Starting phenix.real_space_refine on Fri Aug 9 10:19:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eof_28374/08_2024/8eof_28374.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eof_28374/08_2024/8eof_28374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eof_28374/08_2024/8eof_28374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eof_28374/08_2024/8eof_28374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eof_28374/08_2024/8eof_28374.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eof_28374/08_2024/8eof_28374.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 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 102 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 15723 2.51 5 N 4552 2.21 5 O 5139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25608 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: 9930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9930 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1209} 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: 1 Chain: "R" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 625 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 16, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 24} 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 75.837 25.268 88.543 1.00 40.13 S ATOM 19656 SG CYS D 968 74.555 28.618 89.921 1.00 14.70 S ATOM 19698 SG CYS D 975 76.016 28.337 86.351 1.00 31.54 S ATOM 19716 SG CYS D 978 72.682 26.991 87.125 1.00 38.76 S ATOM 12527 SG CYS D 60 109.712 80.455 114.313 1.00 84.53 S ATOM 12545 SG CYS D 62 111.958 82.928 115.910 1.00 98.06 S ATOM 12654 SG CYS D 75 112.415 79.183 116.650 1.00 99.63 S ATOM 12680 SG CYS D 78 109.515 81.224 118.112 1.00 91.80 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: 16.65, per 1000 atoms: 0.65 Number of scatterers: 25608 At special positions: 0 Unit cell: (132.24, 133.98, 200.1, 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 102 15.00 Mg 1 11.99 O 5139 8.00 N 4552 7.00 C 15723 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: 10.85 Conformation dependent library (CDL) restraints added in 4.0 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 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5566 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 43 sheets defined 35.2% alpha, 13.4% beta 42 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 8.75 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: 3.655A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.682A 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: 3.935A pdb=" N ILE B 110 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.637A pdb=" N ALA B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 4.086A 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: 4.283A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.814A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.778A pdb=" N GLU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.503A 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: 4.283A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 242 " --> pdb=" O LEU C 238 " (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: 3.556A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.571A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.591A pdb=" N LYS C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 removed outlier: 3.980A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.812A pdb=" N ASN C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 removed outlier: 3.556A pdb=" N LEU C 417 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.616A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 4.005A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 removed outlier: 3.898A pdb=" N ARG C 538 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.813A 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: 4.534A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.598A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.599A 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: 3.590A 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: 3.502A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.547A 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: 3.623A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.642A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 removed outlier: 3.561A 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: 3.517A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.827A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.218A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 4.140A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.587A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.515A 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 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: 3.571A pdb=" N LYS D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.623A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.708A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.737A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.888A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' 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: 3.742A pdb=" N LEU D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.616A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.719A 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: 3.726A 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: 3.562A 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: 3.936A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 718 " --> pdb=" O ASP D 714 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 719 " --> pdb=" O LYS D 715 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 763 removed outlier: 4.095A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.800A pdb=" N GLU D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 804 removed outlier: 4.055A 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 866 removed outlier: 3.667A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.574A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.552A 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 1001 removed outlier: 3.725A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1008 removed outlier: 3.528A pdb=" N THR D1008 " --> pdb=" O GLU D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1119 through 1126 removed outlier: 3.818A pdb=" N ARG D1123 " --> pdb=" O HIS D1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.751A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D1139 " --> pdb=" O VAL D1135 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1160 removed outlier: 3.824A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 removed outlier: 3.607A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.620A 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: 3.650A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.784A 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: 3.701A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.357A 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: 4.312A pdb=" N GLU G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 Processing helix chain 'G' and resid 102 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.702A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 192 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 7.006A 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: 6.851A 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: 3.838A 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: 7.037A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.525A 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: 3.591A 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: 3.584A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 191 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.606A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.780A 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 173 removed outlier: 6.873A 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: 6.498A 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: 5.807A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.799A 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: 6.358A 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: 5.122A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.368A 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: 3.552A 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: 6.641A 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: 6.868A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.680A 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: 3.536A pdb=" N GLY C 893 " --> pdb=" O LEU C 885 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.661A 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: 6.685A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.534A 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 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 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: 3.909A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.820A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.623A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.727A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.317A 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: 6.143A 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: 4.598A 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 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 4 through 6 removed outlier: 3.863A pdb=" N ARG G 37 " --> pdb=" O GLU G 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 48 through 49 788 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 226 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 12.71 Time building geometry restraints manager: 11.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6755 1.33 - 1.45: 4739 1.45 - 1.57: 14411 1.57 - 1.69: 200 1.69 - 1.81: 157 Bond restraints: 26262 Sorted by residual: bond pdb=" C3' DG T 31 " pdb=" O3' DG T 31 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" C3' DC T 32 " pdb=" O3' DC T 32 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.89e+00 bond pdb=" CA GLY D 871 " pdb=" C GLY D 871 " ideal model delta sigma weight residual 1.514 1.494 0.020 1.41e-02 5.03e+03 2.06e+00 bond pdb=" C3' DG N 5 " pdb=" O3' DG N 5 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" N PRO D1006 " pdb=" CA PRO D1006 " ideal model delta sigma weight residual 1.469 1.486 -0.017 1.28e-02 6.10e+03 1.79e+00 ... (remaining 26257 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.92: 1161 105.92 - 112.95: 14244 112.95 - 119.99: 9306 119.99 - 127.02: 10858 127.02 - 134.06: 457 Bond angle restraints: 36026 Sorted by residual: angle pdb=" C3' DG T 31 " pdb=" O3' DG T 31 " pdb=" P DC T 32 " ideal model delta sigma weight residual 120.20 127.77 -7.57 1.50e+00 4.44e-01 2.55e+01 angle pdb=" C3' DC T 32 " pdb=" O3' DC T 32 " pdb=" P DA T 33 " ideal model delta sigma weight residual 120.20 126.27 -6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" N TYR D 872 " pdb=" CA TYR D 872 " pdb=" C TYR D 872 " ideal model delta sigma weight residual 112.45 107.39 5.06 1.39e+00 5.18e-01 1.33e+01 angle pdb=" C ILE B 3 " pdb=" N SER B 4 " pdb=" CA SER B 4 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.20e+01 angle pdb=" C ALA D 864 " pdb=" N LEU D 865 " pdb=" CA LEU D 865 " ideal model delta sigma weight residual 120.31 125.56 -5.25 1.52e+00 4.33e-01 1.19e+01 ... (remaining 36021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 14469 35.48 - 70.97: 1353 70.97 - 106.45: 54 106.45 - 141.93: 2 141.93 - 177.41: 2 Dihedral angle restraints: 15880 sinusoidal: 7213 harmonic: 8667 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 -106.00 -176.82 70.82 1 1.70e+01 3.46e-03 2.23e+01 dihedral pdb=" C4' DC T 32 " pdb=" C3' DC T 32 " pdb=" O3' DC T 32 " pdb=" P DA T 33 " ideal model delta sinusoidal sigma weight residual 220.00 42.59 177.41 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG N 5 " pdb=" C3' DG N 5 " pdb=" O3' DG N 5 " pdb=" P DC N 6 " ideal model delta sinusoidal sigma weight residual -140.00 27.96 -167.96 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 15877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2525 0.038 - 0.075: 1119 0.075 - 0.113: 373 0.113 - 0.151: 95 0.151 - 0.188: 10 Chirality restraints: 4122 Sorted by residual: chirality pdb=" P DA T 33 " pdb=" OP1 DA T 33 " pdb=" OP2 DA T 33 " pdb=" O5' DA T 33 " both_signs ideal model delta sigma weight residual True 2.35 -2.53 -0.19 2.00e-01 2.50e+01 8.85e-01 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 -2.52 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ASP D 946 " pdb=" N ASP D 946 " pdb=" C ASP D 946 " pdb=" CB ASP D 946 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 4119 not shown) Planarity restraints: 4374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 870 " 0.029 2.00e-02 2.50e+03 5.86e-02 3.44e+01 pdb=" C SER D 870 " -0.101 2.00e-02 2.50e+03 pdb=" O SER D 870 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY D 871 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 32 " 0.034 2.00e-02 2.50e+03 3.20e-02 2.31e+01 pdb=" N1 DC T 32 " -0.078 2.00e-02 2.50e+03 pdb=" C2 DC T 32 " 0.042 2.00e-02 2.50e+03 pdb=" O2 DC T 32 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC T 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC T 32 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC T 32 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC T 32 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DC T 32 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.069 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO C 82 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.057 5.00e-02 4.00e+02 ... (remaining 4371 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 101 2.55 - 3.14: 17793 3.14 - 3.72: 37018 3.72 - 4.31: 51356 4.31 - 4.90: 88342 Nonbonded interactions: 194610 Sorted by model distance: nonbonded pdb=" O3' A R 30 " pdb="MG MG D2001 " model vdw 1.961 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 2.049 2.170 nonbonded pdb=" O ILE D1210 " pdb=" OG SER D1214 " model vdw 2.136 3.040 nonbonded pdb=" O LYS C 518 " pdb=" OG SER C 525 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASP D 383 " pdb=" OG SER D 403 " model vdw 2.205 3.040 ... (remaining 194605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.930 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: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 83.420 Find NCS groups from input model: 0.530 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.005 0.074 26262 Z= 0.345 Angle : 0.694 8.443 36026 Z= 0.381 Chirality : 0.048 0.188 4122 Planarity : 0.006 0.106 4374 Dihedral : 22.489 177.414 10314 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.59 % Favored : 89.65 % Rotamer: Outliers : 17.49 % Allowed : 25.37 % Favored : 57.13 % 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: -3.14 (0.14), residues: 3018 helix: -1.69 (0.16), residues: 985 sheet: -1.50 (0.27), residues: 371 loop : -2.54 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 944 HIS 0.014 0.002 HIS B 124 PHE 0.019 0.002 PHE C 431 TYR 0.020 0.002 TYR A 168 ARG 0.007 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 444 poor density : 154 time to evaluate : 2.917 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: A 125 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 71 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: C 221 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.6911 (p) REVERT: C 275 LEU cc_start: 0.8416 (mt) cc_final: 0.7999 (mp) REVERT: D 663 MET cc_start: 0.8146 (mmt) cc_final: 0.7862 (mmt) REVERT: D 1081 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8070 (t) REVERT: D 1084 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7195 (pm20) outliers start: 444 outliers final: 104 residues processed: 559 average time/residue: 0.4307 time to fit residues: 358.3232 Evaluate side-chains 214 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 105 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1063 LYS Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1084 GLN Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 98 PRO Chi-restraints excluded: chain G residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 30.0000 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: