Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 05:10:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m64_3449/05_2023/5m64_3449.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m64_3449/05_2023/5m64_3449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m64_3449/05_2023/5m64_3449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m64_3449/05_2023/5m64_3449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m64_3449/05_2023/5m64_3449.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m64_3449/05_2023/5m64_3449.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.011 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 6 6.06 5 P 51 5.49 5 S 171 5.16 5 C 22559 2.51 5 N 6211 2.21 5 O 6878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 956": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1580": "NH1" <-> "NH2" Residue "A ARG 1640": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ARG 909": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1076": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 35876 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1466, 11571 Classifications: {'peptide': 1466} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1406} Chain breaks: 7 Chain: "B" Number of atoms: 9301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9301 Classifications: {'peptide': 1170} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1110} Chain breaks: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 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: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1075 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 472 Classifications: {'peptide': 64} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 60} 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: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2573 Classifications: {'peptide': 323} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 304} Chain breaks: 2 Chain: "N" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 125} Chain breaks: 3 Chain: "S" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 397 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 145 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna3p': 6} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 67.570 103.056 31.016 1.00 64.19 S ATOM 806 SG CYS A 105 69.516 102.164 29.309 1.00 63.96 S ATOM 1609 SG CYS A 233 71.552 105.447 31.007 1.00 63.59 S ATOM 1631 SG CYS A 236 69.020 104.799 28.795 1.00 61.24 S ATOM 461 SG CYS A 62 59.976 55.606 50.322 1.00 58.27 S ATOM 480 SG CYS A 65 62.226 54.447 50.681 1.00 56.92 S ATOM 535 SG CYS A 72 63.472 56.046 52.045 1.00 52.20 S ATOM 20152 SG CYS B1104 76.372 61.136 41.152 1.00 55.81 S ATOM 20178 SG CYS B1107 74.825 63.485 42.814 1.00 61.99 S ATOM 20325 SG CYS B1128 71.993 61.580 41.855 1.00 53.13 S ATOM 20353 SG CYS B1131 73.998 63.232 39.182 1.00 60.07 S ATOM 29091 SG CYS I 13 37.587 138.117 80.860 1.00 79.31 S ATOM 29211 SG CYS I 30 38.503 137.095 77.867 1.00 76.48 S ATOM 29532 SG CYS J 7 76.092 57.993 121.713 1.00 56.17 S ATOM 29555 SG CYS J 10 76.783 55.953 124.171 1.00 54.28 S ATOM 29835 SG CYS J 45 78.966 59.154 123.845 1.00 51.99 S ATOM 29841 SG CYS J 46 76.644 57.270 126.146 1.00 53.86 S ATOM 30867 SG CYS L 31 34.767 56.622 104.678 1.00 59.44 S ATOM 30887 SG CYS L 34 33.287 55.493 106.873 1.00 64.11 S ATOM 30991 SG CYS L 48 32.444 54.794 104.354 1.00 71.34 S ATOM 31014 SG CYS L 51 31.167 58.667 104.592 1.00 67.19 S Time building chain proxies: 19.01, per 1000 atoms: 0.53 Number of scatterers: 35876 At special positions: 0 Unit cell: (156.6, 168.75, 166.05, 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 6 29.99 S 171 16.00 P 51 15.00 O 6878 8.00 N 6211 7.00 C 22559 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: 14.28 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " 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 A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " 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 J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " 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 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 " Number of angles added : 27 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8254 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 54 sheets defined 35.9% alpha, 14.1% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 9.34 Creating SS restraints... Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.271A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.786A pdb=" N GLN A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 4.038A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 199 removed outlier: 3.581A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.906A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.783A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.539A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.055A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 398 removed outlier: 3.946A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.116A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.746A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.090A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.700A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 619 through 625 removed outlier: 3.847A pdb=" N ALA A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 671 through 682 removed outlier: 3.963A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 4.025A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.615A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.728A pdb=" N ASN A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 839 through 849 removed outlier: 3.875A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.657A pdb=" N ALA A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 883 removed outlier: 3.940A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 892 through 911 Processing helix chain 'A' and resid 923 through 932 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.968A pdb=" N GLN A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1025 removed outlier: 3.846A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 4.236A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 3.888A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 removed outlier: 4.051A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1109 removed outlier: 3.999A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A1109 " --> pdb=" O ARG A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.558A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 4.022A pdb=" N GLN A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.604A pdb=" N ILE A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 3.683A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 4.828A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.715A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 4.281A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1337 removed outlier: 4.026A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1484 through 1494 removed outlier: 3.852A pdb=" N ILE A1488 " --> pdb=" O LEU A1484 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1552 Processing helix chain 'A' and resid 1554 through 1572 removed outlier: 3.883A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.886A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.771A pdb=" N ASP A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1653 removed outlier: 3.701A pdb=" N SER A1653 " --> pdb=" O GLY A1650 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.261A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.780A pdb=" N ASN B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 300 through 315 removed outlier: 3.910A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 Processing helix chain 'B' and resid 345 through 356 removed outlier: 4.053A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 365 through 368 removed outlier: 3.869A pdb=" N GLN B 368 " --> pdb=" O ASP B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 369 through 386 Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.605A pdb=" N HIS B 399 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 400 " --> pdb=" O THR B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.833A pdb=" N LEU B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.030A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 598 through 614 removed outlier: 3.714A pdb=" N ASP B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.386A pdb=" N TYR B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 4.066A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.792A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.770A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.124A 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 790 through 797 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 Processing helix chain 'B' and resid 960 through 975 Processing helix chain 'B' and resid 991 through 996 Processing helix chain 'B' and resid 996 through 1004 removed outlier: 3.637A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.710A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1093 removed outlier: 3.704A pdb=" N GLN B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1192 removed outlier: 3.907A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) 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 102 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.182A 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 241 through 251 removed outlier: 3.653A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.620A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 removed outlier: 4.835A pdb=" N ILE C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 48 removed outlier: 4.104A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.402A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 73 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.614A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.978A pdb=" N THR G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.581A pdb=" N ASN H 131 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 133' Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 16 through 28 removed outlier: 4.522A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.624A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.986A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 141 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'M' and resid 209 through 214 removed outlier: 3.648A pdb=" N GLN M 214 " --> pdb=" O LYS M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 247 removed outlier: 4.084A pdb=" N LYS M 246 " --> pdb=" O TYR M 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU M 247 " --> pdb=" O VAL M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 250 No H-bonds generated for 'chain 'M' and resid 248 through 250' Processing helix chain 'M' and resid 252 through 254 No H-bonds generated for 'chain 'M' and resid 252 through 254' Processing helix chain 'M' and resid 255 through 274 removed outlier: 3.823A pdb=" N LEU M 261 " --> pdb=" O THR M 257 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 262 " --> pdb=" O LYS M 258 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER M 266 " --> pdb=" O LEU M 262 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 267 " --> pdb=" O TYR M 263 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY M 270 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL M 271 " --> pdb=" O LEU M 267 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR M 272 " --> pdb=" O LEU M 268 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 285 Processing helix chain 'M' and resid 291 through 303 removed outlier: 3.547A pdb=" N VAL M 295 " --> pdb=" O PRO M 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE M 298 " --> pdb=" O LEU M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 315 removed outlier: 3.967A pdb=" N LYS M 314 " --> pdb=" O PHE M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 340 removed outlier: 3.760A pdb=" N LEU M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS M 330 " --> pdb=" O ASP M 326 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR M 331 " --> pdb=" O LYS M 327 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE M 335 " --> pdb=" O TYR M 331 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE M 336 " --> pdb=" O ILE M 332 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET M 337 " --> pdb=" O LEU M 333 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS M 338 " --> pdb=" O ALA M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 353 Processing helix chain 'M' and resid 356 through 368 removed outlier: 3.513A pdb=" N PHE M 364 " --> pdb=" O VAL M 360 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG M 365 " --> pdb=" O VAL M 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL M 366 " --> pdb=" O SER M 362 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 383 removed outlier: 3.757A pdb=" N GLU M 380 " --> pdb=" O VAL M 376 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE M 382 " --> pdb=" O GLN M 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 389 removed outlier: 3.600A pdb=" N THR M 388 " --> pdb=" O PRO M 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 4.809A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B1199 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.698A pdb=" N ASP A 39 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 85 removed outlier: 10.490A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.535A pdb=" N LEU A 373 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.044A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.569A pdb=" N ASN A 590 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 507 through 510 removed outlier: 7.141A pdb=" N LYS A 576 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE A 536 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR A 578 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 751 removed outlier: 6.621A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB3, first strand: chain 'A' and resid 1504 through 1507 removed outlier: 4.277A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.574A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A1271 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A1295 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A1269 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1275 through 1276 Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.818A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.818A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY G 83 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.176A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 74 removed outlier: 3.836A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP B 143 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.725A pdb=" N VAL B 249 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.212A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.212A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 592 through 597 removed outlier: 4.215A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 639 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 629 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.715A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 769 through 775 removed outlier: 9.362A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 948 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B1031 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 771 " --> pdb=" O VAL B1031 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 769 " --> pdb=" O TYR B1033 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 824 Processing sheet with id=AD1, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD2, first strand: chain 'B' and resid 1099 through 1104 Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD4, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD5, first strand: chain 'C' and resid 41 through 43 removed outlier: 4.172A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 10.338A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.534A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 86 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 169 removed outlier: 6.886A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.960A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN C 158 " --> pdb=" O THR C 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.902A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 234 through 235 removed outlier: 3.531A pdb=" N ASN C 234 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 290 " --> pdb=" O ASN C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 61 removed outlier: 7.110A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 156 removed outlier: 4.237A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 132 through 135 Processing sheet with id=AE6, first strand: chain 'G' and resid 154 through 156 Processing sheet with id=AE7, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AE8, first strand: chain 'H' and resid 37 through 40 removed outlier: 6.805A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 100 through 103 removed outlier: 3.549A pdb=" N TYR H 102 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.510A pdb=" N ASP I 15 " --> pdb=" O CYS I 10 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.744A pdb=" N ASN K 102 " --> pdb=" O SER K 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 37 through 38 Processing sheet with id=AF5, first strand: chain 'N' and resid 30 through 31 removed outlier: 6.067A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 91 through 92 removed outlier: 4.054A pdb=" N GLN M 75 " --> pdb=" O PHE N 58 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE N 58 " --> pdb=" O GLN M 75 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE N 56 " --> pdb=" O VAL M 77 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 80 through 81 removed outlier: 3.534A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 344 through 345 removed outlier: 3.582A pdb=" N LYS M 372 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR M 396 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 88 through 92 1204 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 15.99 Time building geometry restraints manager: 14.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10784 1.34 - 1.45: 5304 1.45 - 1.57: 20205 1.57 - 1.69: 103 1.69 - 1.81: 272 Bond restraints: 36668 Sorted by residual: bond pdb=" N ASP K 57 " pdb=" CA ASP K 57 " ideal model delta sigma weight residual 1.458 1.659 -0.201 1.28e-02 6.10e+03 2.48e+02 bond pdb=" CA GLY A 445 " pdb=" C GLY A 445 " ideal model delta sigma weight residual 1.514 1.350 0.164 1.41e-02 5.03e+03 1.35e+02 bond pdb=" N GLY A 449 " pdb=" CA GLY A 449 " ideal model delta sigma weight residual 1.449 1.599 -0.150 1.45e-02 4.76e+03 1.07e+02 bond pdb=" N LYS B1064 " pdb=" CA LYS B1064 " ideal model delta sigma weight residual 1.456 1.567 -0.111 1.36e-02 5.41e+03 6.70e+01 bond pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 1.531 1.651 -0.120 1.59e-02 3.96e+03 5.72e+01 ... (remaining 36663 not shown) Histogram of bond angle deviations from ideal: 73.00 - 85.20: 3 85.20 - 97.41: 7 97.41 - 109.61: 4064 109.61 - 121.81: 37372 121.81 - 134.02: 8310 Bond angle restraints: 49756 Sorted by residual: angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" C ASP K 57 " ideal model delta sigma weight residual 112.45 73.00 39.45 1.39e+00 5.18e-01 8.06e+02 angle pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" C LYS B1064 " ideal model delta sigma weight residual 114.04 79.22 34.82 1.24e+00 6.50e-01 7.88e+02 angle pdb=" N GLY A 449 " pdb=" CA GLY A 449 " pdb=" C GLY A 449 " ideal model delta sigma weight residual 113.18 79.14 34.04 2.37e+00 1.78e-01 2.06e+02 angle pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.11 87.07 23.04 1.89e+00 2.80e-01 1.49e+02 angle pdb=" N GLY K 58 " pdb=" CA GLY K 58 " pdb=" C GLY K 58 " ideal model delta sigma weight residual 113.18 88.05 25.13 2.37e+00 1.78e-01 1.12e+02 ... (remaining 49751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 20352 17.65 - 35.30: 1383 35.30 - 52.95: 396 52.95 - 70.60: 62 70.60 - 88.25: 12 Dihedral angle restraints: 22205 sinusoidal: 9444 harmonic: 12761 Sorted by residual: dihedral pdb=" C ASP K 57 " pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual -122.60 -85.10 -37.50 0 2.50e+00 1.60e-01 2.25e+02 dihedral pdb=" C LYS B1064 " pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" CB LYS B1064 " ideal model delta harmonic sigma weight residual -122.60 -96.53 -26.07 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual 122.80 97.09 25.71 0 2.50e+00 1.60e-01 1.06e+02 ... (remaining 22202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 5575 0.290 - 0.579: 4 0.579 - 0.869: 0 0.869 - 1.158: 1 1.158 - 1.448: 1 Chirality restraints: 5581 Sorted by residual: chirality pdb=" CA ASP K 57 " pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CB ASP K 57 " both_signs ideal model delta sigma weight residual False 2.51 3.96 -1.45 2.00e-01 2.50e+01 5.24e+01 chirality pdb=" CA LYS B1064 " pdb=" N LYS B1064 " pdb=" C LYS B1064 " pdb=" CB LYS B1064 " both_signs ideal model delta sigma weight residual False 2.51 3.58 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CA LYS A 866 " pdb=" N LYS A 866 " pdb=" C LYS A 866 " pdb=" CB LYS A 866 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 5578 not shown) Planarity restraints: 6243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 58 " -0.030 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C GLY K 58 " 0.102 2.00e-02 2.50e+03 pdb=" O GLY K 58 " -0.038 2.00e-02 2.50e+03 pdb=" N THR K 59 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 247 " 0.030 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C GLY A 247 " -0.101 2.00e-02 2.50e+03 pdb=" O GLY A 247 " 0.038 2.00e-02 2.50e+03 pdb=" N PHE A 248 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 445 " 0.031 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" C GLY A 445 " -0.101 2.00e-02 2.50e+03 pdb=" O GLY A 445 " 0.034 2.00e-02 2.50e+03 pdb=" N ARG A 446 " 0.036 2.00e-02 2.50e+03 ... (remaining 6240 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 5 1.83 - 2.60: 395 2.60 - 3.37: 47401 3.37 - 4.13: 85460 4.13 - 4.90: 148357 Nonbonded interactions: 281618 Sorted by model distance: nonbonded pdb=" NZ LYS A 250 " pdb=" CD1 TYR A 314 " model vdw 1.067 3.420 nonbonded pdb=" OD2 ASP M 197 " pdb=" OE1 GLU M 199 " model vdw 1.529 3.040 nonbonded pdb=" NZ LYS A 250 " pdb=" CG TYR A 314 " model vdw 1.656 3.340 nonbonded pdb=" CA ALA M 369 " pdb=" SD MET M 397 " model vdw 1.783 3.830 nonbonded pdb=" CE LYS A 250 " pdb=" CD1 TYR A 314 " model vdw 1.829 3.740 ... (remaining 281613 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: 0.480 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: 5.210 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 101.000 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 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 : 0.003 0.201 36668 Z= 0.172 Angle : 0.688 39.452 49756 Z= 0.388 Chirality : 0.049 1.448 5581 Planarity : 0.004 0.074 6243 Dihedral : 12.897 88.250 13951 Min Nonbonded Distance : 1.067 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.99 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.31 % 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: -4.55 (0.10), residues: 4313 helix: -3.36 (0.09), residues: 1332 sheet: -2.45 (0.20), residues: 544 loop : -3.02 (0.11), residues: 2437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1253 time to evaluate : 4.340 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 outliers start: 79 outliers final: 16 residues processed: 1304 average time/residue: 0.5408 time to fit residues: 1100.9798 Evaluate side-chains 743 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 727 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3631 time to fit residues: 16.5063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 183 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 341 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 207 optimal weight: 0.2980 chunk 254 optimal weight: 6.9990 chunk 395 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 458 GLN A 470 HIS A 537 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN A 640 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 901 ASN A 939 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1062 HIS A1072 ASN A1191 GLN A1199 GLN A1323 HIS A1454 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 128 GLN B 213 HIS B 231 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN B 504 HIS B 598 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1082 HIS ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1171 ASN C 130 ASN D 17 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS H 134 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 36668 Z= 0.197 Angle : 0.672 10.514 49756 Z= 0.334 Chirality : 0.045 0.268 5581 Planarity : 0.005 0.096 6243 Dihedral : 10.316 89.261 5256 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.35 % Favored : 93.55 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -3.56 (0.11), residues: 4313 helix: -2.11 (0.11), residues: 1364 sheet: -2.02 (0.21), residues: 546 loop : -2.66 (0.11), residues: 2403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 971 time to evaluate : 4.692 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 outliers start: 10 outliers final: 2 residues processed: 977 average time/residue: 0.5222 time to fit residues: 821.3779 Evaluate side-chains 700 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 698 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5660 time to fit residues: 8.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 329 optimal weight: 0.0470 chunk 269 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 428 optimal weight: 9.9990 chunk 353 optimal weight: 8.9990 chunk 393 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 HIS ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 798 HIS ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 ASN A 939 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1072 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN A1320 GLN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 GLN B 87 ASN B 197 ASN B 231 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN B 770 ASN B 944 GLN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 ASN C 88 ASN C 143 ASN C 158 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 174 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN J 53 HIS L 66 GLN M 323 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 36668 Z= 0.322 Angle : 0.764 13.292 49756 Z= 0.392 Chirality : 0.048 0.301 5581 Planarity : 0.006 0.149 6243 Dihedral : 10.639 88.823 5256 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.26 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 4313 helix: -1.42 (0.13), residues: 1353 sheet: -1.77 (0.21), residues: 556 loop : -2.38 (0.12), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8626 Ramachandran restraints generated. 4313 Oldfield, 0 Emsley, 4313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 865 time to evaluate : 5.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 872 average time/residue: 0.5119 time to fit residues: 718.5479 Evaluate side-chains 623 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 621 time to evaluate : 3.952 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7466 time to fit residues: 7.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2255 > 50: distance: 76 - 196: 27.454 distance: 84 - 199: 22.303 distance: 124 - 129: 23.131 distance: 129 - 130: 27.196 distance: 129 - 135: 51.990 distance: 130 - 133: 40.380 distance: 131 - 132: 40.430 distance: 133 - 134: 33.394 distance: 134 - 135: 32.162 distance: 137 - 140: 14.849 distance: 138 - 142: 30.387 distance: 140 - 141: 26.165 distance: 142 - 143: 32.106 distance: 143 - 144: 30.470 distance: 143 - 146: 26.010 distance: 144 - 145: 37.593 distance: 144 - 149: 32.615 distance: 146 - 147: 13.095 distance: 146 - 148: 26.073 distance: 149 - 150: 18.476 distance: 150 - 151: 7.187 distance: 150 - 153: 16.984 distance: 151 - 152: 15.955 distance: 151 - 160: 21.341 distance: 153 - 154: 10.339 distance: 154 - 155: 12.993 distance: 155 - 156: 7.080 distance: 156 - 157: 8.443 distance: 157 - 159: 3.845 distance: 160 - 161: 16.931 distance: 162 - 163: 40.815 distance: 162 - 164: 4.113 distance: 164 - 165: 37.030 distance: 165 - 168: 55.070 distance: 166 - 173: 40.117 distance: 168 - 169: 33.226 distance: 169 - 170: 9.386 distance: 170 - 171: 57.071 distance: 170 - 172: 21.141 distance: 173 - 174: 6.390 distance: 174 - 175: 18.684 distance: 174 - 177: 26.390 distance: 175 - 176: 6.672 distance: 175 - 185: 19.076 distance: 177 - 178: 20.757 distance: 178 - 179: 43.371 distance: 178 - 180: 14.681 distance: 179 - 181: 5.482 distance: 180 - 182: 22.427 distance: 181 - 183: 37.787 distance: 182 - 183: 19.825 distance: 185 - 186: 30.786 distance: 185 - 191: 47.829 distance: 186 - 187: 19.914 distance: 186 - 189: 61.290 distance: 187 - 188: 45.411 distance: 187 - 192: 21.709 distance: 189 - 190: 34.053 distance: 190 - 191: 37.783 distance: 192 - 193: 44.217 distance: 193 - 194: 18.428 distance: 194 - 195: 35.130 distance: 194 - 196: 32.817 distance: 196 - 197: 7.939 distance: 197 - 198: 10.602 distance: 197 - 200: 21.739 distance: 198 - 199: 12.835 distance: 198 - 204: 22.938 distance: 200 - 201: 7.694 distance: 201 - 202: 16.474 distance: 201 - 203: 9.206