Starting phenix.real_space_refine on Sun May 25 10:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pkw_20368/05_2025/6pkw_20368.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pkw_20368/05_2025/6pkw_20368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pkw_20368/05_2025/6pkw_20368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pkw_20368/05_2025/6pkw_20368.map" model { file = "/net/cci-nas-00/data/ceres_data/6pkw_20368/05_2025/6pkw_20368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pkw_20368/05_2025/6pkw_20368.cif" } resolution = 4.5 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 16710 2.51 5 N 4758 2.21 5 O 4742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26262 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 5649 Classifications: {'peptide': 885} Incomplete info: {'truncation_to_alanine': 446} Link IDs: {'PTRANS': 22, 'TRANS': 862} Chain breaks: 14 Unresolved non-hydrogen bonds: 1625 Unresolved non-hydrogen angles: 2047 Unresolved non-hydrogen dihedrals: 1301 Unresolved non-hydrogen chiralities: 159 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 5, 'TYR:plan': 14, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 30, 'PHE:plan': 16, 'GLU:plan': 59, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 903 Chain: "A" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1306 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 8 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 2, 'UNK:plan-1': 22, 'TRP:plan': 2, 'HIS:plan': 3, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 205 Chain: "B" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 4872 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 436} Link IDs: {'PTRANS': 20, 'TRANS': 764} Chain breaks: 20 Unresolved non-hydrogen bonds: 1634 Unresolved non-hydrogen angles: 2070 Unresolved non-hydrogen dihedrals: 1326 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 28, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 9, 'PHE:plan': 21, 'GLU:plan': 54, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 904 Chain: "B" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1304 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 8 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 6, 'ASP:plan': 5, 'TYR:plan': 2, 'UNK:plan-1': 22, 'TRP:plan': 2, 'HIS:plan': 3, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 205 Restraints were copied for chains: D, C Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLU A1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A1272 " occ=0.50 residue: pdb=" N VAL A1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL A1287 " occ=0.50 residue: pdb=" N VAL A1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A1400 " occ=0.50 residue: pdb=" N GLU C1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C1272 " occ=0.50 residue: pdb=" N VAL C1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL C1287 " occ=0.50 residue: pdb=" N VAL C1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C1400 " occ=0.50 residue: pdb=" N GLU B1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B1272 " occ=0.50 residue: pdb=" N VAL B1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL B1287 " occ=0.50 residue: pdb=" N VAL B1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B1400 " occ=0.50 residue: pdb=" N GLU D1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU D1272 " occ=0.50 residue: pdb=" N VAL D1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL D1287 " occ=0.50 residue: pdb=" N VAL D1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D1400 " occ=0.50 Time building chain proxies: 26.54, per 1000 atoms: 1.01 Number of scatterers: 26262 At special positions: 0 Unit cell: (148.174, 146.042, 178.022, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 4742 8.00 N 4758 7.00 C 16710 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 - 3.00 Amino acid : True - 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: 6.05 Conformation dependent library (CDL) restraints added in 3.6 seconds 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7916 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 14 sheets defined 68.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.916A pdb=" N THR A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.838A pdb=" N HIS A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.762A pdb=" N ASN A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 426 through 439 removed outlier: 4.075A pdb=" N ALA A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.837A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 470 removed outlier: 4.116A pdb=" N GLY A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.605A pdb=" N ARG A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.974A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 536 through 548 Processing helix chain 'A' and resid 593 through 605 removed outlier: 3.587A pdb=" N GLN A 605 " --> pdb=" O TRP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.763A pdb=" N ALA A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 639 removed outlier: 3.579A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 672 removed outlier: 3.558A pdb=" N LEU A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.514A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 720 Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.157A pdb=" N ILE A 741 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 808 through 834 removed outlier: 3.634A pdb=" N ASP A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 864 removed outlier: 3.686A pdb=" N HIS A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 Processing helix chain 'A' and resid 880 through 902 Processing helix chain 'A' and resid 904 through 926 removed outlier: 3.932A pdb=" N ILE A 920 " --> pdb=" O CYS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 935 through 949 removed outlier: 4.033A pdb=" N LYS A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 972 Processing helix chain 'A' and resid 978 through 995 removed outlier: 5.456A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 990 - end of helix Processing helix chain 'A' and resid 1036 through 1065 removed outlier: 3.592A pdb=" N THR A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1092 removed outlier: 3.570A pdb=" N ILE A1077 " --> pdb=" O ASN A1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1114 removed outlier: 4.150A pdb=" N LEU A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1156 removed outlier: 3.758A pdb=" N SER A1156 " --> pdb=" O ARG A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1184 Processing helix chain 'A' and resid 1189 through 1206 Processing helix chain 'A' and resid 1370 through 1381 removed outlier: 3.594A pdb=" N LEU A1381 " --> pdb=" O LEU A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1432 Processing helix chain 'A' and resid 1456 through 1467 removed outlier: 3.545A pdb=" N ARG A1460 " --> pdb=" O CYS A1456 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 159 through 178 removed outlier: 3.917A pdb=" N THR C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 removed outlier: 3.839A pdb=" N HIS C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.762A pdb=" N ASN C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 354 through 363 Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 406 through 419 Processing helix chain 'C' and resid 426 through 439 removed outlier: 4.074A pdb=" N ALA C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 448 removed outlier: 3.838A pdb=" N ALA C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 470 removed outlier: 4.117A pdb=" N GLY C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.605A pdb=" N ARG C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.975A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 536 through 548 Processing helix chain 'C' and resid 593 through 605 removed outlier: 3.587A pdb=" N GLN C 605 " --> pdb=" O TRP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 removed outlier: 3.763A pdb=" N ALA C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 639 removed outlier: 3.579A pdb=" N GLU C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 672 removed outlier: 3.558A pdb=" N LEU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 682 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.514A pdb=" N ALA C 706 " --> pdb=" O LYS C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 720 Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 738 through 742 removed outlier: 4.156A pdb=" N ILE C 741 " --> pdb=" O PHE C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 808 through 834 removed outlier: 3.634A pdb=" N ASP C 834 " --> pdb=" O VAL C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 864 removed outlier: 3.686A pdb=" N HIS C 863 " --> pdb=" O ARG C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 880 Processing helix chain 'C' and resid 880 through 902 Processing helix chain 'C' and resid 904 through 926 removed outlier: 3.932A pdb=" N ILE C 920 " --> pdb=" O CYS C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 929 No H-bonds generated for 'chain 'C' and resid 927 through 929' Processing helix chain 'C' and resid 935 through 949 removed outlier: 4.033A pdb=" N LYS C 939 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 947 " --> pdb=" O VAL C 943 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 972 Processing helix chain 'C' and resid 978 through 995 removed outlier: 5.456A pdb=" N GLU C 989 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Proline residue: C 990 - end of helix Processing helix chain 'C' and resid 1036 through 1065 removed outlier: 3.592A pdb=" N THR C1040 " --> pdb=" O PRO C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1092 removed outlier: 3.570A pdb=" N ILE C1077 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C1084 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1096 through 1114 removed outlier: 4.149A pdb=" N LEU C1102 " --> pdb=" O PRO C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1156 removed outlier: 3.758A pdb=" N SER C1156 " --> pdb=" O ARG C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1184 Processing helix chain 'C' and resid 1189 through 1206 Processing helix chain 'C' and resid 1370 through 1381 removed outlier: 3.593A pdb=" N LEU C1381 " --> pdb=" O LEU C1377 " (cutoff:3.500A) Processing helix chain 'C' and resid 1428 through 1432 Processing helix chain 'C' and resid 1456 through 1467 removed outlier: 3.546A pdb=" N ARG C1460 " --> pdb=" O CYS C1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.704A pdb=" N ASN B 47 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.557A pdb=" N LEU B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.734A pdb=" N VAL B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 407 through 421 Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.850A pdb=" N ALA B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'B' and resid 456 through 459 removed outlier: 3.574A pdb=" N ASP B 459 " --> pdb=" O THR B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 460 through 469 Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.565A pdb=" N ARG B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.623A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.923A pdb=" N GLN B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 548 Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 620 through 638 Processing helix chain 'B' and resid 648 through 672 removed outlier: 3.706A pdb=" N VAL B 664 " --> pdb=" O GLN B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.837A pdb=" N ILE B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 720 Processing helix chain 'B' and resid 729 through 737 Processing helix chain 'B' and resid 738 through 743 removed outlier: 4.151A pdb=" N ILE B 741 " --> pdb=" O PHE B 738 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 742 " --> pdb=" O PRO B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 808 through 832 removed outlier: 4.532A pdb=" N MET B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 862 Processing helix chain 'B' and resid 870 through 880 Processing helix chain 'B' and resid 881 through 902 Processing helix chain 'B' and resid 904 through 932 removed outlier: 4.177A pdb=" N LEU B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 925 " --> pdb=" O ILE B 921 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B 930 " --> pdb=" O LEU B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 941 removed outlier: 3.527A pdb=" N LYS B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 949 removed outlier: 4.440A pdb=" N MET B 946 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET B 947 " --> pdb=" O VAL B 943 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU B 948 " --> pdb=" O ARG B 944 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP B 949 " --> pdb=" O ARG B 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 942 through 949' Processing helix chain 'B' and resid 949 through 972 Processing helix chain 'B' and resid 979 through 995 removed outlier: 3.649A pdb=" N ILE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU B 989 " --> pdb=" O GLY B 985 " (cutoff:3.500A) Proline residue: B 990 - end of helix removed outlier: 3.532A pdb=" N ILE B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 995 " --> pdb=" O TYR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1065 Processing helix chain 'B' and resid 1073 through 1092 removed outlier: 3.865A pdb=" N TYR B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU B1084 " --> pdb=" O PHE B1080 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1114 removed outlier: 4.452A pdb=" N LEU B1102 " --> pdb=" O PRO B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1156 Processing helix chain 'B' and resid 1158 through 1184 Processing helix chain 'B' and resid 1189 through 1207 Processing helix chain 'B' and resid 1270 through 1275 Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1456 through 1467 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.703A pdb=" N ASN D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 48 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.557A pdb=" N LEU D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 190 through 201 removed outlier: 3.734A pdb=" N VAL D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 407 through 421 Processing helix chain 'D' and resid 427 through 439 removed outlier: 3.850A pdb=" N ALA D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 Processing helix chain 'D' and resid 456 through 459 removed outlier: 3.573A pdb=" N ASP D 459 " --> pdb=" O THR D 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 459' Processing helix chain 'D' and resid 460 through 469 Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.565A pdb=" N ARG D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 492 through 502 removed outlier: 3.622A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 517 removed outlier: 3.922A pdb=" N GLN D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 548 Processing helix chain 'D' and resid 593 through 606 Processing helix chain 'D' and resid 607 through 618 Processing helix chain 'D' and resid 620 through 638 Processing helix chain 'D' and resid 648 through 672 removed outlier: 3.706A pdb=" N VAL D 664 " --> pdb=" O GLN D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 681 Processing helix chain 'D' and resid 691 through 700 Processing helix chain 'D' and resid 701 through 706 removed outlier: 3.837A pdb=" N ILE D 705 " --> pdb=" O ASP D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 720 Processing helix chain 'D' and resid 729 through 737 Processing helix chain 'D' and resid 738 through 743 removed outlier: 4.150A pdb=" N ILE D 741 " --> pdb=" O PHE D 738 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 742 " --> pdb=" O PRO D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'D' and resid 799 through 807 Processing helix chain 'D' and resid 808 through 832 removed outlier: 4.532A pdb=" N MET D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 862 Processing helix chain 'D' and resid 870 through 880 Processing helix chain 'D' and resid 881 through 902 Processing helix chain 'D' and resid 904 through 932 removed outlier: 4.176A pdb=" N LEU D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 925 " --> pdb=" O ILE D 921 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 929 " --> pdb=" O ARG D 925 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE D 930 " --> pdb=" O LEU D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 935 through 941 removed outlier: 3.527A pdb=" N LYS D 939 " --> pdb=" O THR D 935 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 949 removed outlier: 4.440A pdb=" N MET D 946 " --> pdb=" O ILE D 942 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET D 947 " --> pdb=" O VAL D 943 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU D 948 " --> pdb=" O ARG D 944 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP D 949 " --> pdb=" O ARG D 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 942 through 949' Processing helix chain 'D' and resid 949 through 972 Processing helix chain 'D' and resid 979 through 995 removed outlier: 3.650A pdb=" N ILE D 983 " --> pdb=" O LEU D 979 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Proline residue: D 990 - end of helix removed outlier: 3.532A pdb=" N ILE D 994 " --> pdb=" O PRO D 990 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 995 " --> pdb=" O TYR D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1065 Processing helix chain 'D' and resid 1073 through 1092 removed outlier: 3.865A pdb=" N TYR D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU D1084 " --> pdb=" O PHE D1080 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1114 removed outlier: 4.452A pdb=" N LEU D1102 " --> pdb=" O PRO D1098 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1156 Processing helix chain 'D' and resid 1158 through 1184 Processing helix chain 'D' and resid 1189 through 1207 Processing helix chain 'D' and resid 1270 through 1275 Processing helix chain 'D' and resid 1370 through 1381 Processing helix chain 'D' and resid 1456 through 1467 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 122 removed outlier: 6.063A pdb=" N ILE A 181 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 217 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 147 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N GLY A 184 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N VAL A 149 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 304 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER A 148 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL A 327 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 683 through 684 removed outlier: 3.531A pdb=" N SER A 684 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A 690 " --> pdb=" O SER A 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 5.539A pdb=" N GLY A1323 " --> pdb=" O TRP A1410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU A1412 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASN A1325 " --> pdb=" O GLU A1412 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N SER A1414 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A1327 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE A1416 " --> pdb=" O ILE A1327 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS A1329 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A1418 " --> pdb=" O HIS A1329 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A1331 " --> pdb=" O LEU A1418 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL A1411 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR A1399 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A1413 " --> pdb=" O LYS A1397 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A1397 " --> pdb=" O THR A1413 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A1415 " --> pdb=" O VAL A1395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 6.145A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1346 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 117 through 122 removed outlier: 6.063A pdb=" N ILE C 181 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL C 217 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLY C 184 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL C 149 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL C 304 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER C 148 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL C 327 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 683 through 684 removed outlier: 3.531A pdb=" N SER C 684 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER C 690 " --> pdb=" O SER C 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 5.539A pdb=" N GLY C1323 " --> pdb=" O TRP C1410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU C1412 " --> pdb=" O GLY C1323 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASN C1325 " --> pdb=" O GLU C1412 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER C1414 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C1327 " --> pdb=" O SER C1414 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE C1416 " --> pdb=" O ILE C1327 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS C1329 " --> pdb=" O ILE C1416 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C1418 " --> pdb=" O HIS C1329 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE C1331 " --> pdb=" O LEU C1418 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N VAL C1411 " --> pdb=" O TYR C1399 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR C1399 " --> pdb=" O VAL C1411 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C1413 " --> pdb=" O LYS C1397 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS C1397 " --> pdb=" O THR C1413 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C1415 " --> pdb=" O VAL C1395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 6.145A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C1346 " --> pdb=" O PHE C1332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'B' and resid 1361 through 1362 removed outlier: 5.708A pdb=" N GLY B1323 " --> pdb=" O TRP B1410 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU B1412 " --> pdb=" O GLY B1323 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASN B1325 " --> pdb=" O GLU B1412 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER B1414 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B1327 " --> pdb=" O SER B1414 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE B1416 " --> pdb=" O ILE B1327 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS B1329 " --> pdb=" O ILE B1416 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B1418 " --> pdb=" O HIS B1329 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE B1331 " --> pdb=" O LEU B1418 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL B1411 " --> pdb=" O TYR B1399 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR B1399 " --> pdb=" O VAL B1411 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B1413 " --> pdb=" O LYS B1397 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B1397 " --> pdb=" O THR B1413 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B1415 " --> pdb=" O VAL B1395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1361 through 1362 removed outlier: 6.760A pdb=" N PHE B1332 " --> pdb=" O LEU B1346 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B1346 " --> pdb=" O PHE B1332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 118 through 121 Processing sheet with id=AB4, first strand: chain 'D' and resid 1361 through 1362 removed outlier: 5.708A pdb=" N GLY D1323 " --> pdb=" O TRP D1410 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU D1412 " --> pdb=" O GLY D1323 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASN D1325 " --> pdb=" O GLU D1412 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER D1414 " --> pdb=" O ASN D1325 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE D1327 " --> pdb=" O SER D1414 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE D1416 " --> pdb=" O ILE D1327 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS D1329 " --> pdb=" O ILE D1416 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU D1418 " --> pdb=" O HIS D1329 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE D1331 " --> pdb=" O LEU D1418 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL D1411 " --> pdb=" O TYR D1399 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR D1399 " --> pdb=" O VAL D1411 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR D1413 " --> pdb=" O LYS D1397 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS D1397 " --> pdb=" O THR D1413 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE D1415 " --> pdb=" O VAL D1395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1361 through 1362 removed outlier: 6.760A pdb=" N PHE D1332 " --> pdb=" O LEU D1346 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU D1346 " --> pdb=" O PHE D1332 " (cutoff:3.500A) 1937 hydrogen bonds defined for protein. 5751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.07 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8821 1.34 - 1.46: 5155 1.46 - 1.57: 12710 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 26748 Sorted by residual: bond pdb=" C PHE A 738 " pdb=" N PRO A 739 " ideal model delta sigma weight residual 1.334 1.373 -0.040 8.40e-03 1.42e+04 2.24e+01 bond pdb=" C PHE C 738 " pdb=" N PRO C 739 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.16e+01 bond pdb=" C SER B1281 " pdb=" N PRO B1282 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" C SER D1281 " pdb=" N PRO D1282 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" C SER C1281 " pdb=" N PRO C1282 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 6.94e+00 ... (remaining 26743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 36010 2.72 - 5.44: 711 5.44 - 8.16: 81 8.16 - 10.87: 12 10.87 - 13.59: 8 Bond angle restraints: 36822 Sorted by residual: angle pdb=" N CYS A 621 " pdb=" CA CYS A 621 " pdb=" C CYS A 621 " ideal model delta sigma weight residual 111.28 120.61 -9.33 1.09e+00 8.42e-01 7.32e+01 angle pdb=" N CYS C 621 " pdb=" CA CYS C 621 " pdb=" C CYS C 621 " ideal model delta sigma weight residual 111.28 120.57 -9.29 1.09e+00 8.42e-01 7.26e+01 angle pdb=" N PRO C 504 " pdb=" CA PRO C 504 " pdb=" C PRO C 504 " ideal model delta sigma weight residual 112.47 124.37 -11.90 2.06e+00 2.36e-01 3.33e+01 angle pdb=" N PRO A 504 " pdb=" CA PRO A 504 " pdb=" C PRO A 504 " ideal model delta sigma weight residual 112.47 124.34 -11.87 2.06e+00 2.36e-01 3.32e+01 angle pdb=" N PRO D1097 " pdb=" CA PRO D1097 " pdb=" C PRO D1097 " ideal model delta sigma weight residual 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.50: 14035 11.50 - 23.01: 1022 23.01 - 34.51: 185 34.51 - 46.02: 40 46.02 - 57.52: 6 Dihedral angle restraints: 15288 sinusoidal: 3266 harmonic: 12022 Sorted by residual: dihedral pdb=" CA ILE C 255 " pdb=" C ILE C 255 " pdb=" N ASN C 256 " pdb=" CA ASN C 256 " ideal model delta harmonic sigma weight residual -180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ILE A 255 " pdb=" C ILE A 255 " pdb=" N ASN A 256 " pdb=" CA ASN A 256 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO D1260 " pdb=" C PRO D1260 " pdb=" N ASP D1261 " pdb=" CA ASP D1261 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 15285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3978 0.076 - 0.152: 474 0.152 - 0.227: 58 0.227 - 0.303: 8 0.303 - 0.379: 2 Chirality restraints: 4520 Sorted by residual: chirality pdb=" CA PRO A 504 " pdb=" N PRO A 504 " pdb=" C PRO A 504 " pdb=" CB PRO A 504 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA PRO C 504 " pdb=" N PRO C 504 " pdb=" C PRO C 504 " pdb=" CB PRO C 504 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB VAL D 302 " pdb=" CA VAL D 302 " pdb=" CG1 VAL D 302 " pdb=" CG2 VAL D 302 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 4517 not shown) Planarity restraints: 4802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 503 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LEU C 503 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU C 503 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO C 504 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 503 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C LEU A 503 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU A 503 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO A 504 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 592 " 0.022 2.00e-02 2.50e+03 1.82e-02 8.32e+00 pdb=" CG TRP B 592 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 592 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 592 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 592 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 592 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 592 " 0.001 2.00e-02 2.50e+03 ... (remaining 4799 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5705 2.77 - 3.30: 25742 3.30 - 3.84: 43578 3.84 - 4.37: 43563 4.37 - 4.90: 72022 Nonbonded interactions: 190610 Sorted by model distance: nonbonded pdb=" OH TYR B1259 " pdb=" O VAL B1264 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR D1259 " pdb=" O VAL D1264 " model vdw 2.239 3.040 nonbonded pdb=" O VAL C 301 " pdb=" OG1 THR C 324 " model vdw 2.249 3.040 nonbonded pdb=" O VAL A 301 " pdb=" OG1 THR A 324 " model vdw 2.249 3.040 nonbonded pdb=" O ASN D1073 " pdb=" OG1 THR D1076 " model vdw 2.271 3.040 ... (remaining 190605 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: 0.15 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 68.650 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.007 0.074 26748 Z= 0.347 Angle : 0.940 13.592 36822 Z= 0.535 Chirality : 0.052 0.379 4520 Planarity : 0.007 0.062 4802 Dihedral : 9.190 57.520 7372 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.11), residues: 3848 helix: -1.74 (0.08), residues: 2424 sheet: -2.28 (0.32), residues: 216 loop : -3.23 (0.14), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 592 HIS 0.012 0.003 HIS B 259 PHE 0.023 0.003 PHE C1280 TYR 0.032 0.003 TYR D 131 ARG 0.008 0.001 ARG B1310 Details of bonding type rmsd hydrogen bonds : bond 0.13768 ( 1929) hydrogen bonds : angle 6.62785 ( 5751) covalent geometry : bond 0.00695 (26748) covalent geometry : angle 0.93960 (36822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: B 687 TRP cc_start: 0.8976 (m100) cc_final: 0.8557 (m100) REVERT: B 711 GLN cc_start: 0.9501 (mm-40) cc_final: 0.9207 (mm110) REVERT: B 805 PHE cc_start: 0.9423 (t80) cc_final: 0.9127 (m-80) REVERT: B 1143 MET cc_start: 0.9681 (mmt) cc_final: 0.9385 (mmm) REVERT: B 1169 LYS cc_start: 0.9605 (mttt) cc_final: 0.9401 (tttt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1351 time to fit residues: 14.2057 Evaluate side-chains 45 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.686 Evaluate side-chains 86 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9507 (tp) cc_final: 0.9100 (tt) REVERT: A 438 TRP cc_start: 0.9143 (m-10) cc_final: 0.8616 (m-10) REVERT: A 499 LEU cc_start: 0.9707 (mt) cc_final: 0.9374 (tp) REVERT: A 651 LEU cc_start: 0.9637 (mt) cc_final: 0.9318 (mp) REVERT: A 662 ILE cc_start: 0.9762 (pt) cc_final: 0.9505 (mt) REVERT: A 876 MET cc_start: 0.8593 (mtm) cc_final: 0.8067 (tmm) REVERT: A 1143 MET cc_start: 0.9445 (mmt) cc_final: 0.8899 (mmp) REVERT: A 1429 ASP cc_start: 0.3817 (t0) cc_final: 0.3073 (p0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1623 time to fit residues: 19.7543 Evaluate side-chains 44 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 322 optimal weight: 10.0000 chunk 124 optimal weight: 0.1980 chunk 196 optimal weight: 50.0000 chunk 240 optimal weight: 9.9990 chunk 374 optimal weight: 40.0000 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 HIS D 707 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN C 144 ASN C 259 HIS C 656 HIS C 707 HIS C1081 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.078605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057742 restraints weight = 56451.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057688 restraints weight = 37951.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.058184 restraints weight = 27427.521| |-----------------------------------------------------------------------------| r_work (final): 0.3148 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.042916 restraints weight = 52304.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.043967 restraints weight = 30380.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.044658 restraints weight = 21126.547| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** Sorry: Duplicate selection for occupancies.