0.288 2.00e-02 2.50e+03 1.48e-01 5.49e+02 pdb=" N1 DT T 1 " 0.067 2.00e-02 2.50e+03 pdb=" C2 DT T 1 " 0.161 2.00e-02 2.50e+03 pdb=" O2 DT T 1 " 0.042 2.00e-02 2.50e+03 pdb=" N3 DT T 1 " 0.111 2.00e-02 2.50e+03 pdb=" C4 DT T 1 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT T 1 " -0.281 2.00e-02 2.50e+03 pdb=" C5 DT T 1 " 0.030 2.00e-02 2.50e+03 pdb=" C7 DT T 1 " 0.090 2.00e-02 2.50e+03 pdb=" C6 DT T 1 " 0.065 2.00e-02 2.50e+03 ... (remaining 8109 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 151 1.85 - 2.61: 2357 2.61 - 3.38: 69610 3.38 - 4.14: 121611 4.14 - 4.90: 209817 Nonbonded interactions: 403546 Sorted by model distance: nonbonded pdb=" CD2 HIS P 294 " pdb=" N6 DA T 48 " model vdw 1.089 3.340 nonbonded pdb=" CG PRO O 727 " pdb=" OE2 GLU P 265 " model vdw 1.127 3.440 nonbonded pdb=" O ARG B1105 " pdb=" CG LEU B1196 " model vdw 1.154 3.470 nonbonded pdb=" O HIS O 701 " pdb=" CD2 LEU O 704 " model vdw 1.161 3.460 nonbonded pdb=" NE2 HIS O 571 " pdb=" NZ LYS P 495 " model vdw 1.169 3.200 ... (remaining 403541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.030 Extract box with map and model: 4.510 Check model and map are aligned: 0.720 Set scattering table: 0.430 Process input model: 147.710 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.009 0.151 48460 Z= 0.605 Angle : 1.649 34.351 65937 Z= 1.035 Chirality : 0.100 1.624 7373 Planarity : 0.013 0.201 8112 Dihedral : 14.853 176.029 18511 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 88.79 Ramachandran Plot: Outliers : 4.78 % Allowed : 8.88 % Favored : 86.34 % Rotamer: Outliers : 4.61 % Allowed : 4.93 % Favored : 90.46 % Cbeta Deviations : 1.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.52 (0.09), residues: 5527 helix: -1.91 (0.09), residues: 1945 sheet: -1.62 (0.17), residues: 753 loop : -2.89 (0.10), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP Q 273 HIS 0.017 0.003 HIS O 368 PHE 0.099 0.004 PHE Q 188 TYR 0.097 0.006 TYR Q 443 ARG 0.087 0.010 ARG J 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1877 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1645 time to evaluate : 6.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8501 (tp) cc_final: 0.8279 (tp) REVERT: A 217 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8053 (mttm) REVERT: A 388 LYS cc_start: 0.8148 (tttt) cc_final: 0.7376 (tptm) REVERT: A 472 MET cc_start: 0.8745 (mmp) cc_final: 0.8526 (mmp) REVERT: A 500 VAL cc_start: 0.9300 (p) cc_final: 0.8916 (t) REVERT: A 600 MET cc_start: 0.8112 (ttt) cc_final: 0.7798 (ttt) REVERT: A 635 MET cc_start: 0.7681 (ttp) cc_final: 0.7323 (ttp) REVERT: A 640 ASN cc_start: 0.7957 (t0) cc_final: 0.6939 (m-40) REVERT: A 780 ILE cc_start: 0.8933 (pt) cc_final: 0.8516 (pt) REVERT: A 947 LEU cc_start: 0.7740 (mp) cc_final: 0.7474 (mp) REVERT: A 960 MET cc_start: 0.7998 (mtm) cc_final: 0.7656 (mtp) REVERT: A 995 TYR cc_start: 0.8163 (t80) cc_final: 0.7881 (t80) REVERT: A 1007 ILE cc_start: 0.9149 (mt) cc_final: 0.8723 (mm) REVERT: A 1170 MET cc_start: 0.7986 (mmm) cc_final: 0.7575 (tpp) REVERT: A 1238 MET cc_start: 0.7812 (ttp) cc_final: 0.7282 (ttp) REVERT: A 1588 MET cc_start: 0.7995 (tpt) cc_final: 0.7666 (tpp) REVERT: B 38 LEU cc_start: 0.8645 (tp) cc_final: 0.8434 (tp) REVERT: B 72 VAL cc_start: 0.8453 (t) cc_final: 0.7902 (p) REVERT: B 163 VAL cc_start: 0.8638 (m) cc_final: 0.8328 (t) REVERT: B 242 ASP cc_start: 0.7980 (p0) cc_final: 0.7630 (p0) REVERT: B 270 LEU cc_start: 0.8579 (tp) cc_final: 0.8046 (mt) REVERT: B 378 ILE cc_start: 0.9035 (mt) cc_final: 0.8814 (mm) REVERT: B 411 MET cc_start: 0.8139 (mtp) cc_final: 0.7812 (mtp) REVERT: B 472 SER cc_start: 0.9016 (p) cc_final: 0.8710 (p) REVERT: B 494 TYR cc_start: 0.6722 (m-10) cc_final: 0.6258 (m-10) REVERT: B 521 LEU cc_start: 0.8634 (mt) cc_final: 0.8376 (mm) REVERT: B 531 VAL cc_start: 0.8755 (m) cc_final: 0.8529 (p) REVERT: B 647 SER cc_start: 0.9288 (m) cc_final: 0.9006 (p) REVERT: B 716 MET cc_start: 0.7835 (mtm) cc_final: 0.7550 (mtp) REVERT: B 717 TYR cc_start: 0.7250 (m-10) cc_final: 0.6357 (m-10) REVERT: B 782 ASP cc_start: 0.7292 (p0) cc_final: 0.6857 (p0) REVERT: B 783 MET cc_start: 0.6288 (mtt) cc_final: 0.5910 (mtt) REVERT: B 787 MET cc_start: 0.8685 (ptm) cc_final: 0.8257 (ppp) REVERT: B 788 ILE cc_start: 0.8860 (mm) cc_final: 0.8269 (mm) REVERT: B 791 LYS cc_start: 0.7340 (tttm) cc_final: 0.6996 (tttm) REVERT: B 795 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6739 (mm-30) REVERT: B 918 SER cc_start: 0.8196 (t) cc_final: 0.7893 (t) REVERT: B 959 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8554 (p) REVERT: B 1089 GLN cc_start: 0.7842 (tt0) cc_final: 0.7617 (tt0) REVERT: B 1102 SER cc_start: 0.7598 (m) cc_final: 0.7285 (m) REVERT: B 1117 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8759 (t) REVERT: C 72 ILE cc_start: 0.9016 (mt) cc_final: 0.8771 (mt) REVERT: C 136 LEU cc_start: 0.8257 (tt) cc_final: 0.7971 (tp) REVERT: C 188 ASP cc_start: 0.7144 (m-30) cc_final: 0.6921 (m-30) REVERT: C 220 SER cc_start: 0.9374 (m) cc_final: 0.8912 (p) REVERT: C 313 ILE cc_start: 0.8951 (mt) cc_final: 0.8601 (mt) REVERT: F 130 ILE cc_start: 0.8123 (mt) cc_final: 0.7822 (mt) REVERT: F 142 SER cc_start: 0.8323 (m) cc_final: 0.8034 (p) REVERT: G 96 SER cc_start: 0.3765 (OUTLIER) cc_final: 0.2950 (p) REVERT: G 237 HIS cc_start: 0.5306 (m-70) cc_final: 0.4947 (m-70) REVERT: G 245 VAL cc_start: 0.7149 (t) cc_final: 0.6747 (t) REVERT: I 16 LEU cc_start: 0.7800 (tp) cc_final: 0.7504 (tp) REVERT: J 21 TYR cc_start: 0.8363 (t80) cc_final: 0.8154 (t80) REVERT: J 66 LEU cc_start: 0.7305 (mt) cc_final: 0.7007 (tt) REVERT: K 76 LEU cc_start: 0.8013 (tp) cc_final: 0.7785 (tt) REVERT: K 98 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6519 (mt-10) REVERT: L 46 VAL cc_start: 0.7835 (t) cc_final: 0.7617 (p) REVERT: L 54 ARG cc_start: 0.6149 (mtm180) cc_final: 0.5567 (mtm180) REVERT: M 19 PRO cc_start: 0.7306 (Cg_exo) cc_final: 0.7085 (Cg_endo) REVERT: M 48 LYS cc_start: 0.0671 (OUTLIER) cc_final: -0.0428 (ptmm) REVERT: M 52 VAL cc_start: 0.8327 (t) cc_final: 0.7675 (p) REVERT: M 74 ASN cc_start: 0.7144 (t0) cc_final: 0.6056 (t0) REVERT: M 100 VAL cc_start: 0.7603 (t) cc_final: 0.7299 (m) REVERT: O 463 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6615 (pp) REVERT: P 12 THR cc_start: 0.5525 (p) cc_final: 0.4941 (p) REVERT: P 58 ARG cc_start: 0.1299 (OUTLIER) cc_final: 0.0965 (ttm170) REVERT: P 60 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5475 (mt) REVERT: P 147 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: P 150 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: P 321 ASP cc_start: 0.0311 (OUTLIER) cc_final: -0.0106 (t0) REVERT: P 400 MET cc_start: 0.6318 (mpm) cc_final: 0.4598 (mpp) REVERT: P 419 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6189 (pt) REVERT: P 512 ARG cc_start: 0.3569 (OUTLIER) cc_final: 0.1714 (mtm-85) REVERT: Q 147 GLN cc_start: 0.5818 (OUTLIER) cc_final: 0.4541 (pp30) REVERT: Q 153 ASN cc_start: 0.6990 (OUTLIER) cc_final: 0.6625 (p0) REVERT: Q 202 THR cc_start: 0.7676 (m) cc_final: 0.6883 (t) REVERT: Q 216 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8487 (mp) REVERT: Q 238 THR cc_start: 0.8097 (p) cc_final: 0.7671 (p) REVERT: Q 239 LEU cc_start: 0.7544 (tp) cc_final: 0.7343 (tp) REVERT: Q 290 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5684 (m-10) outliers start: 232 outliers final: 94 residues processed: 1833 average time/residue: 0.6131 time to fit residues: 1814.9783 Evaluate side-chains 1065 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 955 time to evaluate : 5.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 477 optimal weight: 5.9990 chunk 429 optimal weight: 6.9990 chunk 238 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 443 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 513 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 60 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 489 ASN A 553 GLN A 580 HIS A 639 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 926 GLN A 993 GLN A 998 HIS A1108 HIS ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 128 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS B 254 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN B 399 HIS B 462 GLN B 499 HIS ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 999 GLN B1010 ASN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1163 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 335 GLN E 3 GLN E 113 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS H 134 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 267 ASN O 301 GLN O 401 ASN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 ASN O 613 HIS O 617 HIS O 624 GLN ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 701 HIS ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN P 206 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 301 HIS ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN P 511 HIS Q 160 HIS ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 221 HIS ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 260 ASN Q 276 GLN Q 287 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 48460 Z= 0.322 Angle : 0.967 19.357 65937 Z= 0.502 Chirality : 0.053 0.403 7373 Planarity : 0.007 0.161 8112 Dihedral : 13.794 158.195 7276 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 25.98 Ramachandran Plot: Outliers : 1.63 % Allowed : 7.73 % Favored : 90.65 % Rotamer: Outliers : 0.54 % Allowed : 4.15 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.09 % 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: -1.87 (0.11), residues: 5527 helix: -0.32 (0.11), residues: 1980 sheet: -0.99 (0.17), residues: 722 loop : -2.01 (0.11), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP O 399 HIS 0.025 0.002 HIS P 294 PHE 0.043 0.003 PHE O 375 TYR 0.035 0.003 TYR B1184 ARG 0.011 0.001 ARG O 746 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1381 time to evaluate : 5.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8130 (pp) cc_final: 0.7720 (pp) REVERT: A 95 TYR cc_start: 0.7982 (t80) cc_final: 0.7735 (t80) REVERT: A 217 LYS cc_start: 0.8461 (mtmt) cc_final: 0.7855 (mttm) REVERT: A 356 PHE cc_start: 0.6804 (m-10) cc_final: 0.6471 (m-10) REVERT: A 424 MET cc_start: 0.7146 (mmm) cc_final: 0.6531 (mmm) REVERT: A 589 MET cc_start: 0.8299 (mmm) cc_final: 0.8002 (mmm) REVERT: A 640 ASN cc_start: 0.7443 (t0) cc_final: 0.7193 (m-40) REVERT: A 780 ILE cc_start: 0.8694 (pt) cc_final: 0.8473 (pt) REVERT: A 811 SER cc_start: 0.7330 (m) cc_final: 0.7127 (p) REVERT: A 907 VAL cc_start: 0.8663 (t) cc_final: 0.8460 (p) REVERT: A 947 LEU cc_start: 0.7902 (mp) cc_final: 0.7609 (mp) REVERT: A 960 MET cc_start: 0.8029 (mtm) cc_final: 0.7620 (mtp) REVERT: A 1038 ILE cc_start: 0.9088 (mm) cc_final: 0.8858 (mm) REVERT: A 1047 GLN cc_start: 0.7850 (mt0) cc_final: 0.7631 (mt0) REVERT: A 1170 MET cc_start: 0.8118 (mmm) cc_final: 0.7445 (tpp) REVERT: A 1176 ARG cc_start: 0.8049 (mmp-170) cc_final: 0.7742 (mmp80) REVERT: A 1188 ILE cc_start: 0.8422 (mt) cc_final: 0.8054 (tt) REVERT: A 1191 GLN cc_start: 0.8063 (mt0) cc_final: 0.7763 (mt0) REVERT: A 1223 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6640 (ttp80) REVERT: A 1238 MET cc_start: 0.7762 (ttp) cc_final: 0.7211 (ttm) REVERT: A 1556 GLU cc_start: 0.6934 (tp30) cc_final: 0.6537 (tp30) REVERT: A 1573 TYR cc_start: 0.7689 (m-80) cc_final: 0.7369 (m-10) REVERT: A 1588 MET cc_start: 0.8043 (tpt) cc_final: 0.7640 (tpp) REVERT: A 1613 MET cc_start: 0.7235 (ttm) cc_final: 0.6537 (ttm) REVERT: A 1633 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6992 (mm-40) REVERT: B 72 VAL cc_start: 0.8189 (t) cc_final: 0.7975 (p) REVERT: B 125 GLU cc_start: 0.7435 (mp0) cc_final: 0.7211 (mp0) REVERT: B 204 ARG cc_start: 0.8980 (ttm170) cc_final: 0.8772 (ttp80) REVERT: B 242 ASP cc_start: 0.7877 (p0) cc_final: 0.7484 (p0) REVERT: B 270 LEU cc_start: 0.8223 (tp) cc_final: 0.7849 (mt) REVERT: B 378 ILE cc_start: 0.9082 (mt) cc_final: 0.8803 (mm) REVERT: B 380 LYS cc_start: 0.8187 (tttt) cc_final: 0.7707 (ttmm) REVERT: B 411 MET cc_start: 0.7586 (mtp) cc_final: 0.7352 (mtp) REVERT: B 470 LEU cc_start: 0.7887 (mp) cc_final: 0.7686 (mp) REVERT: B 494 TYR cc_start: 0.6696 (m-10) cc_final: 0.6436 (m-80) REVERT: B 531 VAL cc_start: 0.9186 (m) cc_final: 0.8805 (p) REVERT: B 671 TYR cc_start: 0.7722 (m-80) cc_final: 0.7442 (m-80) REVERT: B 782 ASP cc_start: 0.6972 (p0) cc_final: 0.6740 (p0) REVERT: B 783 MET cc_start: 0.6516 (mtt) cc_final: 0.6117 (mtt) REVERT: B 791 LYS cc_start: 0.7292 (tttm) cc_final: 0.6724 (tttm) REVERT: B 900 THR cc_start: 0.8329 (m) cc_final: 0.8025 (p) REVERT: B 918 SER cc_start: 0.7780 (t) cc_final: 0.7462 (t) REVERT: B 1031 VAL cc_start: 0.8840 (t) cc_final: 0.8605 (p) REVERT: B 1077 ASP cc_start: 0.6335 (m-30) cc_final: 0.6054 (m-30) REVERT: B 1093 LEU cc_start: 0.8222 (tp) cc_final: 0.7864 (tp) REVERT: C 101 ILE cc_start: 0.9258 (mt) cc_final: 0.9030 (mm) REVERT: C 166 ASP cc_start: 0.6140 (m-30) cc_final: 0.5841 (m-30) REVERT: C 191 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8594 (mp) REVERT: C 220 SER cc_start: 0.9218 (m) cc_final: 0.8771 (p) REVERT: C 287 ASP cc_start: 0.5212 (p0) cc_final: 0.4959 (p0) REVERT: E 2 ASP cc_start: 0.4374 (p0) cc_final: 0.4086 (p0) REVERT: E 78 LEU cc_start: 0.6410 (tp) cc_final: 0.6145 (tp) REVERT: E 214 CYS cc_start: 0.7289 (t) cc_final: 0.7081 (t) REVERT: F 142 SER cc_start: 0.8469 (m) cc_final: 0.8135 (p) REVERT: J 22 LEU cc_start: 0.8020 (mt) cc_final: 0.7818 (mt) REVERT: J 56 LEU cc_start: 0.8946 (tp) cc_final: 0.8516 (tt) REVERT: K 66 VAL cc_start: 0.9261 (m) cc_final: 0.9046 (t) REVERT: K 81 MET cc_start: 0.7715 (mmm) cc_final: 0.7284 (mmm) REVERT: K 125 MET cc_start: 0.6981 (mtm) cc_final: 0.6641 (mtt) REVERT: K 127 LEU cc_start: 0.8712 (tt) cc_final: 0.8446 (tt) REVERT: K 142 MET cc_start: 0.5981 (ttt) cc_final: 0.5650 (ttm) REVERT: L 46 VAL cc_start: 0.7809 (t) cc_final: 0.7597 (p) REVERT: M 88 ILE cc_start: 0.5030 (tt) cc_final: 0.4552 (tt) REVERT: N 61 ASN cc_start: 0.8402 (p0) cc_final: 0.7927 (p0) REVERT: N 64 ILE cc_start: 0.7414 (mm) cc_final: 0.7198 (mm) REVERT: O 421 ILE cc_start: 0.7871 (mt) cc_final: 0.7431 (mt) REVERT: P 192 TYR cc_start: 0.6016 (t80) cc_final: 0.3766 (t80) REVERT: P 369 TRP cc_start: 0.5817 (m-10) cc_final: 0.5260 (m100) REVERT: Q 214 VAL cc_start: 0.8431 (t) cc_final: 0.8172 (t) REVERT: Q 216 LEU cc_start: 0.8643 (mt) cc_final: 0.8261 (mt) REVERT: Q 238 THR cc_start: 0.8402 (p) cc_final: 0.7879 (p) REVERT: Q 312 TYR cc_start: 0.9087 (t80) cc_final: 0.8702 (t80) outliers start: 27 outliers final: 5 residues processed: 1398 average time/residue: 0.6171 time to fit residues: 1434.0468 Evaluate side-chains 966 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 960 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 285 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 427 optimal weight: 20.0000 chunk 349 optimal weight: 30.0000 chunk 141 optimal weight: 0.9990 chunk 514 optimal weight: 9.9990 chunk 556 optimal weight: 10.0000 chunk 458 optimal weight: 30.0000 chunk 510 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 413 optimal weight: 30.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 383 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1647 ASN B 183 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN B 462 GLN B 469 ASN B 547 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B 999 GLN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN G 65 HIS G 237 HIS I 27 ASN K 118 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 89 GLN O 215 ASN ** O 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 250 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN P 406 GLN P 486 GLN ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 276 GLN Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 48460 Z= 0.356 Angle : 0.877 17.883 65937 Z= 0.456 Chirality : 0.050 0.382 7373 Planarity : 0.007 0.169 8112 Dihedral : 13.817 162.092 7276 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 1.23 % Allowed : 8.29 % Favored : 90.48 % Rotamer: Outliers : 0.26 % Allowed : 3.54 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.09 % 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: -1.34 (0.11), residues: 5527 helix: 0.27 (0.11), residues: 1974 sheet: -0.86 (0.18), residues: 736 loop : -1.77 (0.12), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP N 54 HIS 0.014 0.002 HIS B 282 PHE 0.039 0.003 PHE P 377 TYR 0.034 0.002 TYR Q 131 ARG 0.011 0.001 ARG O 746 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1198 time to evaluate : 5.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.8789 (mtmt) cc_final: 0.7940 (mttm) REVERT: A 339 PHE cc_start: 0.7588 (m-80) cc_final: 0.7357 (m-10) REVERT: A 618 TYR cc_start: 0.8035 (m-80) cc_final: 0.7473 (m-80) REVERT: A 635 MET cc_start: 0.7566 (ttp) cc_final: 0.7206 (ttp) REVERT: A 640 ASN cc_start: 0.7568 (t0) cc_final: 0.7120 (m-40) REVERT: A 947 LEU cc_start: 0.8077 (mp) cc_final: 0.7672 (mp) REVERT: A 960 MET cc_start: 0.7679 (mtm) cc_final: 0.7368 (mtp) REVERT: A 982 VAL cc_start: 0.8182 (t) cc_final: 0.7965 (t) REVERT: A 1038 ILE cc_start: 0.9061 (mm) cc_final: 0.8797 (mm) REVERT: A 1170 MET cc_start: 0.7971 (mmm) cc_final: 0.7514 (tpp) REVERT: A 1191 GLN cc_start: 0.8094 (mt0) cc_final: 0.7809 (mt0) REVERT: A 1238 MET cc_start: 0.7499 (ttp) cc_final: 0.6605 (ttp) REVERT: A 1529 MET cc_start: 0.8140 (mmm) cc_final: 0.7586 (mmp) REVERT: B 205 MET cc_start: 0.8241 (mtm) cc_final: 0.8039 (mtp) REVERT: B 242 ASP cc_start: 0.7929 (p0) cc_final: 0.7461 (p0) REVERT: B 277 LEU cc_start: 0.7928 (mm) cc_final: 0.7694 (mm) REVERT: B 380 LYS cc_start: 0.8319 (tttt) cc_final: 0.7995 (ttmm) REVERT: B 419 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6502 (mm-30) REVERT: B 469 ASN cc_start: 0.8273 (m-40) cc_final: 0.8010 (m110) REVERT: B 480 GLN cc_start: 0.8672 (pm20) cc_final: 0.8466 (pm20) REVERT: B 494 TYR cc_start: 0.6895 (m-10) cc_final: 0.6505 (m-80) REVERT: B 531 VAL cc_start: 0.9149 (m) cc_final: 0.8664 (p) REVERT: B 576 THR cc_start: 0.7397 (p) cc_final: 0.6885 (p) REVERT: B 884 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 924 LYS cc_start: 0.8008 (pttm) cc_final: 0.7511 (pttt) REVERT: B 962 MET cc_start: 0.7774 (tpp) cc_final: 0.7410 (tpp) REVERT: B 1039 MET cc_start: 0.3997 (ttt) cc_final: 0.3661 (ttt) REVERT: B 1057 MET cc_start: 0.8369 (mmp) cc_final: 0.8111 (mmm) REVERT: B 1183 LYS cc_start: 0.8596 (pttt) cc_final: 0.8057 (pttt) REVERT: C 101 ILE cc_start: 0.9233 (mt) cc_final: 0.9014 (mm) REVERT: C 220 SER cc_start: 0.9268 (m) cc_final: 0.8879 (p) REVERT: C 287 ASP cc_start: 0.5342 (p0) cc_final: 0.5108 (p0) REVERT: F 123 LYS cc_start: 0.7355 (mtpt) cc_final: 0.7148 (mtpt) REVERT: F 143 PHE cc_start: 0.7662 (p90) cc_final: 0.7433 (p90) REVERT: H 14 GLU cc_start: 0.6795 (pp20) cc_final: 0.6498 (pp20) REVERT: H 112 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6863 (mp) REVERT: J 27 GLU cc_start: 0.7681 (pp20) cc_final: 0.7325 (pp20) REVERT: J 56 LEU cc_start: 0.9003 (tp) cc_final: 0.8534 (tt) REVERT: K 66 VAL cc_start: 0.9051 (m) cc_final: 0.8815 (t) REVERT: K 125 MET cc_start: 0.7022 (mtm) cc_final: 0.6267 (mtt) REVERT: K 127 LEU cc_start: 0.8846 (tt) cc_final: 0.8462 (tt) REVERT: K 130 VAL cc_start: 0.8976 (t) cc_final: 0.8680 (t) REVERT: M 23 VAL cc_start: 0.7759 (p) cc_final: 0.7245 (m) REVERT: M 100 VAL cc_start: 0.7824 (t) cc_final: 0.7475 (m) REVERT: O 383 ILE cc_start: 0.5841 (mt) cc_final: 0.4644 (mt) REVERT: P 192 TYR cc_start: 0.5827 (t80) cc_final: 0.4918 (t80) REVERT: P 369 TRP cc_start: 0.5498 (m-10) cc_final: 0.4897 (m100) REVERT: P 400 MET cc_start: 0.5667 (mpp) cc_final: 0.5120 (mpp) REVERT: Q 216 LEU cc_start: 0.8479 (mt) cc_final: 0.8180 (mt) REVERT: Q 312 TYR cc_start: 0.8710 (t80) cc_final: 0.8399 (t80) outliers start: 13 outliers final: 1 residues processed: 1208 average time/residue: 0.5791 time to fit residues: 1168.7302 Evaluate side-chains 870 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 868 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 508 optimal weight: 5.9990 chunk 387 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 345 optimal weight: 50.0000 chunk 516 optimal weight: 7.9990 chunk 547 optimal weight: 0.0020 chunk 269 optimal weight: 2.9990 chunk 489 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN A 383 ASN A 425 ASN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A 993 GLN A1026 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN N 128 ASN O 259 ASN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN P 406 GLN ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 48460 Z= 0.229 Angle : 0.797 18.582 65937 Z= 0.411 Chirality : 0.048 0.417 7373 Planarity : 0.006 0.175 8112 Dihedral : 13.827 162.331 7276 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.69 % Favored : 91.10 % Rotamer: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.08 % 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: -1.03 (0.11), residues: 5527 helix: 0.53 (0.11), residues: 1993 sheet: -0.67 (0.18), residues: 738 loop : -1.61 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 125 HIS 0.014 0.001 HIS O 348 PHE 0.035 0.002 PHE P 377 TYR 0.033 0.002 TYR P 366 ARG 0.011 0.001 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1202 time to evaluate : 5.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8774 (pt) cc_final: 0.8170 (pt) REVERT: A 213 ASN cc_start: 0.7885 (t0) cc_final: 0.7488 (t0) REVERT: A 217 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8036 (mttp) REVERT: A 424 MET cc_start: 0.6999 (mmm) cc_final: 0.6707 (mmm) REVERT: A 430 ILE cc_start: 0.8223 (tt) cc_final: 0.7946 (tt) REVERT: A 433 ASP cc_start: 0.6179 (t70) cc_final: 0.5782 (t70) REVERT: A 592 GLN cc_start: 0.6953 (tm-30) cc_final: 0.6369 (tt0) REVERT: A 640 ASN cc_start: 0.7460 (t0) cc_final: 0.7141 (m-40) REVERT: A 659 THR cc_start: 0.9097 (t) cc_final: 0.8736 (m) REVERT: A 780 ILE cc_start: 0.8856 (pt) cc_final: 0.8503 (pt) REVERT: A 907 VAL cc_start: 0.8878 (t) cc_final: 0.8501 (p) REVERT: A 947 LEU cc_start: 0.8188 (mp) cc_final: 0.7513 (mp) REVERT: A 1038 ILE cc_start: 0.9129 (mm) cc_final: 0.8791 (mm) REVERT: A 1047 GLN cc_start: 0.8333 (mt0) cc_final: 0.7834 (mt0) REVERT: A 1170 MET cc_start: 0.7994 (mmm) cc_final: 0.7501 (tpp) REVERT: A 1191 GLN cc_start: 0.8021 (mt0) cc_final: 0.7603 (mt0) REVERT: A 1224 GLU cc_start: 0.7099 (tt0) cc_final: 0.6717 (tt0) REVERT: A 1238 MET cc_start: 0.7273 (ttp) cc_final: 0.7014 (ttm) REVERT: A 1529 MET cc_start: 0.7963 (mmm) cc_final: 0.7716 (mmp) REVERT: A 1613 MET cc_start: 0.7482 (ttm) cc_final: 0.6973 (ttm) REVERT: B 39 GLN cc_start: 0.8052 (pm20) cc_final: 0.7787 (pm20) REVERT: B 242 ASP cc_start: 0.7914 (p0) cc_final: 0.7501 (p0) REVERT: B 380 LYS cc_start: 0.8143 (tttt) cc_final: 0.7762 (ttmm) REVERT: B 531 VAL cc_start: 0.9158 (m) cc_final: 0.8772 (p) REVERT: B 532 HIS cc_start: 0.8459 (t-170) cc_final: 0.8029 (t-170) REVERT: B 565 LEU cc_start: 0.8536 (mt) cc_final: 0.8322 (mt) REVERT: B 671 TYR cc_start: 0.7727 (m-80) cc_final: 0.7458 (m-80) REVERT: B 782 ASP cc_start: 0.6935 (p0) cc_final: 0.6381 (p0) REVERT: B 794 ASP cc_start: 0.6641 (t0) cc_final: 0.6341 (t0) REVERT: B 962 MET cc_start: 0.7694 (tpp) cc_final: 0.7225 (tpp) REVERT: B 1077 ASP cc_start: 0.6310 (m-30) cc_final: 0.6088 (m-30) REVERT: B 1094 ASN cc_start: 0.8439 (m110) cc_final: 0.8102 (m110) REVERT: B 1175 THR cc_start: 0.8822 (m) cc_final: 0.8040 (m) REVERT: B 1183 LYS cc_start: 0.8400 (pttt) cc_final: 0.7803 (pttt) REVERT: C 83 VAL cc_start: 0.8921 (p) cc_final: 0.8644 (m) REVERT: C 93 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7704 (mm-40) REVERT: C 112 MET cc_start: 0.7723 (mmm) cc_final: 0.7145 (mmm) REVERT: C 220 SER cc_start: 0.9199 (m) cc_final: 0.8956 (t) REVERT: E 2 ASP cc_start: 0.4620 (p0) cc_final: 0.3995 (p0) REVERT: E 78 LEU cc_start: 0.6400 (tp) cc_final: 0.6194 (tp) REVERT: E 135 PHE cc_start: 0.7082 (m-80) cc_final: 0.6853 (m-80) REVERT: E 179 GLN cc_start: 0.8140 (mm110) cc_final: 0.7897 (mm110) REVERT: F 74 ILE cc_start: 0.8292 (mm) cc_final: 0.8015 (mm) REVERT: F 82 THR cc_start: 0.8464 (t) cc_final: 0.8123 (p) REVERT: F 89 GLU cc_start: 0.7913 (pt0) cc_final: 0.7657 (pt0) REVERT: F 114 GLU cc_start: 0.7782 (tp30) cc_final: 0.7298 (tp30) REVERT: F 132 LEU cc_start: 0.8659 (mm) cc_final: 0.8292 (mm) REVERT: H 14 GLU cc_start: 0.6429 (pp20) cc_final: 0.5728 (pp20) REVERT: I 4 VAL cc_start: 0.7730 (m) cc_final: 0.7458 (m) REVERT: I 28 VAL cc_start: 0.6162 (t) cc_final: 0.5954 (t) REVERT: I 49 THR cc_start: 0.8204 (p) cc_final: 0.7999 (p) REVERT: J 49 MET cc_start: 0.8792 (tpp) cc_final: 0.8501 (mmm) REVERT: K 66 VAL cc_start: 0.8954 (m) cc_final: 0.8646 (t) REVERT: K 80 ILE cc_start: 0.8779 (mt) cc_final: 0.8553 (mt) REVERT: K 85 ASP cc_start: 0.6572 (t70) cc_final: 0.6099 (t0) REVERT: K 88 PHE cc_start: 0.7558 (t80) cc_final: 0.7248 (t80) REVERT: K 125 MET cc_start: 0.7134 (mtm) cc_final: 0.6571 (mtt) REVERT: K 130 VAL cc_start: 0.8893 (t) cc_final: 0.8680 (t) REVERT: L 53 HIS cc_start: 0.8246 (t-170) cc_final: 0.7944 (t-170) REVERT: M 23 VAL cc_start: 0.7750 (p) cc_final: 0.7337 (m) REVERT: M 52 VAL cc_start: 0.8271 (t) cc_final: 0.7864 (p) REVERT: O 471 MET cc_start: 0.6101 (mmm) cc_final: 0.5510 (mmm) REVERT: P 223 ASN cc_start: 0.4711 (t0) cc_final: 0.4223 (t0) REVERT: P 369 TRP cc_start: 0.5623 (m-10) cc_final: 0.5289 (m100) REVERT: P 400 MET cc_start: 0.5881 (mpp) cc_final: 0.5514 (mpp) REVERT: Q 202 THR cc_start: 0.6955 (m) cc_final: 0.6731 (m) REVERT: Q 216 LEU cc_start: 0.8418 (mt) cc_final: 0.8217 (mt) REVERT: Q 238 THR cc_start: 0.8585 (p) cc_final: 0.7893 (p) REVERT: Q 247 ILE cc_start: 0.7349 (pt) cc_final: 0.6824 (pt) outliers start: 7 outliers final: 1 residues processed: 1206 average time/residue: 0.6142 time to fit residues: 1244.1416 Evaluate side-chains 906 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 905 time to evaluate : 5.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 455 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 7 optimal weight: 0.3980 chunk 407 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 466 optimal weight: 30.0000 chunk 378 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 279 optimal weight: 1.9990 chunk 491 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 383 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN O 313 GLN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 769 GLN P 61 ASN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 402 ASN ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 48460 Z= 0.257 Angle : 0.786 17.375 65937 Z= 0.406 Chirality : 0.047 0.410 7373 Planarity : 0.006 0.157 8112 Dihedral : 13.803 163.787 7276 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.89 % Favored : 91.03 % Rotamer: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.11), residues: 5527 helix: 0.61 (0.11), residues: 1995 sheet: -0.69 (0.18), residues: 743 loop : -1.54 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A1530 HIS 0.012 0.001 HIS O 348 PHE 0.039 0.002 PHE A 57 TYR 0.033 0.002 TYR G 73 ARG 0.009 0.001 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1151 time to evaluate : 6.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.7601 (t0) cc_final: 0.7288 (t0) REVERT: A 217 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7968 (mttp) REVERT: A 424 MET cc_start: 0.6976 (mmm) cc_final: 0.6604 (mmm) REVERT: A 618 TYR cc_start: 0.8129 (m-80) cc_final: 0.7746 (m-10) REVERT: A 640 ASN cc_start: 0.7613 (t0) cc_final: 0.7226 (m-40) REVERT: A 699 CYS cc_start: 0.7924 (p) cc_final: 0.7711 (p) REVERT: A 780 ILE cc_start: 0.8848 (pt) cc_final: 0.8500 (pt) REVERT: A 811 SER cc_start: 0.7772 (p) cc_final: 0.7526 (p) REVERT: A 828 CYS cc_start: 0.8263 (t) cc_final: 0.8044 (t) REVERT: A 907 VAL cc_start: 0.8840 (t) cc_final: 0.8512 (p) REVERT: A 947 LEU cc_start: 0.8206 (mp) cc_final: 0.7565 (mp) REVERT: A 1038 ILE cc_start: 0.9073 (mm) cc_final: 0.8827 (mm) REVERT: A 1047 GLN cc_start: 0.8028 (mt0) cc_final: 0.7804 (mt0) REVERT: A 1049 MET cc_start: 0.7132 (mtp) cc_final: 0.6782 (mmm) REVERT: A 1170 MET cc_start: 0.7906 (mmm) cc_final: 0.7557 (tpp) REVERT: A 1191 GLN cc_start: 0.8429 (mt0) cc_final: 0.8099 (mt0) REVERT: A 1238 MET cc_start: 0.7401 (ttp) cc_final: 0.7016 (ttm) REVERT: A 1491 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6372 (mm-30) REVERT: A 1529 MET cc_start: 0.7905 (mmm) cc_final: 0.7673 (mmp) REVERT: A 1608 SER cc_start: 0.8785 (t) cc_final: 0.8444 (t) REVERT: A 1613 MET cc_start: 0.7207 (ttm) cc_final: 0.6404 (ttm) REVERT: B 242 ASP cc_start: 0.7926 (p0) cc_final: 0.7527 (p0) REVERT: B 270 LEU cc_start: 0.8341 (tp) cc_final: 0.7894 (mt) REVERT: B 277 LEU cc_start: 0.8031 (mm) cc_final: 0.7792 (mm) REVERT: B 380 LYS cc_start: 0.8139 (tttt) cc_final: 0.7737 (ttmm) REVERT: B 467 THR cc_start: 0.7815 (p) cc_final: 0.7579 (p) REVERT: B 703 LEU cc_start: 0.9040 (mt) cc_final: 0.8808 (mp) REVERT: B 762 MET cc_start: 0.7411 (mmm) cc_final: 0.7079 (ttm) REVERT: B 783 MET cc_start: 0.7092 (mtt) cc_final: 0.6677 (mtt) REVERT: B 962 MET cc_start: 0.7726 (tpp) cc_final: 0.7470 (tpp) REVERT: B 1057 MET cc_start: 0.8111 (mmm) cc_final: 0.7700 (mtm) REVERT: B 1094 ASN cc_start: 0.8556 (m110) cc_final: 0.8311 (m110) REVERT: B 1111 LEU cc_start: 0.7893 (tp) cc_final: 0.7630 (tp) REVERT: B 1113 THR cc_start: 0.9190 (p) cc_final: 0.8960 (p) REVERT: B 1175 THR cc_start: 0.8591 (m) cc_final: 0.8061 (m) REVERT: C 93 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7673 (mm-40) REVERT: C 112 MET cc_start: 0.7630 (mmm) cc_final: 0.7199 (mmm) REVERT: C 220 SER cc_start: 0.9233 (m) cc_final: 0.8984 (t) REVERT: D 14 THR cc_start: 0.7993 (p) cc_final: 0.7782 (p) REVERT: D 27 LEU cc_start: 0.7480 (mm) cc_final: 0.7280 (mm) REVERT: E 74 ASP cc_start: 0.6666 (p0) cc_final: 0.6418 (p0) REVERT: E 190 LEU cc_start: 0.7907 (mt) cc_final: 0.7679 (mt) REVERT: E 196 VAL cc_start: 0.7697 (p) cc_final: 0.7483 (m) REVERT: F 132 LEU cc_start: 0.8528 (mm) cc_final: 0.8186 (mm) REVERT: G 116 THR cc_start: 0.6436 (t) cc_final: 0.6164 (t) REVERT: H 112 ILE cc_start: 0.7248 (mp) cc_final: 0.6167 (mp) REVERT: H 125 LEU cc_start: 0.7539 (tp) cc_final: 0.7330 (tp) REVERT: I 4 VAL cc_start: 0.8008 (m) cc_final: 0.7718 (m) REVERT: J 49 MET cc_start: 0.8894 (tpp) cc_final: 0.8671 (mmm) REVERT: J 56 LEU cc_start: 0.8968 (tp) cc_final: 0.8628 (tt) REVERT: J 57 ILE cc_start: 0.9026 (tp) cc_final: 0.8595 (tp) REVERT: K 66 VAL cc_start: 0.8930 (m) cc_final: 0.8557 (t) REVERT: K 85 ASP cc_start: 0.6434 (t70) cc_final: 0.6163 (t0) REVERT: K 125 MET cc_start: 0.7020 (mtm) cc_final: 0.6611 (mtt) REVERT: M 51 PHE cc_start: 0.6619 (m-10) cc_final: 0.6371 (m-10) REVERT: N 38 PHE cc_start: 0.5803 (m-80) cc_final: 0.5406 (m-80) REVERT: O 350 THR cc_start: 0.5269 (p) cc_final: 0.4555 (p) REVERT: O 383 ILE cc_start: 0.5748 (mt) cc_final: 0.4225 (mt) REVERT: O 471 MET cc_start: 0.6176 (mmm) cc_final: 0.5456 (mmm) REVERT: P 41 PHE cc_start: 0.5610 (m-80) cc_final: 0.5354 (m-10) REVERT: P 223 ASN cc_start: 0.5245 (t0) cc_final: 0.4793 (t0) REVERT: P 369 TRP cc_start: 0.5610 (m-10) cc_final: 0.5344 (m100) REVERT: Q 202 THR cc_start: 0.7246 (m) cc_final: 0.6954 (m) REVERT: Q 216 LEU cc_start: 0.8499 (mt) cc_final: 0.8243 (mt) REVERT: Q 238 THR cc_start: 0.8578 (p) cc_final: 0.8118 (p) REVERT: Q 247 ILE cc_start: 0.7932 (pt) cc_final: 0.7591 (pt) outliers start: 3 outliers final: 0 residues processed: 1153 average time/residue: 0.5816 time to fit residues: 1120.4428 Evaluate side-chains 855 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 855 time to evaluate : 5.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 184 optimal weight: 5.9990 chunk 492 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 321 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 547 optimal weight: 0.7980 chunk 454 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 287 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS A 383 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 462 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN I 27 ASN K 99 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 313 GLN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 GLN ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN P 406 GLN ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 48460 Z= 0.340 Angle : 0.803 17.256 65937 Z= 0.415 Chirality : 0.048 0.311 7373 Planarity : 0.006 0.168 8112 Dihedral : 13.894 164.317 7276 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.09 % Favored : 90.90 % Rotamer: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.11), residues: 5527 helix: 0.67 (0.11), residues: 1998 sheet: -0.75 (0.18), residues: 746 loop : -1.53 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP N 54 HIS 0.009 0.001 HIS J 53 PHE 0.033 0.002 PHE Q 127 TYR 0.035 0.002 TYR B1184 ARG 0.017 0.001 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1067 time to evaluate : 5.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8739 (tp) cc_final: 0.8385 (tp) REVERT: A 213 ASN cc_start: 0.7940 (t0) cc_final: 0.7503 (t0) REVERT: A 217 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8131 (mttp) REVERT: A 618 TYR cc_start: 0.8222 (m-80) cc_final: 0.7889 (m-10) REVERT: A 780 ILE cc_start: 0.8871 (pt) cc_final: 0.8639 (pt) REVERT: A 830 MET cc_start: 0.8708 (mmm) cc_final: 0.8336 (tpp) REVERT: A 907 VAL cc_start: 0.8743 (t) cc_final: 0.8423 (p) REVERT: A 947 LEU cc_start: 0.8010 (mp) cc_final: 0.7805 (mt) REVERT: A 982 VAL cc_start: 0.8251 (t) cc_final: 0.8046 (t) REVERT: A 1038 ILE cc_start: 0.9101 (mm) cc_final: 0.8857 (mm) REVERT: A 1049 MET cc_start: 0.7457 (mtp) cc_final: 0.7219 (mmm) REVERT: A 1170 MET cc_start: 0.7823 (mmm) cc_final: 0.7336 (tpp) REVERT: A 1238 MET cc_start: 0.7400 (ttp) cc_final: 0.7052 (ttm) REVERT: A 1491 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6526 (mm-30) REVERT: A 1529 MET cc_start: 0.8033 (mmm) cc_final: 0.7828 (mmp) REVERT: A 1608 SER cc_start: 0.8851 (t) cc_final: 0.8539 (t) REVERT: B 166 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8069 (mm-40) REVERT: B 242 ASP cc_start: 0.8052 (p0) cc_final: 0.7633 (p0) REVERT: B 270 LEU cc_start: 0.8518 (tp) cc_final: 0.8170 (mp) REVERT: B 277 LEU cc_start: 0.8071 (mm) cc_final: 0.7860 (mm) REVERT: B 380 LYS cc_start: 0.8112 (tttt) cc_final: 0.7742 (ttmm) REVERT: B 413 LEU cc_start: 0.9060 (mm) cc_final: 0.8829 (mm) REVERT: B 419 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6628 (tm-30) REVERT: B 783 MET cc_start: 0.7329 (mtt) cc_final: 0.6439 (mtt) REVERT: B 918 SER cc_start: 0.8172 (t) cc_final: 0.7919 (t) REVERT: B 962 MET cc_start: 0.7281 (tpp) cc_final: 0.6996 (tpp) REVERT: B 1057 MET cc_start: 0.8252 (mmm) cc_final: 0.7940 (mtp) REVERT: B 1094 ASN cc_start: 0.8479 (m110) cc_final: 0.8079 (m110) REVERT: B 1111 LEU cc_start: 0.7992 (tp) cc_final: 0.7608 (tp) REVERT: B 1175 THR cc_start: 0.8367 (m) cc_final: 0.7784 (m) REVERT: C 112 MET cc_start: 0.7584 (mmm) cc_final: 0.7167 (mmm) REVERT: C 220 SER cc_start: 0.9307 (m) cc_final: 0.9088 (t) REVERT: C 287 ASP cc_start: 0.5147 (p0) cc_final: 0.4944 (p0) REVERT: E 5 ASN cc_start: 0.5539 (t0) cc_final: 0.5126 (t0) REVERT: E 74 ASP cc_start: 0.6665 (p0) cc_final: 0.6380 (p0) REVERT: F 77 ASP cc_start: 0.7180 (p0) cc_final: 0.6961 (p0) REVERT: F 132 LEU cc_start: 0.8596 (mm) cc_final: 0.8287 (mm) REVERT: H 112 ILE cc_start: 0.6846 (mp) cc_final: 0.6411 (mp) REVERT: J 56 LEU cc_start: 0.8725 (tp) cc_final: 0.8523 (tp) REVERT: K 42 PRO cc_start: 0.7562 (Cg_exo) cc_final: 0.7229 (Cg_endo) REVERT: K 66 VAL cc_start: 0.8931 (m) cc_final: 0.8677 (t) REVERT: K 125 MET cc_start: 0.7089 (mtm) cc_final: 0.6848 (mtt) REVERT: K 127 LEU cc_start: 0.8753 (tt) cc_final: 0.8454 (tt) REVERT: N 38 PHE cc_start: 0.6226 (m-80) cc_final: 0.5677 (m-80) REVERT: O 350 THR cc_start: 0.5261 (p) cc_final: 0.4133 (p) REVERT: O 386 MET cc_start: 0.6732 (mpp) cc_final: 0.6370 (mpp) REVERT: O 471 MET cc_start: 0.6297 (mmm) cc_final: 0.5953 (mmm) REVERT: P 223 ASN cc_start: 0.5203 (t0) cc_final: 0.4720 (t0) REVERT: P 400 MET cc_start: 0.5993 (mpp) cc_final: 0.5703 (mpp) REVERT: P 405 ASP cc_start: 0.6421 (m-30) cc_final: 0.5648 (p0) REVERT: Q 202 THR cc_start: 0.7396 (m) cc_final: 0.7192 (m) REVERT: Q 216 LEU cc_start: 0.8526 (mt) cc_final: 0.8227 (mt) REVERT: Q 238 THR cc_start: 0.8833 (p) cc_final: 0.8542 (p) REVERT: Q 239 LEU cc_start: 0.7961 (tp) cc_final: 0.7690 (tp) REVERT: Q 293 ILE cc_start: 0.8600 (mp) cc_final: 0.8375 (mm) REVERT: Q 312 TYR cc_start: 0.8529 (t80) cc_final: 0.8189 (t80) REVERT: Q 405 ILE cc_start: 0.7160 (tp) cc_final: 0.5967 (tp) outliers start: 5 outliers final: 1 residues processed: 1071 average time/residue: 0.5900 time to fit residues: 1054.6632 Evaluate side-chains 820 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 819 time to evaluate : 5.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 527 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 312 optimal weight: 9.9990 chunk 399 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 460 optimal weight: 6.9990 chunk 305 optimal weight: 20.0000 chunk 545 optimal weight: 0.8980 chunk 341 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 470 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN E 3 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 313 GLN ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 757 GLN P 157 HIS P 294 HIS P 406 GLN ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 48460 Z= 0.237 Angle : 0.778 16.240 65937 Z= 0.400 Chirality : 0.048 0.456 7373 Planarity : 0.006 0.147 8112 Dihedral : 13.895 164.570 7276 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.80 % Favored : 91.24 % Rotamer: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5527 helix: 0.71 (0.12), residues: 1998 sheet: -0.63 (0.18), residues: 743 loop : -1.49 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 143 HIS 0.013 0.001 HIS O 348 PHE 0.034 0.002 PHE O 294 TYR 0.029 0.002 TYR Q 131 ARG 0.023 0.001 ARG P 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1118 time to evaluate : 5.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 213 ASN cc_start: 0.7875 (t0) cc_final: 0.7492 (t0) REVERT: A 217 LYS cc_start: 0.8533 (mtmt) cc_final: 0.7951 (mttp) REVERT: A 592 GLN cc_start: 0.6857 (tm-30) cc_final: 0.6458 (tt0) REVERT: A 601 MET cc_start: 0.7103 (mtp) cc_final: 0.6866 (mtt) REVERT: A 699 CYS cc_start: 0.7695 (p) cc_final: 0.7492 (p) REVERT: A 780 ILE cc_start: 0.8900 (pt) cc_final: 0.8593 (pt) REVERT: A 830 MET cc_start: 0.8446 (mmm) cc_final: 0.8138 (tpp) REVERT: A 907 VAL cc_start: 0.8722 (t) cc_final: 0.8476 (p) REVERT: A 947 LEU cc_start: 0.8072 (mp) cc_final: 0.7440 (mp) REVERT: A 1038 ILE cc_start: 0.9171 (mm) cc_final: 0.8864 (mm) REVERT: A 1049 MET cc_start: 0.7472 (mtp) cc_final: 0.7182 (mmm) REVERT: A 1170 MET cc_start: 0.7830 (mmm) cc_final: 0.7334 (tpp) REVERT: A 1238 MET cc_start: 0.7269 (ttp) cc_final: 0.6908 (ttm) REVERT: A 1529 MET cc_start: 0.7986 (mmm) cc_final: 0.7606 (mmp) REVERT: A 1608 SER cc_start: 0.8838 (t) cc_final: 0.8617 (t) REVERT: A 1613 MET cc_start: 0.7083 (ttp) cc_final: 0.6784 (ttm) REVERT: B 166 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7950 (mm-40) REVERT: B 209 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7068 (tm-30) REVERT: B 242 ASP cc_start: 0.7743 (p0) cc_final: 0.7401 (p0) REVERT: B 270 LEU cc_start: 0.8429 (tp) cc_final: 0.8161 (mp) REVERT: B 307 GLU cc_start: 0.7378 (tt0) cc_final: 0.6784 (tm-30) REVERT: B 309 LEU cc_start: 0.8137 (tp) cc_final: 0.7537 (tp) REVERT: B 419 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6683 (tm-30) REVERT: B 461 MET cc_start: 0.7204 (tpp) cc_final: 0.6613 (tpp) REVERT: B 762 MET cc_start: 0.6952 (mmm) cc_final: 0.6511 (ttm) REVERT: B 783 MET cc_start: 0.7020 (mtt) cc_final: 0.6525 (mtt) REVERT: B 918 SER cc_start: 0.8281 (t) cc_final: 0.8046 (t) REVERT: B 1013 MET cc_start: 0.7023 (mtm) cc_final: 0.6803 (ttm) REVERT: B 1037 ARG cc_start: 0.8337 (ptt90) cc_final: 0.7954 (ptt90) REVERT: B 1057 MET cc_start: 0.8180 (mmm) cc_final: 0.7788 (mtp) REVERT: B 1094 ASN cc_start: 0.8442 (m110) cc_final: 0.8167 (m110) REVERT: C 74 GLU cc_start: 0.7658 (pm20) cc_final: 0.7432 (pm20) REVERT: D 14 THR cc_start: 0.8006 (p) cc_final: 0.7714 (p) REVERT: D 37 LEU cc_start: 0.7298 (pp) cc_final: 0.7027 (mt) REVERT: E 2 ASP cc_start: 0.4283 (p0) cc_final: 0.3803 (p0) REVERT: E 74 ASP cc_start: 0.6985 (p0) cc_final: 0.6615 (p0) REVERT: E 196 VAL cc_start: 0.7521 (p) cc_final: 0.7242 (m) REVERT: F 132 LEU cc_start: 0.8554 (mm) cc_final: 0.8304 (mm) REVERT: G 81 VAL cc_start: 0.7590 (t) cc_final: 0.7379 (t) REVERT: H 112 ILE cc_start: 0.7107 (mp) cc_final: 0.6357 (mp) REVERT: K 66 VAL cc_start: 0.8879 (m) cc_final: 0.8492 (t) REVERT: K 85 ASP cc_start: 0.6065 (t0) cc_final: 0.5695 (t0) REVERT: K 125 MET cc_start: 0.7213 (mtm) cc_final: 0.6760 (mtt) REVERT: M 26 PHE cc_start: 0.7072 (m-10) cc_final: 0.6643 (m-10) REVERT: N 38 PHE cc_start: 0.6337 (m-80) cc_final: 0.6079 (m-80) REVERT: N 80 MET cc_start: 0.6899 (ppp) cc_final: 0.6665 (ppp) REVERT: O 350 THR cc_start: 0.4859 (p) cc_final: 0.4008 (p) REVERT: O 386 MET cc_start: 0.6940 (mpp) cc_final: 0.6645 (mpp) REVERT: O 471 MET cc_start: 0.6276 (mmm) cc_final: 0.5721 (mmm) REVERT: P 41 PHE cc_start: 0.5431 (m-80) cc_final: 0.5031 (m-10) REVERT: P 223 ASN cc_start: 0.5000 (t0) cc_final: 0.4684 (t0) REVERT: P 400 MET cc_start: 0.6070 (mpp) cc_final: 0.5808 (mpp) REVERT: P 405 ASP cc_start: 0.5792 (m-30) cc_final: 0.5374 (p0) REVERT: P 413 LEU cc_start: 0.7230 (mt) cc_final: 0.6839 (mt) REVERT: Q 21 TYR cc_start: 0.6220 (m-80) cc_final: 0.5974 (m-10) REVERT: Q 238 THR cc_start: 0.8833 (p) cc_final: 0.8388 (p) REVERT: Q 239 LEU cc_start: 0.8038 (tp) cc_final: 0.7826 (tp) REVERT: Q 405 ILE cc_start: 0.7252 (tp) cc_final: 0.6186 (tp) outliers start: 2 outliers final: 1 residues processed: 1119 average time/residue: 0.5700 time to fit residues: 1070.3050 Evaluate side-chains 835 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 834 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 337 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 428 optimal weight: 0.0170 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN D 23 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN I 27 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 48460 Z= 0.307 Angle : 0.783 16.169 65937 Z= 0.404 Chirality : 0.048 0.363 7373 Planarity : 0.006 0.148 8112 Dihedral : 13.934 164.778 7276 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.21 % Favored : 90.86 % Rotamer: Outliers : 0.02 % Allowed : 1.19 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.11), residues: 5527 helix: 0.73 (0.12), residues: 2009 sheet: -0.69 (0.18), residues: 739 loop : -1.49 (0.12), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 54 HIS 0.014 0.001 HIS O 479 PHE 0.025 0.002 PHE Q 127 TYR 0.031 0.002 TYR B 566 ARG 0.013 0.001 ARG P 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1041 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.7795 (t0) cc_final: 0.7432 (t0) REVERT: A 217 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8000 (mttp) REVERT: A 589 MET cc_start: 0.8735 (mmm) cc_final: 0.8190 (mmm) REVERT: A 601 MET cc_start: 0.7213 (mtp) cc_final: 0.6903 (mtt) REVERT: A 618 TYR cc_start: 0.8269 (m-10) cc_final: 0.8029 (m-10) REVERT: A 780 ILE cc_start: 0.8922 (pt) cc_final: 0.8680 (pt) REVERT: A 830 MET cc_start: 0.8503 (mmm) cc_final: 0.8024 (tpp) REVERT: A 907 VAL cc_start: 0.8679 (t) cc_final: 0.8435 (p) REVERT: A 947 LEU cc_start: 0.7980 (mp) cc_final: 0.7625 (mp) REVERT: A 982 VAL cc_start: 0.8250 (t) cc_final: 0.8025 (t) REVERT: A 1038 ILE cc_start: 0.9010 (mm) cc_final: 0.8725 (mm) REVERT: A 1053 ASP cc_start: 0.8040 (p0) cc_final: 0.7829 (p0) REVERT: A 1170 MET cc_start: 0.7837 (mmm) cc_final: 0.7432 (tpp) REVERT: A 1238 MET cc_start: 0.7333 (ttp) cc_final: 0.6978 (ttm) REVERT: A 1529 MET cc_start: 0.8000 (mmm) cc_final: 0.7649 (mmp) REVERT: A 1608 SER cc_start: 0.8694 (t) cc_final: 0.8409 (t) REVERT: A 1622 LEU cc_start: 0.8286 (tp) cc_final: 0.7975 (tp) REVERT: B 166 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7999 (mm-40) REVERT: B 242 ASP cc_start: 0.7966 (p0) cc_final: 0.7571 (p0) REVERT: B 270 LEU cc_start: 0.8485 (tp) cc_final: 0.8113 (mp) REVERT: B 277 LEU cc_start: 0.8111 (mm) cc_final: 0.7788 (mm) REVERT: B 307 GLU cc_start: 0.7475 (tt0) cc_final: 0.7029 (tm-30) REVERT: B 309 LEU cc_start: 0.8103 (tp) cc_final: 0.7491 (tp) REVERT: B 413 LEU cc_start: 0.8941 (mm) cc_final: 0.8723 (mm) REVERT: B 527 PHE cc_start: 0.8551 (m-80) cc_final: 0.8076 (m-10) REVERT: B 762 MET cc_start: 0.7108 (mmm) cc_final: 0.6823 (ttm) REVERT: B 783 MET cc_start: 0.7041 (mtt) cc_final: 0.6758 (mtt) REVERT: B 918 SER cc_start: 0.8118 (t) cc_final: 0.7616 (t) REVERT: B 1057 MET cc_start: 0.8069 (mmm) cc_final: 0.7393 (mtp) REVERT: B 1094 ASN cc_start: 0.8531 (m110) cc_final: 0.8113 (m110) REVERT: D 14 THR cc_start: 0.7958 (p) cc_final: 0.7682 (p) REVERT: E 74 ASP cc_start: 0.6977 (p0) cc_final: 0.6754 (p0) REVERT: F 111 LEU cc_start: 0.8329 (tt) cc_final: 0.8027 (tt) REVERT: F 132 LEU cc_start: 0.8522 (mm) cc_final: 0.8320 (mm) REVERT: I 64 LYS cc_start: 0.6100 (tptp) cc_final: 0.5838 (tptp) REVERT: J 57 ILE cc_start: 0.9012 (tp) cc_final: 0.8777 (tp) REVERT: K 85 ASP cc_start: 0.5886 (t0) cc_final: 0.5592 (t0) REVERT: K 88 PHE cc_start: 0.6543 (t80) cc_final: 0.6257 (t80) REVERT: M 26 PHE cc_start: 0.6783 (m-10) cc_final: 0.6450 (m-10) REVERT: M 36 THR cc_start: 0.7845 (m) cc_final: 0.7539 (m) REVERT: N 38 PHE cc_start: 0.6323 (m-80) cc_final: 0.6021 (m-80) REVERT: O 350 THR cc_start: 0.4905 (p) cc_final: 0.4059 (p) REVERT: O 386 MET cc_start: 0.6989 (mpp) cc_final: 0.6641 (mpp) REVERT: O 471 MET cc_start: 0.6296 (mmm) cc_final: 0.5739 (mmm) REVERT: P 41 PHE cc_start: 0.5313 (m-80) cc_final: 0.5065 (m-10) REVERT: P 223 ASN cc_start: 0.5111 (t0) cc_final: 0.4827 (t0) REVERT: P 400 MET cc_start: 0.5920 (mpp) cc_final: 0.5548 (mpp) REVERT: P 405 ASP cc_start: 0.5899 (m-30) cc_final: 0.5689 (p0) REVERT: Q 21 TYR cc_start: 0.6449 (m-80) cc_final: 0.6100 (m-10) REVERT: Q 216 LEU cc_start: 0.8543 (mt) cc_final: 0.8287 (mt) REVERT: Q 239 LEU cc_start: 0.7895 (tp) cc_final: 0.7682 (tp) outliers start: 1 outliers final: 0 residues processed: 1042 average time/residue: 0.5774 time to fit residues: 1006.4488 Evaluate side-chains 804 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 804 time to evaluate : 5.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 496 optimal weight: 2.9990 chunk 522 optimal weight: 40.0000 chunk 476 optimal weight: 6.9990 chunk 508 optimal weight: 7.9990 chunk 305 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 399 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 459 optimal weight: 30.0000 chunk 480 optimal weight: 0.0770 chunk 506 optimal weight: 20.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1336 GLN ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN I 27 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN M 54 HIS ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 ASN ** O 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 179 HIS ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 48460 Z= 0.302 Angle : 0.790 15.860 65937 Z= 0.405 Chirality : 0.048 0.357 7373 Planarity : 0.006 0.148 8112 Dihedral : 13.940 164.231 7276 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.20 % Favored : 90.90 % Rotamer: Outliers : 0.04 % Allowed : 0.66 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.11), residues: 5527 helix: 0.75 (0.12), residues: 2017 sheet: -0.71 (0.18), residues: 769 loop : -1.54 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP N 54 HIS 0.015 0.001 HIS O 479 PHE 0.030 0.002 PHE C 285 TYR 0.041 0.002 TYR B1184 ARG 0.028 0.001 ARG O 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1047 time to evaluate : 5.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7309 (tmm) cc_final: 0.6377 (tmm) REVERT: A 213 ASN cc_start: 0.7861 (t0) cc_final: 0.7555 (t0) REVERT: A 215 GLU cc_start: 0.5953 (tp30) cc_final: 0.5696 (tp30) REVERT: A 217 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8022 (mttp) REVERT: A 592 GLN cc_start: 0.6771 (tm-30) cc_final: 0.5835 (tt0) REVERT: A 601 MET cc_start: 0.7222 (mtp) cc_final: 0.6930 (mtt) REVERT: A 675 SER cc_start: 0.9145 (m) cc_final: 0.8856 (t) REVERT: A 699 CYS cc_start: 0.7796 (p) cc_final: 0.7555 (p) REVERT: A 780 ILE cc_start: 0.8968 (pt) cc_final: 0.8697 (pt) REVERT: A 811 SER cc_start: 0.7854 (p) cc_final: 0.7629 (p) REVERT: A 830 MET cc_start: 0.8431 (mmm) cc_final: 0.8076 (tpp) REVERT: A 907 VAL cc_start: 0.8708 (t) cc_final: 0.8425 (p) REVERT: A 947 LEU cc_start: 0.7970 (mp) cc_final: 0.7637 (mp) REVERT: A 1038 ILE cc_start: 0.9098 (mm) cc_final: 0.8831 (mm) REVERT: A 1053 ASP cc_start: 0.7952 (p0) cc_final: 0.7655 (m-30) REVERT: A 1170 MET cc_start: 0.7934 (mmm) cc_final: 0.7355 (tpp) REVERT: A 1188 ILE cc_start: 0.8531 (mm) cc_final: 0.7952 (tt) REVERT: A 1238 MET cc_start: 0.7278 (ttp) cc_final: 0.6960 (ttm) REVERT: A 1491 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 1492 ILE cc_start: 0.8439 (mm) cc_final: 0.8220 (mm) REVERT: A 1529 MET cc_start: 0.8034 (mmm) cc_final: 0.7677 (mmp) REVERT: A 1608 SER cc_start: 0.8607 (t) cc_final: 0.8385 (t) REVERT: B 70 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 166 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8002 (mm-40) REVERT: B 197 ASN cc_start: 0.8280 (m-40) cc_final: 0.7941 (m-40) REVERT: B 242 ASP cc_start: 0.7901 (p0) cc_final: 0.7600 (p0) REVERT: B 270 LEU cc_start: 0.8466 (tp) cc_final: 0.8119 (mp) REVERT: B 277 LEU cc_start: 0.8001 (mm) cc_final: 0.7796 (mm) REVERT: B 307 GLU cc_start: 0.7315 (tt0) cc_final: 0.6951 (tm-30) REVERT: B 309 LEU cc_start: 0.8009 (tp) cc_final: 0.7372 (tp) REVERT: B 413 LEU cc_start: 0.8799 (mm) cc_final: 0.8479 (mm) REVERT: B 527 PHE cc_start: 0.8460 (m-80) cc_final: 0.8135 (m-10) REVERT: B 918 SER cc_start: 0.8087 (t) cc_final: 0.7641 (t) REVERT: B 1057 MET cc_start: 0.8092 (mmm) cc_final: 0.7378 (mtp) REVERT: B 1086 PHE cc_start: 0.7865 (m-10) cc_final: 0.7461 (m-80) REVERT: B 1094 ASN cc_start: 0.8575 (m110) cc_final: 0.7771 (m110) REVERT: C 72 ILE cc_start: 0.8892 (mm) cc_final: 0.8654 (mm) REVERT: C 112 MET cc_start: 0.7388 (mmm) cc_final: 0.6993 (mmm) REVERT: D 14 THR cc_start: 0.7956 (p) cc_final: 0.7583 (p) REVERT: D 44 ILE cc_start: 0.8455 (pt) cc_final: 0.7595 (pt) REVERT: D 92 ILE cc_start: 0.6811 (mt) cc_final: 0.6534 (mt) REVERT: D 99 LEU cc_start: 0.6322 (pt) cc_final: 0.6116 (pp) REVERT: E 2 ASP cc_start: 0.4377 (p0) cc_final: 0.3729 (p0) REVERT: E 74 ASP cc_start: 0.6903 (p0) cc_final: 0.6675 (p0) REVERT: F 123 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7106 (mtpp) REVERT: F 132 LEU cc_start: 0.8546 (mm) cc_final: 0.8292 (mm) REVERT: G 81 VAL cc_start: 0.7806 (t) cc_final: 0.7499 (t) REVERT: I 2 SER cc_start: 0.7272 (p) cc_final: 0.7032 (p) REVERT: J 22 LEU cc_start: 0.7959 (mt) cc_final: 0.7686 (mt) REVERT: J 36 LEU cc_start: 0.8791 (mt) cc_final: 0.8298 (mt) REVERT: J 47 ARG cc_start: 0.8537 (mmm160) cc_final: 0.7561 (mmm-85) REVERT: K 81 MET cc_start: 0.7398 (mmm) cc_final: 0.7110 (mmm) REVERT: K 85 ASP cc_start: 0.5887 (t0) cc_final: 0.5640 (t0) REVERT: M 26 PHE cc_start: 0.6840 (m-10) cc_final: 0.6534 (m-10) REVERT: M 51 PHE cc_start: 0.6525 (m-10) cc_final: 0.6204 (m-10) REVERT: N 38 PHE cc_start: 0.6076 (m-80) cc_final: 0.5867 (m-80) REVERT: O 386 MET cc_start: 0.7087 (mpp) cc_final: 0.6701 (mpp) REVERT: O 471 MET cc_start: 0.6144 (mmm) cc_final: 0.5601 (mmm) REVERT: P 41 PHE cc_start: 0.5422 (m-80) cc_final: 0.5090 (m-10) REVERT: P 182 ILE cc_start: 0.6589 (pt) cc_final: 0.6348 (pt) REVERT: P 223 ASN cc_start: 0.5401 (t0) cc_final: 0.5036 (t0) REVERT: P 400 MET cc_start: 0.5925 (mpp) cc_final: 0.5637 (mpp) REVERT: Q 21 TYR cc_start: 0.6571 (m-80) cc_final: 0.6099 (m-10) REVERT: Q 216 LEU cc_start: 0.8501 (mt) cc_final: 0.8236 (mt) REVERT: Q 405 ILE cc_start: 0.7272 (tp) cc_final: 0.6304 (tp) REVERT: Q 414 PHE cc_start: 0.5489 (m-80) cc_final: 0.5224 (m-80) outliers start: 2 outliers final: 0 residues processed: 1049 average time/residue: 0.5921 time to fit residues: 1037.2235 Evaluate side-chains 806 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 806 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 333 optimal weight: 10.0000 chunk 537 optimal weight: 8.9990 chunk 328 optimal weight: 30.0000 chunk 255 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 563 optimal weight: 20.0000 chunk 518 optimal weight: 5.9990 chunk 449 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 346 optimal weight: 30.0000 chunk 275 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 693 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN K 118 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 580 ASN ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 HIS P 406 GLN ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.7117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 48460 Z= 0.257 Angle : 0.778 15.699 65937 Z= 0.398 Chirality : 0.048 0.512 7373 Planarity : 0.006 0.147 8112 Dihedral : 13.915 164.112 7276 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.34 % Favored : 90.83 % Rotamer: Outliers : 0.02 % Allowed : 0.48 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 5527 helix: 0.78 (0.12), residues: 2029 sheet: -0.72 (0.18), residues: 763 loop : -1.48 (0.12), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP N 54 HIS 0.015 0.001 HIS Q 407 PHE 0.039 0.002 PHE Q 127 TYR 0.043 0.002 TYR B1184 ARG 0.015 0.001 ARG Q 412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1045 time to evaluate : 5.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7617 (pp) cc_final: 0.7398 (pp) REVERT: A 213 ASN cc_start: 0.7747 (t0) cc_final: 0.7480 (t0) REVERT: A 217 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8087 (mttp) REVERT: A 506 THR cc_start: 0.8950 (p) cc_final: 0.8679 (p) REVERT: A 621 THR cc_start: 0.8436 (p) cc_final: 0.8145 (t) REVERT: A 659 THR cc_start: 0.9009 (t) cc_final: 0.8624 (m) REVERT: A 830 MET cc_start: 0.8273 (mmm) cc_final: 0.7922 (tpp) REVERT: A 947 LEU cc_start: 0.8039 (mp) cc_final: 0.7571 (mp) REVERT: A 982 VAL cc_start: 0.8298 (t) cc_final: 0.8058 (t) REVERT: A 1038 ILE cc_start: 0.9086 (mm) cc_final: 0.8763 (mm) REVERT: A 1170 MET cc_start: 0.7856 (mmm) cc_final: 0.7358 (tpp) REVERT: A 1188 ILE cc_start: 0.8519 (mm) cc_final: 0.8009 (tt) REVERT: A 1238 MET cc_start: 0.7217 (ttp) cc_final: 0.6888 (ttm) REVERT: A 1529 MET cc_start: 0.7992 (mmm) cc_final: 0.7658 (mmp) REVERT: A 1608 SER cc_start: 0.8667 (t) cc_final: 0.8395 (t) REVERT: B 70 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 166 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8011 (mm-40) REVERT: B 197 ASN cc_start: 0.8230 (m-40) cc_final: 0.7859 (m-40) REVERT: B 242 ASP cc_start: 0.7921 (p0) cc_final: 0.7492 (p0) REVERT: B 270 LEU cc_start: 0.8462 (tp) cc_final: 0.8122 (mp) REVERT: B 277 LEU cc_start: 0.8009 (mm) cc_final: 0.7786 (mm) REVERT: B 307 GLU cc_start: 0.7392 (tt0) cc_final: 0.6748 (tm-30) REVERT: B 309 LEU cc_start: 0.8065 (tp) cc_final: 0.7432 (tp) REVERT: B 476 LEU cc_start: 0.8802 (mp) cc_final: 0.8580 (mp) REVERT: B 502 MET cc_start: 0.8018 (ttp) cc_final: 0.7497 (tmm) REVERT: B 527 PHE cc_start: 0.8454 (m-80) cc_final: 0.7931 (m-10) REVERT: B 918 SER cc_start: 0.7933 (t) cc_final: 0.7555 (t) REVERT: B 1057 MET cc_start: 0.8068 (mmm) cc_final: 0.7669 (mtp) REVERT: B 1061 LYS cc_start: 0.6719 (ptmt) cc_final: 0.6486 (pttt) REVERT: B 1086 PHE cc_start: 0.7391 (m-10) cc_final: 0.7149 (m-10) REVERT: B 1093 LEU cc_start: 0.8440 (tp) cc_final: 0.8200 (tp) REVERT: B 1094 ASN cc_start: 0.8626 (m110) cc_final: 0.7868 (m110) REVERT: B 1113 THR cc_start: 0.9262 (p) cc_final: 0.8883 (t) REVERT: C 112 MET cc_start: 0.7232 (mmm) cc_final: 0.6826 (mmm) REVERT: D 99 LEU cc_start: 0.6293 (pt) cc_final: 0.6054 (pp) REVERT: E 74 ASP cc_start: 0.6836 (p0) cc_final: 0.6561 (p0) REVERT: G 81 VAL cc_start: 0.7720 (t) cc_final: 0.7504 (t) REVERT: I 31 SER cc_start: 0.7313 (m) cc_final: 0.7011 (t) REVERT: I 64 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6808 (tptp) REVERT: J 57 ILE cc_start: 0.8973 (tp) cc_final: 0.8714 (tp) REVERT: K 85 ASP cc_start: 0.5910 (t0) cc_final: 0.5648 (t0) REVERT: M 51 PHE cc_start: 0.6735 (m-10) cc_final: 0.6479 (m-10) REVERT: N 38 PHE cc_start: 0.6080 (m-80) cc_final: 0.5805 (m-80) REVERT: O 386 MET cc_start: 0.6996 (mpp) cc_final: 0.6646 (mpp) REVERT: O 471 MET cc_start: 0.6182 (mmm) cc_final: 0.5602 (mmm) REVERT: P 41 PHE cc_start: 0.5220 (m-80) cc_final: 0.4922 (m-10) REVERT: P 223 ASN cc_start: 0.5301 (t0) cc_final: 0.4901 (t0) REVERT: Q 21 TYR cc_start: 0.6444 (m-80) cc_final: 0.6044 (m-10) REVERT: Q 216 LEU cc_start: 0.8476 (mt) cc_final: 0.8209 (mt) REVERT: Q 239 LEU cc_start: 0.7785 (tp) cc_final: 0.7486 (tp) REVERT: Q 293 ILE cc_start: 0.8260 (mp) cc_final: 0.8034 (mm) REVERT: Q 405 ILE cc_start: 0.7273 (tp) cc_final: 0.6340 (tp) outliers start: 1 outliers final: 0 residues processed: 1046 average time/residue: 0.5951 time to fit residues: 1039.0949 Evaluate side-chains 799 residues out of total 5033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 799 time to evaluate : 5.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 356 optimal weight: 7.9990 chunk 478 optimal weight: 30.0000 chunk 137 optimal weight: 7.9990 chunk 414 optimal weight: 30.0000 chunk 66 optimal weight: 0.1980 chunk 124 optimal weight: 20.0000 chunk 449 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 461 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A1047 GLN A1336 GLN ** A1500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 161 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN K 118 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 179 HIS ** Q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.069428 restraints weight = 150789.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.071678 restraints weight = 82920.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073153 restraints weight = 56326.683| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 48460 Z= 0.301 Angle : 0.793 15.237 65937 Z= 0.405 Chirality : 0.048 0.494 7373 Planarity : 0.006 0.147 8112 Dihedral : 13.932 163.715 7276 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.78 % Allowed : 8.49 % Favored : 90.74 % Rotamer: Outliers : 0.02 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 5527 helix: 0.79 (0.12), residues: 2021 sheet: -0.74 (0.18), residues: 790 loop : -1.51 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP A 530 HIS 0.013 0.001 HIS O 479 PHE 0.035 0.002 PHE B 25 TYR 0.043 0.002 TYR B1184 ARG 0.017 0.001 ARG Q 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16610.05 seconds wall clock time: 298 minutes 41.85 seconds (17921.85 seconds total)