Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 16:17:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoe_28373/08_2023/8eoe_28373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoe_28373/08_2023/8eoe_28373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoe_28373/08_2023/8eoe_28373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoe_28373/08_2023/8eoe_28373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoe_28373/08_2023/8eoe_28373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoe_28373/08_2023/8eoe_28373.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 88 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 15585 2.51 5 N 4497 2.21 5 O 5039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 25301 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8549 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1043} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9919 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1208} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} bond proxies already assigned to first conformer: 877 Chain: "T" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 772 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "N" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 713 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 2 Chain: "R" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 329 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19089 SG CYS D 891 76.718 24.605 87.413 1.00 62.79 S ATOM 19656 SG CYS D 968 75.454 27.919 88.920 1.00 58.47 S ATOM 19698 SG CYS D 975 76.959 27.807 85.389 1.00 56.89 S ATOM 19716 SG CYS D 978 73.604 26.370 86.027 1.00 57.17 S ATOM 12527 SG CYS D 60 108.742 79.963 115.702 1.00 98.93 S ATOM 12545 SG CYS D 62 110.825 82.452 117.535 1.00108.10 S ATOM 12654 SG CYS D 75 111.202 78.681 118.251 1.00 98.26 S ATOM 12680 SG CYS D 78 108.181 80.701 119.486 1.00102.05 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU G 15 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU G 15 " occ=0.50 Time building chain proxies: 13.60, per 1000 atoms: 0.54 Number of scatterers: 25301 At special positions: 0 Unit cell: (127.89, 141.81, 199.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 88 15.00 Mg 1 11.99 O 5039 8.00 N 4497 7.00 C 15585 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: 10.25 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 968 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 75 " Number of angles added : 12 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5564 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 44 sheets defined 35.3% alpha, 13.6% beta 35 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 8.60 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.675A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.653A pdb=" N LEU B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.936A pdb=" N ILE B 110 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.596A pdb=" N ALA B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.290A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.795A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.704A pdb=" N GLU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 226 through 229 Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.219A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.690A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.565A pdb=" N LYS C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 removed outlier: 4.026A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.739A pdb=" N ASN C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.622A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.969A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 removed outlier: 3.897A pdb=" N ARG C 538 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS C 539 " --> pdb=" O GLU C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 539' Processing helix chain 'C' and resid 582 through 587 removed outlier: 4.569A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.575A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.500A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.568A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 637' Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.633A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.564A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 removed outlier: 3.549A pdb=" N LEU C 985 " --> pdb=" O GLN C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.505A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.808A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.188A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 4.193A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.505A pdb=" N PHE D 7 " --> pdb=" O VAL D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.604A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 147 through 184 Processing helix chain 'D' and resid 191 through 228 Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.531A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.590A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.739A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.766A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 342 through 359 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.746A pdb=" N LEU D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 402 through 406' Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.659A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.830A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 removed outlier: 3.665A pdb=" N THR D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.602A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.884A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 763 removed outlier: 4.025A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 779 Processing helix chain 'D' and resid 780 through 793 removed outlier: 3.773A pdb=" N GLU D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 804 removed outlier: 4.058A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 819 Processing helix chain 'D' and resid 845 through 853 removed outlier: 3.717A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 866 removed outlier: 4.008A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.540A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 880 " --> pdb=" O ARG D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.542A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1004 removed outlier: 3.711A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1119 through 1126 removed outlier: 3.828A pdb=" N ARG D1123 " --> pdb=" O HIS D1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.746A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN D1139 " --> pdb=" O VAL D1135 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.176A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 removed outlier: 3.653A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.629A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.629A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 72 removed outlier: 3.743A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'G' and resid 14 through 28 removed outlier: 4.298A pdb=" N GLU G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 79 removed outlier: 3.680A pdb=" N TYR G 77 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.636A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 192 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.726A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.848A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.967A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.618A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.640A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 191 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 177 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 100 removed outlier: 6.564A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 174 removed outlier: 6.939A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.601A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.623A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.319A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'C' and resid 190 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.205A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.627A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.661A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.915A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.502A pdb=" N GLY C 893 " --> pdb=" O LEU C 885 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.636A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.601A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.506A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.917A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.811A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.619A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.540A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 443 through 444 removed outlier: 6.173A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.608A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE3, first strand: chain 'D' and resid 1061 through 1063 removed outlier: 3.617A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE6, first strand: chain 'G' and resid 5 through 6 removed outlier: 7.139A pdb=" N GLU G 68 " --> pdb=" O PHE G 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 43 through 44 removed outlier: 4.307A pdb=" N LYS G 58 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 48 through 49 790 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 11.97 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7512 1.33 - 1.45: 3902 1.45 - 1.57: 14178 1.57 - 1.69: 171 1.69 - 1.81: 157 Bond restraints: 25920 Sorted by residual: bond pdb=" CB PRO D1006 " pdb=" CG PRO D1006 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.40e+00 bond pdb=" C3' DC T 32 " pdb=" O3' DC T 32 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.10e+00 bond pdb=" C LEU D1028 " pdb=" N PRO D1029 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.66e+00 bond pdb=" N LEU D 184 " pdb=" CA LEU D 184 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.31e+00 bond pdb=" C3' DG N 5 " pdb=" O3' DG N 5 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.26e+00 ... (remaining 25915 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.71: 1067 105.71 - 112.80: 13929 112.80 - 119.88: 8878 119.88 - 126.96: 11169 126.96 - 134.04: 451 Bond angle restraints: 35494 Sorted by residual: angle pdb=" O3' DC T 32 " pdb=" C3' DC T 32 " pdb=" C2' DC T 32 " ideal model delta sigma weight residual 111.50 120.13 -8.63 1.50e+00 4.44e-01 3.31e+01 angle pdb=" C ASP G 73 " pdb=" N ASP G 74 " pdb=" CA ASP G 74 " ideal model delta sigma weight residual 120.31 128.71 -8.40 1.52e+00 4.33e-01 3.05e+01 angle pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 112.29 107.33 4.96 9.40e-01 1.13e+00 2.79e+01 angle pdb=" C4' DC T 32 " pdb=" C3' DC T 32 " pdb=" O3' DC T 32 " ideal model delta sigma weight residual 110.00 115.70 -5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" N TYR D 872 " pdb=" CA TYR D 872 " pdb=" C TYR D 872 " ideal model delta sigma weight residual 112.90 108.15 4.75 1.31e+00 5.83e-01 1.31e+01 ... (remaining 35489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 14172 35.35 - 70.70: 1314 70.70 - 106.05: 44 106.05 - 141.40: 3 141.40 - 176.75: 2 Dihedral angle restraints: 15535 sinusoidal: 6871 harmonic: 8664 Sorted by residual: dihedral pdb=" O4' A R 21 " pdb=" C1' A R 21 " pdb=" N9 A R 21 " pdb=" C4 A R 21 " ideal model delta sinusoidal sigma weight residual 254.00 168.28 85.72 1 1.70e+01 3.46e-03 3.07e+01 dihedral pdb=" O4' C R 20 " pdb=" C1' C R 20 " pdb=" N1 C R 20 " pdb=" C2 C R 20 " ideal model delta sinusoidal sigma weight residual -128.00 -67.21 -60.79 1 1.70e+01 3.46e-03 1.70e+01 dihedral pdb=" C4' DC T 23 " pdb=" C3' DC T 23 " pdb=" O3' DC T 23 " pdb=" P DA T 24 " ideal model delta sinusoidal sigma weight residual 220.00 43.25 176.75 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 15532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4038 0.137 - 0.275: 12 0.275 - 0.412: 0 0.412 - 0.549: 0 0.549 - 0.686: 1 Chirality restraints: 4051 Sorted by residual: chirality pdb=" C3' DC T 32 " pdb=" C4' DC T 32 " pdb=" O3' DC T 32 " pdb=" C2' DC T 32 " both_signs ideal model delta sigma weight residual False -2.66 -1.97 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C3' DG T 31 " pdb=" C4' DG T 31 " pdb=" O3' DG T 31 " pdb=" C2' DG T 31 " both_signs ideal model delta sigma weight residual False -2.66 -2.41 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" P DC N 6 " pdb=" OP1 DC N 6 " pdb=" OP2 DC N 6 " pdb=" O5' DC N 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4048 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 82 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 143 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C MET D 143 " 0.071 2.00e-02 2.50e+03 pdb=" O MET D 143 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG D 144 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 197 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C VAL D 197 " 0.069 2.00e-02 2.50e+03 pdb=" O VAL D 197 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG D 198 " -0.024 2.00e-02 2.50e+03 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 118 2.57 - 3.15: 18076 3.15 - 3.73: 36827 3.73 - 4.32: 51266 4.32 - 4.90: 87462 Nonbonded interactions: 193749 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 1.984 2.170 nonbonded pdb=" O3' A R 30 " pdb="MG MG D2001 " model vdw 2.041 2.170 nonbonded pdb=" O ILE D1210 " pdb=" OG SER D1214 " model vdw 2.163 2.440 nonbonded pdb=" OH TYR C 278 " pdb=" OE1 GLU C 285 " model vdw 2.223 2.440 nonbonded pdb=" O THR C 433 " pdb=" OG1 THR C 433 " model vdw 2.237 2.440 ... (remaining 193744 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 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 1 through 226) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 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: 0.020 Extract box with map and model: 15.620 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 77.440 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 0.078 25920 Z= 0.210 Angle : 0.629 8.630 35494 Z= 0.353 Chirality : 0.046 0.686 4051 Planarity : 0.006 0.104 4358 Dihedral : 22.186 176.754 9971 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.44 % Rotamer Outliers : 17.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.14 (0.14), residues: 3017 helix: -1.65 (0.16), residues: 984 sheet: -1.64 (0.26), residues: 401 loop : -2.53 (0.13), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 440 poor density : 160 time to evaluate : 3.138 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 outliers start: 440 outliers final: 105 residues processed: 556 average time/residue: 0.4469 time to fit residues: 369.3226 Evaluate side-chains 201 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 96 time to evaluate : 2.968 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 1 residues processed: 105 average time/residue: 0.3490 time to fit residues: 68.6594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 20.0000 chunk 232 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 278 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 61 HIS A 79 ASN A 152 ASN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS C 323 HIS C 435 GLN C 610 ASN ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN C 751 HIS C1062 GLN C1066 GLN C1077 GLN C1111 ASN C1129 GLN D 5 ASN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 262 GLN D 352 ASN D 368 ASN D 410 GLN D 505 HIS D 525 HIS D 533 ASN D 564 ASN D 657 GLN D 693 GLN D 759 GLN D 852 ASN D 882 GLN D1109 GLN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1273 GLN E 63 GLN G 9 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 25920 Z= 0.467 Angle : 0.697 10.125 35494 Z= 0.367 Chirality : 0.047 0.243 4051 Planarity : 0.006 0.071 4358 Dihedral : 16.416 174.447 4215 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.40 % Favored : 93.50 % Rotamer Outliers : 4.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.31 (0.14), residues: 3017 helix: -0.56 (0.16), residues: 1009 sheet: -1.23 (0.25), residues: 431 loop : -2.32 (0.14), residues: 1577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 102 time to evaluate : 2.890 Fit side-chains outliers start: 116 outliers final: 40 residues processed: 210 average time/residue: 0.3660 time to fit residues: 124.8526 Evaluate side-chains 137 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 3.051 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2274 time to fit residues: 20.9739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 543 GLN ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 25920 Z= 0.215 Angle : 0.554 8.943 35494 Z= 0.292 Chirality : 0.042 0.158 4051 Planarity : 0.005 0.055 4358 Dihedral : 16.165 177.199 4215 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.37 % Favored : 94.56 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.65 (0.15), residues: 3017 helix: 0.18 (0.17), residues: 994 sheet: -0.77 (0.26), residues: 420 loop : -2.08 (0.14), residues: 1603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 101 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 17 residues processed: 152 average time/residue: 0.4071 time to fit residues: 98.7411 Evaluate side-chains 110 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 3.073 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2330 time to fit residues: 11.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 187 optimal weight: 0.3980 chunk 280 optimal weight: 0.8980 chunk 296 optimal weight: 5.9990 chunk 146 optimal weight: 0.2980 chunk 265 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 141 ASN C 479 HIS ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 25920 Z= 0.199 Angle : 0.529 9.727 35494 Z= 0.277 Chirality : 0.042 0.164 4051 Planarity : 0.004 0.059 4358 Dihedral : 15.971 177.885 4215 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.96 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.27 (0.15), residues: 3017 helix: 0.58 (0.17), residues: 999 sheet: -0.57 (0.26), residues: 421 loop : -1.93 (0.14), residues: 1597 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 94 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 17 residues processed: 146 average time/residue: 0.4388 time to fit residues: 104.2837 Evaluate side-chains 109 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 3.027 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2560 time to fit residues: 12.0080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 220 optimal weight: 0.0060 chunk 122 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 891 ASN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 25920 Z= 0.394 Angle : 0.585 9.338 35494 Z= 0.308 Chirality : 0.044 0.154 4051 Planarity : 0.004 0.059 4358 Dihedral : 15.941 176.862 4215 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.07 % Favored : 93.86 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.23 (0.15), residues: 3017 helix: 0.62 (0.17), residues: 1004 sheet: -0.55 (0.25), residues: 440 loop : -1.93 (0.14), residues: 1573 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 96 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 131 average time/residue: 0.3912 time to fit residues: 83.4146 Evaluate side-chains 111 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 2.896 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2349 time to fit residues: 11.9494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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: 53.5404 > 50: distance: 61 - 161: 16.156 distance: 110 - 116: 15.285 distance: 116 - 117: 15.180 distance: 117 - 118: 15.739 distance: 117 - 120: 13.589 distance: 118 - 119: 21.815 distance: 118 - 121: 29.378 distance: 121 - 122: 12.135 distance: 122 - 123: 20.524 distance: 122 - 125: 11.339 distance: 123 - 124: 8.540 distance: 123 - 130: 8.978 distance: 125 - 126: 16.850 distance: 126 - 127: 7.291 distance: 127 - 128: 3.671 distance: 127 - 129: 4.355 distance: 130 - 131: 9.074 distance: 130 - 136: 30.173 distance: 131 - 132: 18.964 distance: 131 - 134: 26.786 distance: 132 - 133: 11.318 distance: 132 - 137: 3.785 distance: 134 - 135: 12.746 distance: 135 - 136: 38.562 distance: 137 - 138: 10.311 distance: 138 - 139: 4.115 distance: 138 - 141: 7.189 distance: 139 - 140: 6.826 distance: 139 - 145: 5.303 distance: 141 - 142: 4.217 distance: 142 - 143: 4.215 distance: 142 - 144: 3.027 distance: 145 - 146: 4.198 distance: 146 - 147: 4.623 distance: 146 - 149: 5.649 distance: 147 - 148: 9.358 distance: 147 - 150: 6.216 distance: 151 - 152: 4.346 distance: 151 - 154: 3.630 distance: 152 - 153: 8.577 distance: 154 - 156: 6.540 distance: 158 - 159: 7.772 distance: 159 - 160: 11.009 distance: 159 - 162: 4.621 distance: 160 - 161: 7.896 distance: 160 - 165: 12.141 distance: 162 - 163: 12.442 distance: 162 - 164: 7.841 distance: 165 - 166: 11.742 distance: 166 - 167: 14.947 distance: 166 - 169: 14.233 distance: 167 - 168: 11.876 distance: 167 - 171: 20.017 distance: 169 - 170: 17.262 distance: 171 - 172: 8.290 distance: 172 - 173: 13.985 distance: 172 - 175: 6.861 distance: 173 - 174: 16.142 distance: 173 - 178: 8.376 distance: 175 - 176: 14.301 distance: 175 - 177: 6.073 distance: 178 - 184: 8.827 distance: 179 - 180: 3.302 distance: 179 - 182: 5.591 distance: 180 - 181: 7.554 distance: 180 - 185: 5.807 distance: 182 - 183: 10.351 distance: 183 - 184: 5.068