Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 15:56:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/10_2023/6ahu_9627_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/10_2023/6ahu_9627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/10_2023/6ahu_9627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/10_2023/6ahu_9627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/10_2023/6ahu_9627_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/10_2023/6ahu_9627_neut.pdb" } resolution = 3.66 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= 0.008 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 1 6.06 5 P 413 5.49 5 S 112 5.16 5 C 17011 2.51 5 N 5269 2.21 5 O 6580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "B ARG 831": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B ARG 1008": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 29386 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 7295 Classifications: {'RNA': 341} Modifications used: {'rna2p_pur': 28, 'rna2p_pyr': 20, 'rna3p_pur': 152, 'rna3p_pyr': 141} Link IDs: {'rna2p': 48, 'rna3p': 292} Chain: "B" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6142 Classifications: {'peptide': 774} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 723} Chain breaks: 4 Chain: "C" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1448 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain breaks: 1 Chain: "D" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "E" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1197 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 10, 'TRANS': 118} Chain breaks: 2 Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1021 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1824 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "J" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1905 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "K" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 979 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2939 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 341} Chain: "T" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1535 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 61} Chain: "K" 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 24659 SG CYS K 92 68.808 76.740 55.775 1.00101.00 S Time building chain proxies: 15.47, per 1000 atoms: 0.53 Number of scatterers: 29386 At special positions: 0 Unit cell: (146.52, 129.36, 200.64, 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 1 29.99 S 112 16.00 P 413 15.00 O 6580 8.00 N 5269 7.00 C 17011 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: 13.33 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 92 " 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 23 sheets defined 36.5% alpha, 16.9% beta 85 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 9.94 Creating SS restraints... Processing helix chain 'B' and resid 100 through 127 removed outlier: 3.766A pdb=" N THR B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.949A pdb=" N ARG B 140 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.106A pdb=" N ARG B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.771A pdb=" N GLU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 204 through 211 removed outlier: 4.105A pdb=" N LYS B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 211 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 4.074A pdb=" N TYR B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.916A pdb=" N CYS B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.590A pdb=" N LEU B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.717A pdb=" N THR B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 removed outlier: 4.141A pdb=" N VAL B 455 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 456' Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.576A pdb=" N ILE B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 490 removed outlier: 3.612A pdb=" N VAL B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 removed outlier: 3.655A pdb=" N VAL B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 542 " --> pdb=" O GLN B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.594A pdb=" N TRP B 554 " --> pdb=" O SER B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 555 through 565 removed outlier: 3.509A pdb=" N CYS B 559 " --> pdb=" O ASN B 555 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 580 removed outlier: 3.642A pdb=" N MET B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Proline residue: B 633 - end of helix removed outlier: 3.922A pdb=" N TYR B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 4.299A pdb=" N SER B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 653 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.603A pdb=" N LEU B 680 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 682 " --> pdb=" O LYS B 678 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 720 removed outlier: 3.878A pdb=" N THR B 712 " --> pdb=" O TRP B 708 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 716 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL B 719 " --> pdb=" O TRP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 820 removed outlier: 3.543A pdb=" N ALA B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B 818 " --> pdb=" O GLN B 814 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS B 819 " --> pdb=" O LEU B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 removed outlier: 3.767A pdb=" N CYS B 845 " --> pdb=" O THR B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 889 removed outlier: 4.014A pdb=" N PHE B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 884 " --> pdb=" O LYS B 880 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 885 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 886 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 904 No H-bonds generated for 'chain 'B' and resid 902 through 904' Processing helix chain 'B' and resid 905 through 920 removed outlier: 3.918A pdb=" N LEU B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 910 " --> pdb=" O SER B 906 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 920 " --> pdb=" O LYS B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 957 removed outlier: 4.012A pdb=" N VAL B 955 " --> pdb=" O PRO B 951 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 951 through 957' Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.623A pdb=" N MET B 993 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 996 " --> pdb=" O ASP B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.662A pdb=" N GLN C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 54 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.549A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.641A pdb=" N ARG C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.649A pdb=" N GLN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.576A pdb=" N LEU C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.854A pdb=" N GLN D 94 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 112 removed outlier: 3.775A pdb=" N ARG D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.622A pdb=" N LEU E 22 " --> pdb=" O PRO E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 41 removed outlier: 3.613A pdb=" N ARG E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 73 through 81 removed outlier: 4.293A pdb=" N VAL E 77 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 removed outlier: 3.572A pdb=" N LEU E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 124 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.524A pdb=" N GLU E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.219A pdb=" N PHE F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP F 30 " --> pdb=" O GLY F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 59 removed outlier: 3.769A pdb=" N ALA F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 75 Processing helix chain 'F' and resid 76 through 86 removed outlier: 3.776A pdb=" N LEU F 84 " --> pdb=" O CYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 77 through 93 removed outlier: 3.625A pdb=" N ILE G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN G 83 " --> pdb=" O ASN G 79 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 52 removed outlier: 3.605A pdb=" N LYS H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 58 removed outlier: 3.824A pdb=" N ALA H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 89 removed outlier: 3.717A pdb=" N TRP H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'I' and resid 14 through 29 removed outlier: 3.586A pdb=" N LEU I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 83 through 91 removed outlier: 3.658A pdb=" N CYS I 87 " --> pdb=" O ASP I 83 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN I 88 " --> pdb=" O PRO I 84 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL I 89 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG I 91 " --> pdb=" O CYS I 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 91' Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.980A pdb=" N ARG I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 97' Processing helix chain 'I' and resid 109 through 119 removed outlier: 3.712A pdb=" N ILE I 115 " --> pdb=" O LYS I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.692A pdb=" N ILE I 142 " --> pdb=" O LYS I 138 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP I 147 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 181 removed outlier: 4.104A pdb=" N TYR I 168 " --> pdb=" O THR I 164 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR I 169 " --> pdb=" O MET I 165 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 173 " --> pdb=" O THR I 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU I 174 " --> pdb=" O ILE I 170 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS I 181 " --> pdb=" O MET I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 210 removed outlier: 3.660A pdb=" N LEU I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 237 removed outlier: 3.578A pdb=" N SER I 222 " --> pdb=" O LYS I 218 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN I 224 " --> pdb=" O ALA I 220 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N CYS I 225 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA I 228 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU I 229 " --> pdb=" O CYS I 225 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG I 235 " --> pdb=" O HIS I 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 3.634A pdb=" N GLY J 20 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU J 28 " --> pdb=" O THR J 24 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 removed outlier: 3.638A pdb=" N CYS J 87 " --> pdb=" O ASP J 83 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN J 88 " --> pdb=" O PRO J 84 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU J 90 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 109 through 119 removed outlier: 3.555A pdb=" N HIS J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 149 removed outlier: 3.675A pdb=" N VAL J 144 " --> pdb=" O PRO J 140 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA J 145 " --> pdb=" O PRO J 141 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP J 147 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 178 removed outlier: 3.961A pdb=" N TYR J 168 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE J 170 " --> pdb=" O ARG J 166 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 172 " --> pdb=" O TYR J 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 210 removed outlier: 3.646A pdb=" N ALA J 204 " --> pdb=" O PRO J 200 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN J 205 " --> pdb=" O TYR J 201 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 237 removed outlier: 3.758A pdb=" N ALA J 219 " --> pdb=" O SER J 215 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL J 221 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER J 222 " --> pdb=" O LYS J 218 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN J 224 " --> pdb=" O ALA J 220 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS J 225 " --> pdb=" O VAL J 221 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU J 233 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 28 removed outlier: 4.214A pdb=" N ALA K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE K 11 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG K 13 " --> pdb=" O GLU K 9 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN K 15 " --> pdb=" O PHE K 11 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS K 22 " --> pdb=" O TYR K 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN K 27 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 49 Processing helix chain 'K' and resid 54 through 59 Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.738A pdb=" N LEU K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'L' and resid 30 through 35 Processing helix chain 'L' and resid 53 through 61 removed outlier: 3.558A pdb=" N MET L 61 " --> pdb=" O LYS L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.693A pdb=" N GLU L 125 " --> pdb=" O LYS L 121 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY L 128 " --> pdb=" O TYR L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 154 Processing helix chain 'L' and resid 159 through 171 removed outlier: 3.527A pdb=" N GLU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU L 171 " --> pdb=" O TRP L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 197 removed outlier: 3.945A pdb=" N TYR L 196 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 249 removed outlier: 3.606A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP L 242 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY L 245 " --> pdb=" O PHE L 241 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA L 246 " --> pdb=" O ASP L 242 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 247 " --> pdb=" O TRP L 243 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE L 248 " --> pdb=" O LEU L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.641A pdb=" N ILE L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 303 removed outlier: 4.467A pdb=" N GLU L 303 " --> pdb=" O TYR L 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 300 through 303' Processing sheet with id=AA1, first strand: chain 'B' and resid 212 through 215 removed outlier: 4.264A pdb=" N ARG B 225 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 215 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY B 223 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 243 through 244 removed outlier: 3.524A pdb=" N LEU B 507 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS B 448 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 252 through 256 removed outlier: 3.558A pdb=" N TRP B 413 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 289 through 294 removed outlier: 3.788A pdb=" N THR B 309 " --> pdb=" O TRP B 330 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 330 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 311 " --> pdb=" O TRP B 328 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP B 328 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS B 313 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 326 " --> pdb=" O LYS B 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.259A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B1006 " --> pdb=" O CYS B 876 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 875 " --> pdb=" O LEU B 964 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR B 962 " --> pdb=" O VAL B 877 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.259A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 861 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY B 979 " --> pdb=" O LEU B 863 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 980 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP B 971 " --> pdb=" O GLU B 980 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 25 Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 115 removed outlier: 4.036A pdb=" N GLN C 112 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE C 182 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 131 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL C 156 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 174 through 178 removed outlier: 3.929A pdb=" N ILE D 177 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE D 165 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE D 140 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU D 187 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL D 142 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR D 185 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 144 " --> pdb=" O VAL D 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 55 through 59 removed outlier: 6.919A pdb=" N VAL E 55 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG E 68 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR E 57 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E 59 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE E 64 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 9 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 10 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU E 101 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU E 12 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASN E 99 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'F' and resid 34 through 35 removed outlier: 6.637A pdb=" N GLY F 34 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 38 removed outlier: 6.482A pdb=" N ASN G 35 " --> pdb=" O TYR G 70 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N HIS G 72 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE G 37 " --> pdb=" O HIS G 72 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE G 69 " --> pdb=" O VAL G 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 103 through 109 removed outlier: 3.510A pdb=" N SER G 103 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA G 129 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP G 109 " --> pdb=" O ARG G 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 9 through 14 removed outlier: 3.622A pdb=" N GLU H 9 " --> pdb=" O LYS L 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS L 19 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL H 11 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU L 14 " --> pdb=" O VAL L 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL L 16 " --> pdb=" O MET L 353 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR L 349 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP L 348 " --> pdb=" O PHE L 344 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TRP L 309 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE L 44 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS L 279 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE L 46 " --> pdb=" O TYR L 277 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER L 270 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL L 272 " --> pdb=" O GLN L 218 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN L 218 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA L 274 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.643A pdb=" N ILE H 77 " --> pdb=" O HIS H 20 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN H 106 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS H 25 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL H 104 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU H 27 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE H 102 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.741A pdb=" N ALA I 34 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL I 33 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ARG I 76 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE I 35 " --> pdb=" O ARG I 76 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR I 78 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL I 39 " --> pdb=" O ILE I 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.741A pdb=" N ALA I 34 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL I 33 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ARG I 76 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE I 35 " --> pdb=" O ARG I 76 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR I 78 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N VAL I 102 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR I 75 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ALA I 104 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU I 77 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE I 106 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 79 " --> pdb=" O PHE I 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 34 through 35 removed outlier: 5.934A pdb=" N ILE J 35 " --> pdb=" O ARG J 76 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR J 78 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL J 39 " --> pdb=" O ILE J 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 34 through 35 removed outlier: 5.934A pdb=" N ILE J 35 " --> pdb=" O ARG J 76 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR J 78 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR J 75 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ALA J 104 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU J 77 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE J 106 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE J 79 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL J 103 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N CYS J 126 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL J 105 " --> pdb=" O CYS J 126 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL J 125 " --> pdb=" O GLU J 153 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL J 155 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 188 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 76 through 81 removed outlier: 3.659A pdb=" N THR K 76 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 131 through 133 removed outlier: 4.085A pdb=" N ALA L 94 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER L 91 " --> pdb=" O HIS L 184 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA L 182 " --> pdb=" O TYR L 93 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L 95 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE L 177 " --> pdb=" O ASN L 71 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN L 201 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 322 through 323 610 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 215 hydrogen bonds 386 hydrogen bond angles 0 basepair planarities 85 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 12.37 Time building geometry restraints manager: 14.19 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: 7978 1.34 - 1.46: 9164 1.46 - 1.58: 12734 1.58 - 1.70: 824 1.70 - 1.83: 147 Bond restraints: 30847 Sorted by residual: bond pdb=" C VAL B 659 " pdb=" N PRO B 660 " ideal model delta sigma weight residual 1.334 1.404 -0.070 2.34e-02 1.83e+03 8.91e+00 bond pdb=" C ASP B 406 " pdb=" N PRO B 407 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.63e+00 bond pdb=" C LYS D 118 " pdb=" N PRO D 119 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.36e+00 bond pdb=" C ALA B 832 " pdb=" N PRO B 833 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.92e+00 bond pdb=" C ASN H 15 " pdb=" N PRO H 16 " ideal model delta sigma weight residual 1.332 1.350 -0.017 8.20e-03 1.49e+04 4.47e+00 ... (remaining 30842 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.41: 3038 106.41 - 113.35: 17367 113.35 - 120.30: 11609 120.30 - 127.24: 10681 127.24 - 134.18: 1058 Bond angle restraints: 43753 Sorted by residual: angle pdb=" C LEU K 69 " pdb=" N VAL K 70 " pdb=" CA VAL K 70 " ideal model delta sigma weight residual 120.24 124.86 -4.62 6.30e-01 2.52e+00 5.38e+01 angle pdb=" C ARG G 23 " pdb=" N LYS G 24 " pdb=" CA LYS G 24 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C ARG G 25 " pdb=" N LEU G 26 " pdb=" CA LEU G 26 " ideal model delta sigma weight residual 120.58 127.45 -6.87 1.32e+00 5.74e-01 2.71e+01 angle pdb=" C THR E 106 " pdb=" N ILE E 107 " pdb=" CA ILE E 107 " ideal model delta sigma weight residual 120.53 127.69 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" CA LEU H 92 " pdb=" CB LEU H 92 " pdb=" CG LEU H 92 " ideal model delta sigma weight residual 116.30 132.91 -16.61 3.50e+00 8.16e-02 2.25e+01 ... (remaining 43748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.64: 17349 30.64 - 61.27: 396 61.27 - 91.91: 44 91.91 - 122.55: 7 122.55 - 153.19: 2 Dihedral angle restraints: 17798 sinusoidal: 10247 harmonic: 7551 Sorted by residual: dihedral pdb=" CA GLU D 171 " pdb=" C GLU D 171 " pdb=" N ASP D 172 " pdb=" CA ASP D 172 " ideal model delta harmonic sigma weight residual 180.00 -134.69 -45.31 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA PRO B 463 " pdb=" C PRO B 463 " pdb=" N HIS B 464 " pdb=" CA HIS B 464 " ideal model delta harmonic sigma weight residual 180.00 -135.69 -44.31 0 5.00e+00 4.00e-02 7.85e+01 dihedral pdb=" CA LYS D 170 " pdb=" C LYS D 170 " pdb=" N GLU D 171 " pdb=" CA GLU D 171 " ideal model delta harmonic sigma weight residual -180.00 -141.70 -38.30 0 5.00e+00 4.00e-02 5.87e+01 ... (remaining 17795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4970 0.089 - 0.178: 298 0.178 - 0.266: 12 0.266 - 0.355: 2 0.355 - 0.444: 1 Chirality restraints: 5283 Sorted by residual: chirality pdb=" CB ILE B 499 " pdb=" CA ILE B 499 " pdb=" CG1 ILE B 499 " pdb=" CG2 ILE B 499 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C3' G A 261 " pdb=" C4' G A 261 " pdb=" O3' G A 261 " pdb=" C2' G A 261 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C3' C A 326 " pdb=" C4' C A 326 " pdb=" O3' C A 326 " pdb=" C2' C A 326 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 5280 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 463 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C PRO B 463 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO B 463 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS B 464 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 30 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO G 31 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 31 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 31 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 170 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C LYS D 170 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS D 170 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU D 171 " -0.015 2.00e-02 2.50e+03 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 7234 2.81 - 3.33: 23352 3.33 - 3.85: 50440 3.85 - 4.38: 58503 4.38 - 4.90: 88564 Nonbonded interactions: 228093 Sorted by model distance: nonbonded pdb=" OH TYR J 30 " pdb=" O ARG J 198 " model vdw 2.284 2.440 nonbonded pdb=" O TRP H 86 " pdb=" OG1 THR H 90 " model vdw 2.291 2.440 nonbonded pdb=" O ILE B 493 " pdb=" NH2 ARG G 25 " model vdw 2.294 2.520 nonbonded pdb=" O2' A A 32 " pdb=" O VAL G 39 " model vdw 2.301 2.440 nonbonded pdb=" O2' A T 58 " pdb=" OP2 A T 60 " model vdw 2.322 2.440 ... (remaining 228088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'J' and resid 2 through 237) } 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=0.50 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: 0.740 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: 5.470 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 87.130 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 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: 97.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 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 0.070 30847 Z= 0.202 Angle : 0.770 16.606 43753 Z= 0.422 Chirality : 0.041 0.444 5283 Planarity : 0.006 0.066 4022 Dihedral : 11.492 153.187 12894 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.85 % Favored : 89.92 % Rotamer: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.16 % 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: -5.26 (0.12), residues: 2559 helix: -4.73 (0.06), residues: 738 sheet: -1.92 (0.21), residues: 512 loop : -3.42 (0.13), residues: 1309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 925 time to evaluate : 2.900 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 outliers start: 2 outliers final: 0 residues processed: 927 average time/residue: 0.5030 time to fit residues: 688.6090 Evaluate side-chains 434 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 2.851 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 119 optimal weight: 0.2980 chunk 232 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS B 958 HIS ** B 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS E 75 GLN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 148 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN I 27 HIS I 88 ASN I 143 ASN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 HIS J 143 ASN J 231 HIS ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS L 39 ASN L 203 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 337 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 30847 Z= 0.293 Angle : 0.736 15.151 43753 Z= 0.372 Chirality : 0.042 0.312 5283 Planarity : 0.006 0.065 4022 Dihedral : 12.453 155.266 7781 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.82 % Favored : 89.10 % Rotamer: Outliers : 4.67 % Allowed : 12.61 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.07 (0.14), residues: 2559 helix: -2.81 (0.13), residues: 793 sheet: -1.51 (0.22), residues: 507 loop : -3.16 (0.15), residues: 1259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 474 time to evaluate : 2.777 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 outliers start: 106 outliers final: 70 residues processed: 545 average time/residue: 0.4306 time to fit residues: 364.7490 Evaluate side-chains 438 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 368 time to evaluate : 2.700 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 70 outliers final: 1 residues processed: 70 average time/residue: 0.2845 time to fit residues: 39.5081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 69.3517 > 50: distance: 35 - 40: 31.672 distance: 40 - 41: 45.651 distance: 41 - 42: 47.828 distance: 41 - 44: 29.435 distance: 42 - 43: 45.954 distance: 42 - 48: 42.850 distance: 44 - 45: 25.143 distance: 45 - 46: 17.594 distance: 45 - 47: 15.352 distance: 48 - 49: 35.919 distance: 48 - 54: 3.013 distance: 49 - 50: 55.831 distance: 49 - 52: 36.635 distance: 50 - 51: 55.749 distance: 50 - 55: 55.797 distance: 52 - 53: 3.649 distance: 53 - 54: 5.188 distance: 55 - 56: 27.858 distance: 56 - 57: 30.849 distance: 56 - 59: 38.449 distance: 57 - 58: 22.082 distance: 57 - 63: 57.862 distance: 59 - 60: 39.943 distance: 59 - 61: 48.272 distance: 60 - 62: 26.228 distance: 63 - 64: 39.541 distance: 64 - 65: 40.225 distance: 64 - 67: 30.603 distance: 65 - 66: 53.366 distance: 65 - 70: 43.515 distance: 67 - 68: 44.226 distance: 67 - 69: 27.383 distance: 70 - 71: 19.389 distance: 71 - 72: 45.669 distance: 71 - 74: 16.889 distance: 72 - 73: 41.803 distance: 72 - 79: 47.815 distance: 74 - 75: 45.088 distance: 75 - 76: 50.370 distance: 76 - 77: 50.329 distance: 76 - 78: 21.409 distance: 79 - 80: 48.768 distance: 81 - 82: 20.996 distance: 81 - 83: 40.059 distance: 83 - 84: 29.933 distance: 84 - 85: 20.670 distance: 84 - 87: 23.469 distance: 85 - 86: 45.980 distance: 87 - 88: 22.155 distance: 88 - 89: 13.374 distance: 89 - 90: 21.144 distance: 90 - 91: 26.654 distance: 92 - 93: 57.707 distance: 93 - 94: 41.328 distance: 93 - 96: 15.597 distance: 94 - 95: 4.561 distance: 94 - 98: 16.113 distance: 96 - 97: 39.072 distance: 98 - 99: 15.863 distance: 99 - 100: 20.705 distance: 99 - 102: 28.943 distance: 100 - 101: 42.288 distance: 100 - 109: 60.304 distance: 102 - 103: 8.573 distance: 103 - 104: 27.160 distance: 105 - 106: 15.765 distance: 106 - 107: 9.560 distance: 106 - 108: 23.965 distance: 109 - 110: 58.003 distance: 110 - 111: 55.763 distance: 110 - 113: 65.914 distance: 111 - 112: 27.275 distance: 111 - 116: 34.344 distance: 113 - 114: 36.778