Starting phenix.real_space_refine on Sun Nov 19 10:19:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkw_20368/11_2023/6pkw_20368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkw_20368/11_2023/6pkw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkw_20368/11_2023/6pkw_20368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkw_20368/11_2023/6pkw_20368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkw_20368/11_2023/6pkw_20368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkw_20368/11_2023/6pkw_20368.pdb" } 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 Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A ARG 1092": "NH1" <-> "NH2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 689": "NH1" <-> "NH2" Residue "C ARG 1092": "NH1" <-> "NH2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 689": "NH1" <-> "NH2" Residue "D PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 26262 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 6955 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 537} Link IDs: {'PTRANS': 33, 'TRANS': 1052} Chain breaks: 23 Unresolved non-hydrogen bonds: 1942 Unresolved non-hydrogen angles: 2456 Unresolved non-hydrogen dihedrals: 1552 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 8, 'UNK:plan-1': 22, 'TYR:plan': 16, 'ASN:plan1': 25, 'TRP:plan': 4, 'ASP:plan': 35, 'PHE:plan': 16, 'GLU:plan': 65, 'ARG:plan': 50} Unresolved non-hydrogen planarities: 1108 Chain: "C" Number of atoms: 6955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 6955 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 537} Link IDs: {'PTRANS': 33, 'TRANS': 1052} Chain breaks: 23 Unresolved non-hydrogen bonds: 1942 Unresolved non-hydrogen angles: 2456 Unresolved non-hydrogen dihedrals: 1552 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 8, 'UNK:plan-1': 22, 'TYR:plan': 16, 'ASN:plan1': 25, 'TRP:plan': 4, 'ASP:plan': 35, 'PHE:plan': 16, 'GLU:plan': 65, 'ARG:plan': 50} Unresolved non-hydrogen planarities: 1108 Chain: "B" Number of atoms: 6176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 6176 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 528} Link IDs: {'PTRANS': 31, 'TRANS': 954} Chain breaks: 29 Unresolved non-hydrogen bonds: 1953 Unresolved non-hydrogen angles: 2482 Unresolved non-hydrogen dihedrals: 1578 Unresolved non-hydrogen chiralities: 178 Planarities with less than four sites: {'GLN:plan1': 28, 'UNK:plan-1': 22, 'ASP:plan': 33, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 7, 'HIS:plan': 12, 'PHE:plan': 21, 'GLU:plan': 60, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 1109 Chain: "D" Number of atoms: 6176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 6176 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 528} Link IDs: {'PTRANS': 31, 'TRANS': 954} Chain breaks: 29 Unresolved non-hydrogen bonds: 1953 Unresolved non-hydrogen angles: 2482 Unresolved non-hydrogen dihedrals: 1578 Unresolved non-hydrogen chiralities: 178 Planarities with less than four sites: {'GLN:plan1': 28, 'UNK:plan-1': 22, 'ASP:plan': 33, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 7, 'HIS:plan': 12, 'PHE:plan': 21, 'GLU:plan': 60, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 1109 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: 14.57, per 1000 atoms: 0.55 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 - 3.50 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: 11.03 Conformation dependent library (CDL) restraints added in 5.6 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: 2.92 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: 11.37 Time building geometry restraints manager: 11.79 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: 99.05 - 106.08: 499 106.08 - 113.10: 15007 113.10 - 120.13: 9025 120.13 - 127.16: 11883 127.16 - 134.18: 408 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 2.440 nonbonded pdb=" OH TYR D1259 " pdb=" O VAL D1264 " model vdw 2.239 2.440 nonbonded pdb=" O VAL C 301 " pdb=" OG1 THR C 324 " model vdw 2.249 2.440 nonbonded pdb=" O VAL A 301 " pdb=" OG1 THR A 324 " model vdw 2.249 2.440 nonbonded pdb=" O ASN D1073 " pdb=" OG1 THR D1076 " model vdw 2.271 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 49 or resid 116 through 137 or resid 164 throug \ h 169 or (resid 170 through 172 and (name N or name CA or name C or name O or na \ me CB )) or resid 173 through 175 or (resid 182 through 183 and (name N or name \ CA or name C or name O or name CB )) or resid 184 through 197 or (resid 198 thro \ ugh 202 and (name N or name CA or name C or name O or name CB )) or resid 259 th \ rough 260 or (resid 261 through 265 and (name N or name CA or name C or name O o \ r name CB )) or (resid 266 through 271 and (name N or name CA or name C or name \ O or name CB )) or resid 272 through 277 or (resid 278 through 285 and (name N o \ r name CA or name C or name O or name CB )) or resid 286 or (resid 287 through 2 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 296 through \ 302 or (resid 303 through 304 and (name N or name CA or name C or name O or nam \ e CB )) or resid 313 through 315 or (resid 316 through 318 and (name N or name C \ A or name C or name O or name CB )) or resid 319 through 325 or (resid 326 throu \ gh 327 and (name N or name CA or name C or name O or name CB )) or resid 353 thr \ ough 364 or resid 372 through 389 or (resid 390 through 394 and (name N or name \ CA or name C or name O or name CB )) or (resid 406 through 412 and (name N or na \ me CA or name C or name O or name CB )) or resid 413 through 421 or (resid 426 t \ hrough 431 and (name N or name CA or name C or name O or name CB )) or resid 432 \ through 433 or (resid 434 through 435 and (name N or name CA or name C or name \ O or name CB )) or resid 436 through 437 or (resid 438 through 439 and (name N o \ r name CA or name C or name O or name CB )) or resid 440 or (resid 441 through 4 \ 50 and (name N or name CA or name C or name O or name CB )) or (resid 455 throug \ h 459 and (name N or name CA or name C or name O or name CB )) or resid 460 thro \ ugh 474 or (resid 475 and (name N or name CA or name C or name O or name CB )) o \ r resid 476 through 477 or (resid 478 through 479 and (name N or name CA or name \ C or name O or name CB )) or resid 480 through 499 or (resid 500 and (name N or \ name CA or name C or name O or name CB )) or resid 501 through 507 or (resid 50 \ 8 through 515 and (name N or name CA or name C or name O or name CB )) or resid \ 516 through 537 or (resid 538 through 539 and (name N or name CA or name C or na \ me O or name CB )) or resid 540 through 544 or (resid 545 through 547 and (name \ N or name CA or name C or name O or name CB )) or resid 548 through 596 or (resi \ d 597 through 598 and (name N or name CA or name C or name O or name CB )) or re \ sid 599 through 603 or (resid 604 and (name N or name CA or name C or name O or \ name CB )) or resid 605 through 609 or (resid 610 through 611 and (name N or nam \ e CA or name C or name O or name CB )) or resid 612 through 631 or (resid 632 an \ d (name N or name CA or name C or name O or name CB )) or resid 633 through 639 \ or resid 646 through 649 or (resid 650 through 652 and (name N or name CA or nam \ e C or name O or name CB )) or resid 653 through 694 or (resid 695 through 696 a \ nd (name N or name CA or name C or name O or name CB )) or resid 697 through 702 \ or (resid 703 and (name N or name CA or name C or name O or name CB )) or resid \ 704 through 739 or (resid 740 through 743 and (name N or name CA or name C or n \ ame O or name CB )) or resid 744 or (resid 745 through 798 and (name N or name C \ A or name C or name O or name CB )) or resid 799 or (resid 800 through 804 and ( \ name N or name CA or name C or name O or name CB )) or resid 805 through 806 or \ (resid 807 and (name N or name CA or name C or name O or name CB )) or resid 808 \ through 811 or (resid 812 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 820 or (resid 821 and (name N or name CA or name C or n \ ame O or name CB )) or resid 822 through 823 or (resid 824 through 825 and (name \ N or name CA or name C or name O or name CB )) or resid 826 through 828 or (res \ id 829 through 832 and (name N or name CA or name C or name O or name CB )) or r \ esid 840 through 841 or (resid 842 through 845 and (name N or name CA or name C \ or name O or name CB )) or resid 846 through 854 or (resid 855 through 860 and ( \ name N or name CA or name C or name O or name CB )) or resid 861 through 862 or \ (resid 863 through 864 and (name N or name CA or name C or name O or name CB )) \ or (resid 869 through 881 and (name N or name CA or name C or name O or name CB \ )) or resid 882 through 884 or (resid 885 and (name N or name CA or name C or na \ me O or name CB )) or resid 886 through 889 or (resid 890 through 892 and (name \ N or name CA or name C or name O or name CB )) or resid 893 through 917 or (resi \ d 918 through 921 and (name N or name CA or name C or name O or name CB )) or re \ sid 922 through 925 or (resid 926 through 930 and (name N or name CA or name C o \ r name O or name CB )) or resid 931 or (resid 932 through 936 and (name N or nam \ e CA or name C or name O or name CB )) or resid 937 through 980 or (resid 981 th \ rough 984 and (name N or name CA or name C or name O or name CB )) or resid 985 \ through 994 or (resid 995 through 1032 and (name N or name CA or name C or name \ O or name CB )) or resid 1033 through 1051 or (resid 1052 through 1074 and (name \ N or name CA or name C or name O or name CB )) or resid 1075 through 1080 or (r \ esid 1081 and (name N or name CA or name C or name O or name CB )) or resid 1082 \ through 1100 or (resid 1101 through 1102 and (name N or name CA or name C or na \ me O or name CB )) or resid 1103 or (resid 1104 through 1108 and (name N or name \ CA or name C or name O or name CB )) or resid 1109 through 1126 or (resid 1127 \ and (name N or name CA or name C or name O or name CB )) or resid 1128 through 1 \ 134 or (resid 1135 and (name N or name CA or name C or name O or name CB )) or r \ esid 1136 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 through 1153 or (resid 1154 and (name \ N or name CA or name C or name O or name CB )) or resid 1155 through 1159 or (re \ sid 1160 and (name N or name CA or name C or name O or name CB )) or resid 1161 \ through 1172 or (resid 1173 and (name N or name CA or name C or name O or name C \ B )) or resid 1174 through 1448 or (resid 1449 through 1453 and (name N or name \ CA or name C or name O or name CB )) or resid 1454 through 1467)) selection = (chain 'B' and (resid 40 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 or (resid 119 through 124 and (name N o \ r name CA or name C or name O or name CB )) or resid 125 or (resid 126 through 1 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 134 or (resid 135 through 165 and (name N or name CA or name C or name O or nam \ e CB )) or resid 166 through 198 or (resid 199 through 202 and (name N or name C \ A or name C or name O or name CB )) or resid 259 through 262 or (resid 263 throu \ gh 265 and (name N or name CA or name C or name O or name CB )) or (resid 266 th \ rough 271 and (name N or name CA or name C or name O or name CB )) or resid 272 \ through 314 or (resid 315 through 318 and (name N or name CA or name C or name O \ or name CB )) or resid 319 through 321 or (resid 322 through 323 and (name N or \ name CA or name C or name O or name CB )) or resid 324 through 327 or (resid 35 \ 3 through 374 and (name N or name CA or name C or name O or name CB )) or resid \ 375 through 380 or (resid 381 through 388 and (name N or name CA or name C or na \ me O or name CB )) or resid 389 through 391 or (resid 392 through 412 and (name \ N or name CA or name C or name O or name CB )) or resid 413 through 418 or (resi \ d 419 through 431 and (name N or name CA or name C or name O or name CB )) or re \ sid 432 through 620 or (resid 621 and (name N or name CA or name C or name O or \ name CB )) or resid 622 through 680 or (resid 681 through 682 and (name N or nam \ e CA or name C or name O or name CB )) or resid 683 through 718 or (resid 719 an \ d (name N or name CA or name C or name O or name CB )) or (resid 720 through 726 \ and (name N or name CA or name C or name O or name CB )) or resid 727 through 7 \ 33 or (resid 734 through 738 and (name N or name CA or name C or name O or name \ CB )) or resid 739 through 810 or (resid 811 through 812 and (name N or name CA \ or name C or name O or name CB )) or resid 813 through 824 or (resid 825 and (na \ me N or name CA or name C or name O or name CB )) or resid 826 through 857 or (r \ esid 858 through 860 and (name N or name CA or name C or name O or name CB )) or \ resid 861 through 863 or (resid 864 and (name N or name CA or name C or name O \ or name CB )) or resid 869 through 890 or (resid 891 through 892 and (name N or \ name CA or name C or name O or name CB )) or resid 893 through 912 or (resid 913 \ through 921 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 22 through 934 or (resid 935 through 936 and (name N or name CA or name C or nam \ e O or name CB )) or resid 937 through 981 or (resid 982 through 984 and (name N \ or name CA or name C or name O or name CB )) or (resid 985 through 989 and (nam \ e N or name CA or name C or name O or name CB )) or resid 990 through 1047 or (r \ esid 1048 through 1074 and (name N or name CA or name C or name O or name CB )) \ or resid 1075 through 1086 or (resid 1087 through 1088 and (name N or name CA or \ name C or name O or name CB )) or resid 1089 through 1131 or (resid 1132 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1133 through 1467)) selection = (chain 'C' and (resid 40 through 49 or resid 116 through 137 or resid 164 throug \ h 169 or (resid 170 through 172 and (name N or name CA or name C or name O or na \ me CB )) or resid 173 through 175 or (resid 182 through 183 and (name N or name \ CA or name C or name O or name CB )) or resid 184 through 197 or (resid 198 thro \ ugh 202 and (name N or name CA or name C or name O or name CB )) or resid 259 th \ rough 260 or (resid 261 through 265 and (name N or name CA or name C or name O o \ r name CB )) or (resid 266 through 271 and (name N or name CA or name C or name \ O or name CB )) or resid 272 through 277 or (resid 278 through 285 and (name N o \ r name CA or name C or name O or name CB )) or resid 286 or (resid 287 through 2 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 296 through \ 302 or (resid 303 through 304 and (name N or name CA or name C or name O or nam \ e CB )) or resid 313 through 315 or (resid 316 through 318 and (name N or name C \ A or name C or name O or name CB )) or resid 319 through 325 or (resid 326 throu \ gh 327 and (name N or name CA or name C or name O or name CB )) or resid 353 thr \ ough 364 or resid 372 through 389 or (resid 390 through 394 and (name N or name \ CA or name C or name O or name CB )) or (resid 406 through 412 and (name N or na \ me CA or name C or name O or name CB )) or resid 413 through 421 or (resid 426 t \ hrough 431 and (name N or name CA or name C or name O or name CB )) or resid 432 \ through 433 or (resid 434 through 435 and (name N or name CA or name C or name \ O or name CB )) or resid 436 through 437 or (resid 438 through 439 and (name N o \ r name CA or name C or name O or name CB )) or resid 440 or (resid 441 through 4 \ 50 and (name N or name CA or name C or name O or name CB )) or (resid 455 throug \ h 459 and (name N or name CA or name C or name O or name CB )) or resid 460 thro \ ugh 474 or (resid 475 and (name N or name CA or name C or name O or name CB )) o \ r resid 476 through 477 or (resid 478 through 479 and (name N or name CA or name \ C or name O or name CB )) or resid 480 through 499 or (resid 500 and (name N or \ name CA or name C or name O or name CB )) or resid 501 through 507 or (resid 50 \ 8 through 515 and (name N or name CA or name C or name O or name CB )) or resid \ 516 through 537 or (resid 538 through 539 and (name N or name CA or name C or na \ me O or name CB )) or resid 540 through 544 or (resid 545 through 547 and (name \ N or name CA or name C or name O or name CB )) or resid 548 through 596 or (resi \ d 597 through 598 and (name N or name CA or name C or name O or name CB )) or re \ sid 599 through 603 or (resid 604 and (name N or name CA or name C or name O or \ name CB )) or resid 605 through 609 or (resid 610 through 611 and (name N or nam \ e CA or name C or name O or name CB )) or resid 612 through 631 or (resid 632 an \ d (name N or name CA or name C or name O or name CB )) or resid 633 through 639 \ or resid 646 through 649 or (resid 650 through 652 and (name N or name CA or nam \ e C or name O or name CB )) or resid 653 through 694 or (resid 695 through 696 a \ nd (name N or name CA or name C or name O or name CB )) or resid 697 through 702 \ or (resid 703 and (name N or name CA or name C or name O or name CB )) or resid \ 704 through 739 or (resid 740 through 743 and (name N or name CA or name C or n \ ame O or name CB )) or resid 744 or (resid 745 through 798 and (name N or name C \ A or name C or name O or name CB )) or resid 799 or (resid 800 through 804 and ( \ name N or name CA or name C or name O or name CB )) or resid 805 through 806 or \ (resid 807 and (name N or name CA or name C or name O or name CB )) or resid 808 \ through 811 or (resid 812 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 820 or (resid 821 and (name N or name CA or name C or n \ ame O or name CB )) or resid 822 through 823 or (resid 824 through 825 and (name \ N or name CA or name C or name O or name CB )) or resid 826 through 828 or (res \ id 829 through 832 and (name N or name CA or name C or name O or name CB )) or r \ esid 840 through 841 or (resid 842 through 845 and (name N or name CA or name C \ or name O or name CB )) or resid 846 through 854 or (resid 855 through 860 and ( \ name N or name CA or name C or name O or name CB )) or resid 861 through 862 or \ (resid 863 through 864 and (name N or name CA or name C or name O or name CB )) \ or (resid 869 through 881 and (name N or name CA or name C or name O or name CB \ )) or resid 882 through 884 or (resid 885 and (name N or name CA or name C or na \ me O or name CB )) or resid 886 through 889 or (resid 890 through 892 and (name \ N or name CA or name C or name O or name CB )) or resid 893 through 917 or (resi \ d 918 through 921 and (name N or name CA or name C or name O or name CB )) or re \ sid 922 through 925 or (resid 926 through 930 and (name N or name CA or name C o \ r name O or name CB )) or resid 931 or (resid 932 through 936 and (name N or nam \ e CA or name C or name O or name CB )) or resid 937 through 980 or (resid 981 th \ rough 984 and (name N or name CA or name C or name O or name CB )) or resid 985 \ through 994 or (resid 995 through 1032 and (name N or name CA or name C or name \ O or name CB )) or resid 1033 through 1051 or (resid 1052 through 1074 and (name \ N or name CA or name C or name O or name CB )) or resid 1075 through 1080 or (r \ esid 1081 and (name N or name CA or name C or name O or name CB )) or resid 1082 \ through 1100 or (resid 1101 through 1102 and (name N or name CA or name C or na \ me O or name CB )) or resid 1103 or (resid 1104 through 1108 and (name N or name \ CA or name C or name O or name CB )) or resid 1109 through 1126 or (resid 1127 \ and (name N or name CA or name C or name O or name CB )) or resid 1128 through 1 \ 134 or (resid 1135 and (name N or name CA or name C or name O or name CB )) or r \ esid 1136 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 through 1153 or (resid 1154 and (name \ N or name CA or name C or name O or name CB )) or resid 1155 through 1159 or (re \ sid 1160 and (name N or name CA or name C or name O or name CB )) or resid 1161 \ through 1172 or (resid 1173 and (name N or name CA or name C or name O or name C \ B )) or resid 1174 through 1448 or (resid 1449 through 1453 and (name N or name \ CA or name C or name O or name CB )) or resid 1454 through 1467)) selection = (chain 'D' and (resid 40 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 or (resid 119 through 124 and (name N o \ r name CA or name C or name O or name CB )) or resid 125 or (resid 126 through 1 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 134 or (resid 135 through 165 and (name N or name CA or name C or name O or nam \ e CB )) or resid 166 through 198 or (resid 199 through 202 and (name N or name C \ A or name C or name O or name CB )) or resid 259 through 262 or (resid 263 throu \ gh 265 and (name N or name CA or name C or name O or name CB )) or (resid 266 th \ rough 271 and (name N or name CA or name C or name O or name CB )) or resid 272 \ through 314 or (resid 315 through 318 and (name N or name CA or name C or name O \ or name CB )) or resid 319 through 321 or (resid 322 through 323 and (name N or \ name CA or name C or name O or name CB )) or resid 324 through 327 or (resid 35 \ 3 through 374 and (name N or name CA or name C or name O or name CB )) or resid \ 375 through 380 or (resid 381 through 388 and (name N or name CA or name C or na \ me O or name CB )) or resid 389 through 391 or (resid 392 through 412 and (name \ N or name CA or name C or name O or name CB )) or resid 413 through 418 or (resi \ d 419 through 431 and (name N or name CA or name C or name O or name CB )) or re \ sid 432 through 620 or (resid 621 and (name N or name CA or name C or name O or \ name CB )) or resid 622 through 680 or (resid 681 through 682 and (name N or nam \ e CA or name C or name O or name CB )) or resid 683 through 718 or (resid 719 an \ d (name N or name CA or name C or name O or name CB )) or (resid 720 through 726 \ and (name N or name CA or name C or name O or name CB )) or resid 727 through 7 \ 33 or (resid 734 through 738 and (name N or name CA or name C or name O or name \ CB )) or resid 739 through 810 or (resid 811 through 812 and (name N or name CA \ or name C or name O or name CB )) or resid 813 through 824 or (resid 825 and (na \ me N or name CA or name C or name O or name CB )) or resid 826 through 857 or (r \ esid 858 through 860 and (name N or name CA or name C or name O or name CB )) or \ resid 861 through 863 or (resid 864 and (name N or name CA or name C or name O \ or name CB )) or resid 869 through 890 or (resid 891 through 892 and (name N or \ name CA or name C or name O or name CB )) or resid 893 through 912 or (resid 913 \ through 921 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 22 through 934 or (resid 935 through 936 and (name N or name CA or name C or nam \ e O or name CB )) or resid 937 through 981 or (resid 982 through 984 and (name N \ or name CA or name C or name O or name CB )) or (resid 985 through 989 and (nam \ e N or name CA or name C or name O or name CB )) or resid 990 through 1047 or (r \ esid 1048 through 1074 and (name N or name CA or name C or name O or name CB )) \ or resid 1075 through 1086 or (resid 1087 through 1088 and (name N or name CA or \ name C or name O or name CB )) or resid 1089 through 1131 or (resid 1132 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1133 through 1467)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 5.120 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 72.050 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.140 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.190 ------------------------------------------------------------------------------- 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= 0.474 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 *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3300 time to fit residues: 170.1434 Evaluate side-chains 167 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8239 ------------------------------------------------------------------------------- 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: 9.9990 chunk 312 optimal weight: 0.1980 chunk 173 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 210 optimal weight: 50.0000 chunk 166 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 196 optimal weight: 50.0000 chunk 240 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 259 HIS A 605 GLN A 656 HIS A 707 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 ASN C 47 ASN C 259 HIS C 605 GLN C 656 HIS C 707 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 707 HIS B1164 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 HIS D 707 HIS D1164 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26748 Z= 0.254 Angle : 0.576 8.508 36822 Z= 0.320 Chirality : 0.038 0.141 4520 Planarity : 0.005 0.054 4802 Dihedral : 5.517 25.001 4184 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: -0.87 (0.13), residues: 3848 helix: 0.53 (0.10), residues: 2520 sheet: -1.97 (0.33), residues: 216 loop : -2.83 (0.17), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 2 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2762 time to fit residues: 104.8758 Evaluate side-chains 165 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.192 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 40.0000 chunk 116 optimal weight: 20.0000 chunk 311 optimal weight: 50.0000 chunk 254 optimal weight: 9.9990 chunk 103 optimal weight: 50.0000 chunk 374 optimal weight: 8.9990 chunk 404 optimal weight: 50.0000 chunk 333 optimal weight: 9.9990 chunk 371 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 300 optimal weight: 30.0000 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 144 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN D 711 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26748 Z= 0.393 Angle : 0.703 9.961 36822 Z= 0.388 Chirality : 0.040 0.177 4520 Planarity : 0.005 0.054 4802 Dihedral : 5.602 25.171 4184 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.26 % Allowed : 5.46 % Favored : 94.28 % 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: -0.28 (0.14), residues: 3848 helix: 1.01 (0.10), residues: 2508 sheet: -2.22 (0.32), residues: 240 loop : -2.52 (0.18), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 3 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 3.196 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 178 average time/residue: 0.2622 time to fit residues: 87.8978 Evaluate side-chains 156 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 3.006 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2249 time to fit residues: 4.6087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 20.0000 chunk 281 optimal weight: 40.0000 chunk 194 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 178 optimal weight: 50.0000 chunk 251 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 398 optimal weight: 0.3980 chunk 196 optimal weight: 50.0000 chunk 356 optimal weight: 0.0170 chunk 107 optimal weight: 5.9990 overall best weight: 2.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 GLN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26748 Z= 0.145 Angle : 0.488 7.081 36822 Z= 0.263 Chirality : 0.037 0.135 4520 Planarity : 0.004 0.050 4802 Dihedral : 4.803 24.039 4184 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 0.79 (0.14), residues: 3848 helix: 1.91 (0.10), residues: 2522 sheet: -1.96 (0.33), residues: 232 loop : -2.33 (0.18), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 4 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2746 time to fit residues: 113.1856 Evaluate side-chains 164 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 0.0050 chunk 226 optimal weight: 0.4980 chunk 5 optimal weight: 20.0000 chunk 296 optimal weight: 50.0000 chunk 164 optimal weight: 6.9990 chunk 339 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 overall best weight: 3.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26748 Z= 0.172 Angle : 0.485 7.003 36822 Z= 0.261 Chirality : 0.036 0.136 4520 Planarity : 0.004 0.049 4802 Dihedral : 4.460 24.224 4184 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 1.36 (0.14), residues: 3848 helix: 2.36 (0.10), residues: 2530 sheet: -1.72 (0.33), residues: 250 loop : -2.19 (0.19), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 5 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2806 time to fit residues: 101.8327 Evaluate side-chains 165 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 3.9990 chunk 358 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 398 optimal weight: 0.0470 chunk 330 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 overall best weight: 4.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26748 Z= 0.202 Angle : 0.495 9.778 36822 Z= 0.268 Chirality : 0.036 0.135 4520 Planarity : 0.004 0.059 4802 Dihedral : 4.400 23.855 4184 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 1.49 (0.14), residues: 3848 helix: 2.47 (0.10), residues: 2532 sheet: -1.65 (0.34), residues: 248 loop : -2.19 (0.19), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 6 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2713 time to fit residues: 98.3933 Evaluate side-chains 163 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.060 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 335 optimal weight: 2.9990 chunk 222 optimal weight: 30.0000 chunk 397 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26748 Z= 0.198 Angle : 0.492 7.393 36822 Z= 0.266 Chirality : 0.036 0.166 4520 Planarity : 0.004 0.051 4802 Dihedral : 4.345 23.416 4184 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 1.59 (0.14), residues: 3848 helix: 2.51 (0.10), residues: 2558 sheet: -1.31 (0.38), residues: 214 loop : -2.25 (0.19), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 7 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.032 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2793 time to fit residues: 95.9521 Evaluate side-chains 153 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 196 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 312 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26748 Z= 0.201 Angle : 0.497 6.910 36822 Z= 0.269 Chirality : 0.037 0.151 4520 Planarity : 0.004 0.055 4802 Dihedral : 4.326 23.074 4184 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 1.64 (0.14), residues: 3848 helix: 2.55 (0.10), residues: 2556 sheet: -1.24 (0.38), residues: 214 loop : -2.21 (0.19), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 8 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 3.241 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2712 time to fit residues: 90.6875 Evaluate side-chains 153 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 9.9990 chunk 380 optimal weight: 50.0000 chunk 347 optimal weight: 20.0000 chunk 370 optimal weight: 30.0000 chunk 222 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 chunk 290 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 349 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26748 Z= 0.229 Angle : 0.518 6.830 36822 Z= 0.281 Chirality : 0.037 0.176 4520 Planarity : 0.004 0.054 4802 Dihedral : 4.381 22.818 4184 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.57 (0.14), residues: 3848 helix: 2.49 (0.10), residues: 2566 sheet: -1.23 (0.39), residues: 214 loop : -2.30 (0.19), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 9 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 3.300 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2737 time to fit residues: 91.3220 Evaluate side-chains 154 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 8.9990 chunk 391 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 185 optimal weight: 30.0000 chunk 272 optimal weight: 40.0000 chunk 410 optimal weight: 20.0000 chunk 377 optimal weight: 30.0000 chunk 326 optimal weight: 50.0000 chunk 33 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1329 HIS D1329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26748 Z= 0.300 Angle : 0.595 8.207 36822 Z= 0.325 Chirality : 0.039 0.152 4520 Planarity : 0.004 0.055 4802 Dihedral : 4.787 22.913 4184 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 1.14 (0.14), residues: 3848 helix: 2.15 (0.10), residues: 2546 sheet: -1.51 (0.39), residues: 210 loop : -2.29 (0.18), residues: 1092 ********************** REFINEMENT MACRO_CYCLE 10 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.956 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2763 time to fit residues: 88.5171 Evaluate side-chains 148 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 8.9990 chunk 348 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 301 optimal weight: 50.0000 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 50.0000 chunk 327 optimal weight: 50.0000 chunk 137 optimal weight: 0.9990 chunk 336 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.055986 restraints weight = 193439.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056895 restraints weight = 124388.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057593 restraints weight = 92014.001| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26748 Z= 0.160 Angle : 0.483 6.683 36822 Z= 0.259 Chirality : 0.037 0.138 4520 Planarity : 0.004 0.055 4802 Dihedral : 4.355 23.058 4184 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.62 (0.14), residues: 3848 helix: 2.52 (0.10), residues: 2558 sheet: -1.24 (0.40), residues: 206 loop : -2.18 (0.19), residues: 1084 =============================================================================== Job complete usr+sys time: 4037.27 seconds wall clock time: 74 minutes 28.79 seconds (4468.79 seconds total)