Starting phenix.real_space_refine on Thu Feb 22 00:38:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkx_20369/02_2024/6pkx_20369_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkx_20369/02_2024/6pkx_20369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkx_20369/02_2024/6pkx_20369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkx_20369/02_2024/6pkx_20369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkx_20369/02_2024/6pkx_20369_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pkx_20369/02_2024/6pkx_20369_trim_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 116 5.16 5 C 20956 2.51 5 N 5670 2.21 5 O 5700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 280": "NH1" <-> "NH2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 750": "NH1" <-> "NH2" Residue "B ARG 944": "NH1" <-> "NH2" Residue "B TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1162": "NH1" <-> "NH2" Residue "B PHE 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "D TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 750": "NH1" <-> "NH2" Residue "D ARG 944": "NH1" <-> "NH2" Residue "D TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1162": "NH1" <-> "NH2" Residue "D PHE 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32448 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 8049 Classifications: {'peptide': 1206} Incomplete info: {'truncation_to_alanine': 465} Link IDs: {'PTRANS': 44, 'TRANS': 1161} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1725 Unresolved non-hydrogen angles: 2165 Unresolved non-hydrogen dihedrals: 1389 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 31, 'UNK:plan-1': 22, 'ASP:plan': 38, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 12, 'GLU:plan': 72, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1063 Chain: "B" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 8138 Classifications: {'peptide': 1218} Incomplete info: {'truncation_to_alanine': 493} Link IDs: {'PTRANS': 46, 'TRANS': 1171} Chain breaks: 16 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1763 Unresolved non-hydrogen angles: 2198 Unresolved non-hydrogen dihedrals: 1406 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 11, 'UNK:plan-1': 22, 'TYR:plan': 7, 'ASN:plan1': 20, 'TRP:plan': 2, 'ASP:plan': 41, 'PHE:plan': 10, 'GLU:plan': 74, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1050 Chain: "C" Number of atoms: 8049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 8049 Classifications: {'peptide': 1206} Incomplete info: {'truncation_to_alanine': 465} Link IDs: {'PTRANS': 44, 'TRANS': 1161} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1725 Unresolved non-hydrogen angles: 2165 Unresolved non-hydrogen dihedrals: 1389 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 31, 'UNK:plan-1': 22, 'ASP:plan': 38, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 12, 'GLU:plan': 72, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1063 Chain: "D" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 8138 Classifications: {'peptide': 1218} Incomplete info: {'truncation_to_alanine': 493} Link IDs: {'PTRANS': 46, 'TRANS': 1171} Chain breaks: 16 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1763 Unresolved non-hydrogen angles: 2198 Unresolved non-hydrogen dihedrals: 1406 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 11, 'UNK:plan-1': 22, 'TYR:plan': 7, 'ASN:plan1': 20, 'TRP:plan': 2, 'ASP:plan': 41, 'PHE:plan': 10, 'GLU:plan': 74, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1050 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'AR6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'AR6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLU A1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A1272 " 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 ARG A1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG A1447 " occ=0.50 residue: pdb=" N GLU B1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B1272 " 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 ARG B1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG B1447 " occ=0.50 residue: pdb=" N GLU C1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU C1272 " 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 ARG C1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG C1447 " occ=0.50 residue: pdb=" N GLU D1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D1272 " occ=0.50 residue: pdb=" N VAL D1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D1400 " occ=0.50 residue: pdb=" N ARG D1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG D1447 " occ=0.50 Time building chain proxies: 17.50, per 1000 atoms: 0.54 Number of scatterers: 32448 At special positions: 0 Unit cell: (165.41, 162.63, 179.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 116 16.00 P 4 15.00 O 5700 8.00 N 5670 7.00 C 20956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.02 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1024 " distance=2.01 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.00 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1024 " distance=2.06 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.02 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1024 " distance=2.01 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.00 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1024 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.12 Conformation dependent library (CDL) restraints added in 6.3 seconds 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 203 helices and 12 sheets defined 53.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.26 Creating SS restraints... Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.538A pdb=" N SER A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.888A pdb=" N ALA A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 366 through 369 Processing helix chain 'A' and resid 372 through 388 removed outlier: 3.865A pdb=" N MET A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 Processing helix chain 'A' and resid 427 through 438 Processing helix chain 'A' and resid 441 through 448 removed outlier: 3.936A pdb=" N SER A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 473 through 482 Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'A' and resid 594 through 604 removed outlier: 4.115A pdb=" N TRP A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 644 through 671 Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.002A pdb=" N ILE A 741 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 742 " --> pdb=" O PRO A 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 742' Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 799 through 806 Processing helix chain 'A' and resid 809 through 833 Processing helix chain 'A' and resid 841 through 863 removed outlier: 3.695A pdb=" N THR A 851 " --> pdb=" O TYR A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 876 Processing helix chain 'A' and resid 882 through 900 removed outlier: 4.249A pdb=" N ILE A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 922 Processing helix chain 'A' and resid 924 through 929 removed outlier: 4.541A pdb=" N ALA A 928 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 972 removed outlier: 4.756A pdb=" N LEU A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 4.735A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 990 - end of helix removed outlier: 3.625A pdb=" N ILE A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 removed outlier: 4.239A pdb=" N ASN A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 997 through 1001' Processing helix chain 'A' and resid 1039 through 1066 removed outlier: 3.913A pdb=" N MET A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A1049 " --> pdb=" O CYS A1045 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A1050 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A1066 " --> pdb=" O ILE A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1070 No H-bonds generated for 'chain 'A' and resid 1068 through 1070' Processing helix chain 'A' and resid 1074 through 1091 removed outlier: 4.511A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1085 " --> pdb=" O GLN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1111 Processing helix chain 'A' and resid 1130 through 1156 Processing helix chain 'A' and resid 1159 through 1183 Processing helix chain 'A' and resid 1189 through 1208 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1370 through 1379 Processing helix chain 'A' and resid 1428 through 1431 No H-bonds generated for 'chain 'A' and resid 1428 through 1431' Processing helix chain 'A' and resid 1438 through 1440 No H-bonds generated for 'chain 'A' and resid 1438 through 1440' Processing helix chain 'A' and resid 1457 through 1468 removed outlier: 3.611A pdb=" N ALA A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 160 through 177 removed outlier: 4.101A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.610A pdb=" N ILE B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA B 279 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 4.720A pdb=" N ASN B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 405 through 418 Processing helix chain 'B' and resid 427 through 437 removed outlier: 4.299A pdb=" N ALA B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 447 Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.525A pdb=" N HIS B 461 " --> pdb=" O SER B 458 " (cutoff:3.500A) Proline residue: B 462 - end of helix Processing helix chain 'B' and resid 473 through 482 Processing helix chain 'B' and resid 486 through 489 No H-bonds generated for 'chain 'B' and resid 486 through 489' Processing helix chain 'B' and resid 493 through 501 Processing helix chain 'B' and resid 507 through 516 removed outlier: 4.202A pdb=" N LYS B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.876A pdb=" N SER B 540 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 541 " --> pdb=" O HIS B 538 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B 545 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 605 Processing helix chain 'B' and resid 608 through 616 removed outlier: 4.029A pdb=" N ILE B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 637 Processing helix chain 'B' and resid 644 through 671 Processing helix chain 'B' and resid 674 through 680 Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 708 through 719 Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 749 through 764 removed outlier: 3.585A pdb=" N THR B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 806 Processing helix chain 'B' and resid 809 through 832 removed outlier: 3.932A pdb=" N MET B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 863 Processing helix chain 'B' and resid 870 through 878 Processing helix chain 'B' and resid 882 through 899 Processing helix chain 'B' and resid 905 through 929 Processing helix chain 'B' and resid 937 through 971 removed outlier: 3.598A pdb=" N ASP B 949 " --> pdb=" O ARG B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 986 removed outlier: 3.790A pdb=" N ILE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 995 Processing helix chain 'B' and resid 1037 through 1070 removed outlier: 3.935A pdb=" N TYR B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1089 removed outlier: 3.540A pdb=" N TYR B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1108 removed outlier: 5.267A pdb=" N LEU B1102 " --> pdb=" O PRO B1098 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B1105 " --> pdb=" O LEU B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1155 removed outlier: 4.094A pdb=" N GLU B1134 " --> pdb=" O GLN B1130 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU B1135 " --> pdb=" O THR B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1182 removed outlier: 4.576A pdb=" N HIS B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1208 Processing helix chain 'B' and resid 1252 through 1255 Processing helix chain 'B' and resid 1370 through 1380 Processing helix chain 'B' and resid 1428 through 1432 Processing helix chain 'B' and resid 1452 through 1454 No H-bonds generated for 'chain 'B' and resid 1452 through 1454' Processing helix chain 'B' and resid 1457 through 1469 Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 190 through 204 removed outlier: 3.539A pdb=" N SER C 204 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 275 through 286 removed outlier: 3.888A pdb=" N ALA C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 366 through 369 Processing helix chain 'C' and resid 372 through 388 removed outlier: 3.865A pdb=" N MET C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 417 Processing helix chain 'C' and resid 427 through 438 Processing helix chain 'C' and resid 441 through 448 removed outlier: 3.937A pdb=" N SER C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 473 through 482 Processing helix chain 'C' and resid 486 through 489 No H-bonds generated for 'chain 'C' and resid 486 through 489' Processing helix chain 'C' and resid 493 through 501 Processing helix chain 'C' and resid 507 through 516 Processing helix chain 'C' and resid 536 through 547 Processing helix chain 'C' and resid 594 through 604 removed outlier: 4.115A pdb=" N TRP C 601 " --> pdb=" O ASP C 597 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 617 Processing helix chain 'C' and resid 621 through 639 Processing helix chain 'C' and resid 644 through 671 Processing helix chain 'C' and resid 676 through 680 Processing helix chain 'C' and resid 692 through 699 Processing helix chain 'C' and resid 708 through 718 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 738 through 742 removed outlier: 4.001A pdb=" N ILE C 741 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C 742 " --> pdb=" O PRO C 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 742' Processing helix chain 'C' and resid 749 through 759 Processing helix chain 'C' and resid 799 through 806 Processing helix chain 'C' and resid 809 through 833 Processing helix chain 'C' and resid 841 through 863 removed outlier: 3.696A pdb=" N THR C 851 " --> pdb=" O TYR C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 876 Processing helix chain 'C' and resid 882 through 900 removed outlier: 4.250A pdb=" N ILE C 894 " --> pdb=" O ILE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 922 Processing helix chain 'C' and resid 924 through 929 removed outlier: 4.542A pdb=" N ALA C 928 " --> pdb=" O ARG C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 972 removed outlier: 4.756A pdb=" N LEU C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 994 removed outlier: 4.735A pdb=" N GLU C 989 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Proline residue: C 990 - end of helix removed outlier: 3.624A pdb=" N ILE C 994 " --> pdb=" O PRO C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1066 removed outlier: 3.913A pdb=" N MET C1043 " --> pdb=" O LEU C1039 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS C1045 " --> pdb=" O ILE C1041 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C1049 " --> pdb=" O CYS C1045 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE C1050 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C1066 " --> pdb=" O ILE C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1070 No H-bonds generated for 'chain 'C' and resid 1068 through 1070' Processing helix chain 'C' and resid 1074 through 1091 removed outlier: 4.511A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU C1084 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C1085 " --> pdb=" O GLN C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1111 Processing helix chain 'C' and resid 1130 through 1156 Processing helix chain 'C' and resid 1159 through 1183 Processing helix chain 'C' and resid 1189 through 1208 Processing helix chain 'C' and resid 1253 through 1255 No H-bonds generated for 'chain 'C' and resid 1253 through 1255' Processing helix chain 'C' and resid 1370 through 1379 Processing helix chain 'C' and resid 1428 through 1431 No H-bonds generated for 'chain 'C' and resid 1428 through 1431' Processing helix chain 'C' and resid 1438 through 1440 No H-bonds generated for 'chain 'C' and resid 1438 through 1440' Processing helix chain 'C' and resid 1457 through 1468 removed outlier: 3.610A pdb=" N ALA C1467 " --> pdb=" O LEU C1463 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 160 through 177 removed outlier: 4.102A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 272 through 287 removed outlier: 3.611A pdb=" N ILE D 275 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 276 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA D 279 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 4.719A pdb=" N ASN D 322 " --> pdb=" O ASN D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 352 through 361 Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 427 through 437 removed outlier: 4.300A pdb=" N ALA D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 447 Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.525A pdb=" N HIS D 461 " --> pdb=" O SER D 458 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 482 Processing helix chain 'D' and resid 486 through 489 No H-bonds generated for 'chain 'D' and resid 486 through 489' Processing helix chain 'D' and resid 493 through 501 Processing helix chain 'D' and resid 507 through 516 removed outlier: 4.202A pdb=" N LYS D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG D 515 " --> pdb=" O LYS D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 546 removed outlier: 3.876A pdb=" N SER D 540 " --> pdb=" O SER D 537 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 541 " --> pdb=" O HIS D 538 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 544 " --> pdb=" O GLU D 541 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 545 " --> pdb=" O GLU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 605 Processing helix chain 'D' and resid 608 through 616 removed outlier: 4.029A pdb=" N ILE D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 637 Processing helix chain 'D' and resid 644 through 671 Processing helix chain 'D' and resid 674 through 680 Processing helix chain 'D' and resid 692 through 699 Processing helix chain 'D' and resid 708 through 719 Processing helix chain 'D' and resid 728 through 736 Processing helix chain 'D' and resid 739 through 743 Processing helix chain 'D' and resid 749 through 764 removed outlier: 3.586A pdb=" N THR D 761 " --> pdb=" O GLN D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 806 Processing helix chain 'D' and resid 809 through 832 removed outlier: 3.932A pdb=" N MET D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 863 Processing helix chain 'D' and resid 870 through 878 Processing helix chain 'D' and resid 882 through 899 Processing helix chain 'D' and resid 905 through 929 Processing helix chain 'D' and resid 937 through 971 removed outlier: 3.599A pdb=" N ASP D 949 " --> pdb=" O ARG D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 986 removed outlier: 3.790A pdb=" N ILE D 983 " --> pdb=" O LEU D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 995 Processing helix chain 'D' and resid 1037 through 1070 removed outlier: 3.935A pdb=" N TYR D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1089 removed outlier: 3.540A pdb=" N TYR D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1108 removed outlier: 5.269A pdb=" N LEU D1102 " --> pdb=" O PRO D1098 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D1105 " --> pdb=" O LEU D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1155 removed outlier: 4.094A pdb=" N GLU D1134 " --> pdb=" O GLN D1130 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU D1135 " --> pdb=" O THR D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1159 through 1182 removed outlier: 4.576A pdb=" N HIS D1164 " --> pdb=" O GLU D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1189 through 1208 Processing helix chain 'D' and resid 1252 through 1255 Processing helix chain 'D' and resid 1370 through 1380 Processing helix chain 'D' and resid 1428 through 1432 Processing helix chain 'D' and resid 1452 through 1454 No H-bonds generated for 'chain 'D' and resid 1452 through 1454' Processing helix chain 'D' and resid 1457 through 1469 Processing sheet with id= A, first strand: chain 'A' and resid 237 through 239 removed outlier: 7.798A pdb=" N ALA A 238 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP A 105 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 181 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 217 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY A 184 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 302 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL A 305 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 327 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1326 through 1329 removed outlier: 6.552A pdb=" N GLU A1412 " --> pdb=" O ILE A1327 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N HIS A1329 " --> pdb=" O GLU A1412 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER A1414 " --> pdb=" O HIS A1329 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 105 through 107 Processing sheet with id= D, first strand: chain 'B' and resid 117 through 122 removed outlier: 6.106A pdb=" N ILE B 181 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL B 217 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY B 184 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1325 through 1329 Processing sheet with id= F, first strand: chain 'B' and resid 1345 through 1348 Processing sheet with id= G, first strand: chain 'C' and resid 237 through 239 removed outlier: 7.798A pdb=" N ALA C 238 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP C 105 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE C 181 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL C 217 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLY C 184 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 302 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL C 305 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 327 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 1326 through 1329 removed outlier: 6.551A pdb=" N GLU C1412 " --> pdb=" O ILE C1327 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N HIS C1329 " --> pdb=" O GLU C1412 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N SER C1414 " --> pdb=" O HIS C1329 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 105 through 107 Processing sheet with id= J, first strand: chain 'D' and resid 117 through 122 removed outlier: 6.107A pdb=" N ILE D 181 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL D 217 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY D 184 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 1325 through 1329 Processing sheet with id= L, first strand: chain 'D' and resid 1345 through 1348 1784 hydrogen bonds defined for protein. 5163 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: 12.45 Time building geometry restraints manager: 14.17 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: 10581 1.34 - 1.46: 8386 1.46 - 1.59: 14047 1.59 - 1.71: 12 1.71 - 1.83: 164 Bond restraints: 33190 Sorted by residual: bond pdb=" C3D AR6 D1602 " pdb=" C4D AR6 D1602 " ideal model delta sigma weight residual 1.529 1.300 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3D AR6 B1602 " pdb=" C4D AR6 B1602 " ideal model delta sigma weight residual 1.529 1.300 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1' AR6 B1602 " pdb=" C2' AR6 B1602 " ideal model delta sigma weight residual 1.529 1.304 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' AR6 D1602 " pdb=" C2' AR6 D1602 " ideal model delta sigma weight residual 1.529 1.304 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C1' AR6 B1602 " pdb=" O4' AR6 B1602 " ideal model delta sigma weight residual 1.396 1.608 -0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 33185 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.72: 695 105.72 - 112.94: 18127 112.94 - 120.16: 12267 120.16 - 127.39: 14159 127.39 - 134.61: 466 Bond angle restraints: 45714 Sorted by residual: angle pdb=" N ILE D 275 " pdb=" CA ILE D 275 " pdb=" C ILE D 275 " ideal model delta sigma weight residual 110.62 118.74 -8.12 1.02e+00 9.61e-01 6.35e+01 angle pdb=" N ILE B 275 " pdb=" CA ILE B 275 " pdb=" C ILE B 275 " ideal model delta sigma weight residual 110.62 118.73 -8.11 1.02e+00 9.61e-01 6.32e+01 angle pdb=" N GLY D 272 " pdb=" CA GLY D 272 " pdb=" C GLY D 272 " ideal model delta sigma weight residual 113.24 123.63 -10.39 1.31e+00 5.83e-01 6.29e+01 angle pdb=" N GLY B 272 " pdb=" CA GLY B 272 " pdb=" C GLY B 272 " ideal model delta sigma weight residual 113.24 123.61 -10.37 1.31e+00 5.83e-01 6.27e+01 angle pdb=" N ARG D 278 " pdb=" CA ARG D 278 " pdb=" C ARG D 278 " ideal model delta sigma weight residual 111.07 119.18 -8.11 1.07e+00 8.73e-01 5.74e+01 ... (remaining 45709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 17890 15.16 - 30.31: 902 30.31 - 45.47: 200 45.47 - 60.62: 42 60.62 - 75.78: 22 Dihedral angle restraints: 19056 sinusoidal: 4954 harmonic: 14102 Sorted by residual: dihedral pdb=" CA SER D1011 " pdb=" C SER D1011 " pdb=" N CYS D1012 " pdb=" CA CYS D1012 " ideal model delta harmonic sigma weight residual 180.00 125.40 54.60 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA SER B1011 " pdb=" C SER B1011 " pdb=" N CYS B1012 " pdb=" CA CYS B1012 " ideal model delta harmonic sigma weight residual 180.00 125.47 54.53 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ASP A 620 " pdb=" C ASP A 620 " pdb=" N CYS A 621 " pdb=" CA CYS A 621 " ideal model delta harmonic sigma weight residual -180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 19053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4687 0.072 - 0.144: 796 0.144 - 0.216: 82 0.216 - 0.288: 15 0.288 - 0.360: 4 Chirality restraints: 5584 Sorted by residual: chirality pdb=" CA CYS B1012 " pdb=" N CYS B1012 " pdb=" C CYS B1012 " pdb=" CB CYS B1012 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA CYS D1012 " pdb=" N CYS D1012 " pdb=" C CYS D1012 " pdb=" CB CYS D1012 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ARG D 278 " pdb=" N ARG D 278 " pdb=" C ARG D 278 " pdb=" CB ARG D 278 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 5581 not shown) Planarity restraints: 5844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 592 " 0.018 2.00e-02 2.50e+03 1.95e-02 9.47e+00 pdb=" CG TRP B 592 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 592 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 592 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 592 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 592 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 592 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 592 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP B 592 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 592 " -0.019 2.00e-02 2.50e+03 1.94e-02 9.45e+00 pdb=" CG TRP D 592 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 592 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 592 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 592 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 592 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 592 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 592 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 592 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP D 592 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 378 " 0.017 2.00e-02 2.50e+03 1.91e-02 9.10e+00 pdb=" CG TRP B 378 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 378 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 378 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 378 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 378 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 378 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 378 " -0.010 2.00e-02 2.50e+03 ... (remaining 5841 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 850 2.70 - 3.25: 32170 3.25 - 3.80: 50787 3.80 - 4.35: 55954 4.35 - 4.90: 92062 Nonbonded interactions: 231823 Sorted by model distance: nonbonded pdb=" O ARG D 249 " pdb=" OH TYR D 271 " model vdw 2.151 2.440 nonbonded pdb=" O ARG B 249 " pdb=" OH TYR B 271 " model vdw 2.151 2.440 nonbonded pdb=" CB UNK B1209 " pdb=" CB UNK C1209 " model vdw 2.190 3.840 nonbonded pdb=" CB UNK A1209 " pdb=" CB UNK D1209 " model vdw 2.229 3.840 nonbonded pdb=" OD1 ASN D 356 " pdb=" OH TYR D 367 " model vdw 2.316 2.440 ... (remaining 231818 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 98 and (name N or name CA or name C or name O or name CB \ )) or resid 99 through 102 or (resid 103 and (name N or name CA or name C or nam \ e O or name CB )) or resid 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 106 through 107 or (resid 108 and (name N or name \ CA or name C or name O or name CB )) or resid 114 through 122 or (resid 123 thr \ ough 124 and (name N or name CA or name C or name O or name CB )) or resid 125 t \ hrough 149 or (resid 150 and (name N or name CA or name C or name O or name CB ) \ ) or resid 151 or (resid 154 through 155 and (name N or name CA or name C or nam \ e O or name CB )) or resid 156 or (resid 157 and (name N or name CA or name C or \ name O or name CB )) or resid 158 through 162 or (resid 163 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or resid 164 through \ 166 or (resid 167 through 168 and (name N or name CA or name C or name O or nam \ e CB )) or resid 169 through 171 or (resid 172 and (name N or name CA or name C \ or name O or name CB )) or resid 173 through 174 or (resid 175 through 177 and ( \ name N or name CA or name C or name O or name CB )) or resid 178 through 190 or \ (resid 191 and (name N or name CA or name C or name O or name CB or name CG )) o \ r (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 93 through 195 or (resid 196 through 197 and (name N or name CA or name C or nam \ e O or name CB )) or resid 198 through 207 or (resid 208 through 209 and (name N \ or name CA or name C or name O or name CB )) or resid 210 through 224 or (resid \ 225 through 231 and (name N or name CA or name C or name O or name CB )) or res \ id 232 through 238 or (resid 239 through 245 and (name N or name CA or name C or \ name O or name CB )) or (resid 246 through 252 and (name N or name CA or name C \ or name O or name CB )) or resid 253 through 255 or (resid 256 and (name N or n \ ame CA or name C or name O or name CB )) or resid 257 through 272 or (resid 273 \ through 274 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 5 through 289 or (resid 297 and (name N or name CA or name C or name O or name C \ B )) or resid 298 through 320 or (resid 321 and (name N or name CA or name C or \ name O or name CB )) or resid 322 through 336 or (resid 337 and (name N or name \ CA or name C or name O or name CB )) or resid 338 through 340 or (resid 341 and \ (name N or name CA or name C or name O or name CB )) or resid 342 through 343 or \ (resid 344 through 345 and (name N or name CA or name C or name O or name CB )) \ or resid 346 or (resid 347 through 350 and (name N or name CA or name C or name \ O or name CB )) or resid 351 or (resid 352 through 353 and (name N or name CA o \ r name C or name O or name CB )) or resid 354 through 357 or (resid 358 through \ 361 and (name N or name CA or name C or name O or name CB )) or resid 362 throug \ h 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or \ resid 371 through 373 or (resid 374 and (name N or name CA or name C or name O o \ r name CB )) or resid 375 through 382 or (resid 383 through 384 and (name N or n \ ame CA or name C or name O or name CB )) or resid 385 through 386 or (resid 387 \ and (name N or name CA or name C or name O or name CB )) or resid 388 through 39 \ 3 or (resid 394 through 406 and (name N or name CA or name C or name O or name C \ B )) or resid 407 through 426 or (resid 427 through 431 and (name N or name CA o \ r name C or name O or name CB )) or resid 432 through 444 or (resid 445 and (nam \ e N or name CA or name C or name O or name CB )) or resid 446 through 452 or (re \ sid 453 through 454 and (name N or name CA or name C or name O or name CB )) or \ resid 455 through 460 or (resid 461 and (name N or name CA or name C or name O o \ r name CB )) or resid 462 through 483 or (resid 484 through 488 and (name N or n \ ame CA or name C or name O or name CB )) or resid 489 or (resid 490 through 499 \ and (name N or name CA or name C or name O or name CB )) or resid 500 through 50 \ 2 or (resid 503 and (name N or name CA or name C or name O or name CB )) or resi \ d 504 or (resid 505 through 506 and (name N or name CA or name C or name O or na \ me CB )) or resid 507 through 543 or (resid 544 and (name N or name CA or name C \ or name O or name CB )) or resid 545 through 549 or (resid 550 and (name N or n \ ame CA or name C or name O or name CB )) or resid 551 or (resid 552 and (name N \ or name CA or name C or name O or name CB )) or resid 553 through 554 or (resid \ 555 through 558 and (name N or name CA or name C or name O or name CB )) or resi \ d 591 through 595 or (resid 596 through 598 and (name N or name CA or name C or \ name O or name CB )) or resid 599 through 606 or (resid 607 through 609 and (nam \ e N or name CA or name C or name O or name CB )) or resid 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O or name CB \ )) or resid 703 through 721 or (resid 722 and (name N or name CA or name C or n \ ame O or name CB )) or resid 723 through 731 or (resid 732 through 738 and (name \ N or name CA or name C or name O or name CB )) or resid 739 through 740 or (res \ id 741 and (name N or name CA or name C or name O or name CB )) or resid 742 thr \ ough 748 or (resid 749 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE )) or resid 750 through 835 or (resid 836 through \ 838 and (name N or name CA or name C or name O or name CB )) or resid 839 throug \ h 841 or (resid 842 through 845 and (name N or name CA or name C or name O or na \ me CB )) or resid 846 through 851 or (resid 852 and (name N or name CA or name C \ or name O or name CB )) or resid 853 through 864 or resid 869 through 899 or (r \ esid 900 and (name N or name CA or name C or name O or name CB )) or resid 901 t \ hrough 904 or (resid 905 and (name N or name CA or name C or name O or name CB ) \ ) or resid 906 through 909 or (resid 910 and (name N or name CA or name C or nam \ e O or name CB )) or resid 911 through 915 or (resid 916 and (name N or name CA \ or name C or name O or name CB )) or resid 917 through 930 or (resid 931 through \ 935 and (name N or name CA or name C or name O or name CB )) or resid 936 throu \ gh 941 or (resid 942 through 950 and (name N or name CA or name C or name O or n \ ame CB )) or resid 951 through 952 or (resid 953 through 954 and (name N or name \ CA or name C or name O or name CB )) or resid 955 through 961 or (resid 962 thr \ ough 963 and (name N or name CA or name C or name O or name CB )) or resid 964 t \ hrough 974 or (resid 975 through 979 and (name N or name CA or name C or name O \ or name CB )) or resid 980 through 982 or (resid 983 through 984 and (name N or \ name CA or name C or name O or name CB )) or resid 985 through 1047 or (resid 10 \ 48 through 1049 and (name N or name CA or name C or name O or name CB )) or resi \ d 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(name N or name CA or name C or name O or name CB )) or resid 1130 thr \ ough 1132 or (resid 1133 through 1134 and (name N or name CA or name C or name O \ or name CB )) or resid 1135 through 1143 or (resid 1144 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE )) or resid 1145 \ through 1154 or (resid 1155 and (name N or name CA or name C or name O or name \ CB )) or resid 1156 through 1159 or (resid 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 o \ r name CA or name C or name O or name CB or name CG )) or resid 1174 through 117 \ 5 or (resid 1176 and (name N or name CA or name C or name O or name CB )) or res \ id 1177 through 1437 or resid 1444 through 1470)) selection = (chain 'B' and (resid 98 through 213 or (resid 214 and (name N or name CA or nam \ e C or name O or name CB )) or resid 215 through 394 or (resid 395 through 406 a \ nd (name N or name CA or name C or name 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\ id 1104 through 1105 and (name N or name CA or name C or name O or name CB )) or \ resid 1106 through 1108 or (resid 1109 through 1110 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1111 or resid 1120 through 1128 or (resid \ 1129 and (name N or name CA or name C or name O or name CB )) or resid 1130 thr \ ough 1132 or (resid 1133 through 1134 and (name N or name CA or name C or name O \ or name CB )) or resid 1135 through 1143 or (resid 1144 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE )) or resid 1145 \ through 1154 or (resid 1155 and (name N or name CA or name C or name O or name \ CB )) or resid 1156 through 1159 or (resid 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 o \ r name CA or name C or name O or name CB or name CG )) or resid 1174 through 117 \ 5 or (resid 1176 and (name N or name CA or name C or name O or name CB )) or res \ id 1177 through 1437 or resid 1444 through 1470)) selection = (chain 'D' and (resid 98 through 213 or (resid 214 and (name N or name CA or nam \ e C or name O or name CB )) or resid 215 through 394 or (resid 395 through 406 a \ nd (name N or name CA or name C or name O or name CB )) or resid 407 through 409 \ or (resid 410 through 416 and (name N or name CA or name C or name O or name CB \ )) or resid 417 or (resid 418 through 423 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 424 through 431 and (name N or name CA or name C o \ r name O or name CB )) or resid 432 through 433 or (resid 434 through 445 and (n \ ame N or name CA or name C or name O or name CB )) or resid 446 through 447 or ( \ resid 448 and (name N or name CA or name C or name O or name CB )) or resid 449 \ through 480 or (resid 481 through 482 and (name N or name CA or name C or name O \ or name CB )) or resid 483 through 494 or (resid 495 through 499 and (name N or \ name CA or name C or name O or name CB )) or resid 500 through 509 or (resid 51 \ 0 through 515 and (name N or name CA or name C or name O or name CB )) or resid \ 516 through 517 or (resid 535 through 536 and (name N or name CA or name C or na \ me O or name CB )) or resid 537 or (resid 538 and (name N or name CA or name C o \ r name O or name CB )) or resid 539 through 546 or (resid 547 and (name N or nam \ e CA or name C or name O or name CB )) or resid 548 or (resid 549 through 550 an \ d (name N or name CA or name C or name O or name CB )) or resid 551 through 558 \ or resid 591 through 597 or (resid 598 and (name N or name CA or name C or name \ O or name CB )) or resid 599 through 607 or (resid 608 through 609 and (name N o \ r name CA or name C or name O or name CB )) or resid 610 through 618 or (resid 6 \ 19 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE )) or (resid 620 and (name N or name CA or name C or name O or name CB \ )) or resid 621 through 645 or (resid 646 through 647 and (name N or name CA or \ name C or name O or name CB )) or resid 648 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 671 or (res \ id 672 through 678 and (name N or name CA or name C or name O or name CB )) or r \ esid 679 through 681 or (resid 682 and (name N or name CA or name C or name O or \ name CB )) or resid 683 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 710 or (resid 711 through 712 a \ nd (name N or name CA or name C or name O or name CB )) or resid 713 through 745 \ or (resid 746 through 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 or (resid 750 through 753 and (name N or name CA or name C or n \ ame O or name CB )) or resid 754 or (resid 755 through 761 and (name N or name C \ A or name C or name O or name CB )) or (resid 798 and (name N or name CA or name \ C or name O or name CB )) or resid 799 through 800 or (resid 801 and (name N or \ name CA or name C or name O or name CB )) or resid 802 through 811 or (resid 81 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 813 through \ 815 or (resid 816 and (name N or name CA or name C or name O or name CB )) or re \ sid 817 through 842 or (resid 843 through 845 and (name N or name CA or name C o \ r name O or name CB )) or resid 846 through 849 or (resid 850 and (name N or nam \ e CA or name C or name O or name CB )) or resid 851 through 853 or (resid 854 an \ d (name N or name CA or name C or name O or name CB )) or resid 855 through 869 \ or (resid 870 through 879 and (name N or name CA or name C or name O or name CB \ )) or resid 881 through 889 or (resid 890 and (name N or name CA or name C or na \ me O or name CB )) or resid 891 through 903 or (resid 904 through 905 and (name \ N or name CA or name C or name O or name CB )) or resid 906 through 924 or (resi \ d 925 and (name N or name CA or name C or name O or name CB )) or resid 926 thro \ ugh 933 or (resid 934 through 935 and (name N or name CA or name C or name O or \ name CB )) or resid 936 through 943 or (resid 944 through 950 and (name N or nam \ e CA or name C or name O or name CB )) or resid 951 through 955 or (resid 956 an \ d (name N or name CA or name C or name O or name CB )) or resid 957 through 968 \ or (resid 969 and (name N or name CA or name C or name O or name CB )) or resid \ 970 through 990 or (resid 991 through 995 and (name N or name CA or name C or na \ me O or name CB )) or (resid 996 through 998 and (name N or name CA or name C or \ name O or name CB )) or resid 999 through 1022 or (resid 1023 and (name N or na \ me CA or name C or name O or name CB )) or resid 1024 through 1027 or (resid 102 \ 8 through 1032 and (name N or name CA or name C or name O or name CB )) or resid \ 1033 through 1034 or (resid 1035 and (name N or name CA or name C or name O or \ name CB )) or resid 1036 through 1038 or (resid 1039 through 1044 and (name N or \ name CA or name C or name O or name CB )) or resid 1045 or (resid 1046 through \ 1049 and (name N or name CA or name C or name O or name CB )) or resid 1050 thro \ ugh 1057 or (resid 1058 through 1062 and (name N or name CA or name C or name O \ or name CB )) or resid 1063 through 1065 or (resid 1066 and (name N or name CA o \ r name C or name O or name CB )) or resid 1067 through 1083 or (resid 1084 and ( \ name N or name CA or name C or name O or name CB )) or resid 1085 through 1087 o \ r (resid 1088 through 1089 and (name N or name CA or name C or name O or name CB \ )) or resid 1090 through 1091 or (resid 1092 and (name N or name CA or name C o \ r name O or name CB )) or resid 1093 through 1094 or (resid 1095 and (name N or \ name CA or name C or name O or name CB )) or resid 1096 through 1122 or (resid 1 \ 123 and (name N or name CA or name C or name O or name CB )) or resid 1124 throu \ gh 1126 or (resid 1127 and (name N or name CA or name C or name O or name CB )) \ or resid 1128 through 1151 or (resid 1152 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name NE )) or resid 1153 through 1161 o \ r (resid 1162 and (name N or name CA or name C or name O or name CB )) or resid \ 1163 through 1209 or resid 1252 through 1257 or (resid 1258 through 1259 and (na \ me N or name CA or name C or name O or name CB )) or resid 1260 through 1291 or \ resid 1303 through 1355 or (resid 1356 through 1359 and (name N or name CA or na \ me C or name O or name CB )) or resid 1360 through 1437 or resid 1444 through 14 \ 70)) } 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.570 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 85.970 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.008 0.229 33190 Z= 0.514 Angle : 1.024 15.898 45714 Z= 0.560 Chirality : 0.055 0.360 5584 Planarity : 0.007 0.070 5844 Dihedral : 11.028 75.776 9824 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.99 (0.10), residues: 4640 helix: -2.18 (0.08), residues: 2542 sheet: -1.98 (0.30), residues: 278 loop : -3.33 (0.12), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP B 378 HIS 0.009 0.002 HIS B1329 PHE 0.026 0.003 PHE B 156 TYR 0.036 0.003 TYR C 847 ARG 0.010 0.001 ARG A1082 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1154 ASP cc_start: 0.8221 (m-30) cc_final: 0.8000 (m-30) REVERT: A 1173 MET cc_start: 0.6975 (ttp) cc_final: 0.6692 (ttm) REVERT: B 410 LEU cc_start: 0.9276 (mt) cc_final: 0.9028 (tp) REVERT: B 601 TRP cc_start: 0.8790 (t60) cc_final: 0.8520 (t60) REVERT: B 669 HIS cc_start: 0.8312 (t70) cc_final: 0.8002 (t-90) REVERT: B 923 CYS cc_start: 0.8078 (t) cc_final: 0.7600 (t) REVERT: B 1045 CYS cc_start: 0.8312 (m) cc_final: 0.7999 (t) REVERT: B 1252 MET cc_start: 0.7176 (mtm) cc_final: 0.6647 (pmm) REVERT: B 1290 GLN cc_start: 0.6786 (mm-40) cc_final: 0.6257 (pt0) REVERT: B 1305 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7376 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3395 (m100) cc_final: 0.2442 (m100) REVERT: B 1356 TRP cc_start: 0.5727 (m-90) cc_final: 0.5370 (m100) REVERT: C 1154 ASP cc_start: 0.8236 (m-30) cc_final: 0.7986 (m-30) REVERT: C 1173 MET cc_start: 0.6979 (ttp) cc_final: 0.6681 (ttm) REVERT: D 410 LEU cc_start: 0.9281 (mt) cc_final: 0.9027 (tp) REVERT: D 601 TRP cc_start: 0.8798 (t60) cc_final: 0.8590 (t60) REVERT: D 669 HIS cc_start: 0.8319 (t70) cc_final: 0.8037 (t70) REVERT: D 923 CYS cc_start: 0.7929 (t) cc_final: 0.7471 (t) REVERT: D 1045 CYS cc_start: 0.8225 (m) cc_final: 0.7964 (t) REVERT: D 1252 MET cc_start: 0.7176 (mtm) cc_final: 0.6647 (pmm) REVERT: D 1290 GLN cc_start: 0.6792 (mm-40) cc_final: 0.6257 (pt0) REVERT: D 1305 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7476 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3410 (m100) cc_final: 0.2474 (m100) REVERT: D 1356 TRP cc_start: 0.5734 (m-90) cc_final: 0.5370 (m100) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 0.3713 time to fit residues: 390.1850 Evaluate side-chains 358 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 407 optimal weight: 1.9990 chunk 365 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 229 optimal weight: 30.0000 chunk 281 optimal weight: 6.9990 chunk 437 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 256 ASN A 259 HIS A 707 HIS A1064 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 HIS A1419 HIS B 193 HIS B 259 HIS B 390 HIS B 707 HIS B 969 GLN B1164 HIS B1290 GLN B1329 HIS ** B1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 256 ASN C 259 HIS C 707 HIS C1064 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1326 HIS C1419 HIS C1431 ASN D 193 HIS D 259 HIS D 390 HIS D 707 HIS D 969 GLN D1164 HIS D1290 GLN D1329 HIS ** D1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33190 Z= 0.308 Angle : 0.671 8.991 45714 Z= 0.356 Chirality : 0.042 0.317 5584 Planarity : 0.005 0.059 5844 Dihedral : 6.144 80.159 5086 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.12), residues: 4640 helix: -0.27 (0.10), residues: 2536 sheet: -2.01 (0.27), residues: 306 loop : -2.87 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 592 HIS 0.008 0.001 HIS D 193 PHE 0.027 0.002 PHE C 922 TYR 0.024 0.002 TYR D1083 ARG 0.005 0.001 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 GLU cc_start: 0.7641 (pp20) cc_final: 0.7397 (pp20) REVERT: A 832 MET cc_start: 0.6215 (ttp) cc_final: 0.5968 (ttp) REVERT: A 1173 MET cc_start: 0.7130 (ttp) cc_final: 0.6808 (ttm) REVERT: B 410 LEU cc_start: 0.9356 (mt) cc_final: 0.9074 (tp) REVERT: B 1045 CYS cc_start: 0.8320 (m) cc_final: 0.8021 (p) REVERT: B 1252 MET cc_start: 0.7400 (mtm) cc_final: 0.6753 (pmm) REVERT: B 1290 GLN cc_start: 0.7110 (mm110) cc_final: 0.6345 (pt0) REVERT: B 1305 ARG cc_start: 0.8294 (mtm180) cc_final: 0.7598 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3674 (m100) cc_final: 0.2596 (m100) REVERT: B 1356 TRP cc_start: 0.5825 (m-90) cc_final: 0.5490 (m100) REVERT: C 445 GLU cc_start: 0.7623 (pp20) cc_final: 0.7370 (pp20) REVERT: C 832 MET cc_start: 0.6271 (ttp) cc_final: 0.5969 (ttp) REVERT: C 916 CYS cc_start: 0.8034 (m) cc_final: 0.7742 (t) REVERT: C 1049 LEU cc_start: 0.7153 (pp) cc_final: 0.6803 (tp) REVERT: C 1173 MET cc_start: 0.6873 (ttp) cc_final: 0.6530 (ttm) REVERT: D 410 LEU cc_start: 0.9369 (mt) cc_final: 0.9049 (tp) REVERT: D 1045 CYS cc_start: 0.8324 (m) cc_final: 0.7989 (p) REVERT: D 1252 MET cc_start: 0.7511 (mtm) cc_final: 0.6841 (pmm) REVERT: D 1290 GLN cc_start: 0.6989 (mm110) cc_final: 0.6260 (pt0) REVERT: D 1305 ARG cc_start: 0.8300 (mtm180) cc_final: 0.7600 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3817 (m100) cc_final: 0.2758 (m100) REVERT: D 1356 TRP cc_start: 0.5714 (m-90) cc_final: 0.5419 (m100) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.3391 time to fit residues: 256.7728 Evaluate side-chains 325 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 243 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 chunk 298 optimal weight: 0.0070 chunk 120 optimal weight: 0.0970 chunk 438 optimal weight: 5.9990 chunk 473 optimal weight: 0.1980 chunk 390 optimal weight: 0.8980 chunk 434 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 351 optimal weight: 50.0000 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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** A1161 HIS A1290 GLN ** A1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1161 HIS C1290 GLN D 426 HIS ** D1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33190 Z= 0.145 Angle : 0.544 7.697 45714 Z= 0.283 Chirality : 0.038 0.276 5584 Planarity : 0.004 0.046 5844 Dihedral : 5.292 83.958 5086 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.08 (0.12), residues: 4640 helix: 0.69 (0.10), residues: 2528 sheet: -1.88 (0.27), residues: 312 loop : -2.63 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP D 815 HIS 0.003 0.000 HIS A 193 PHE 0.021 0.001 PHE A 922 TYR 0.019 0.001 TYR B 118 ARG 0.004 0.000 ARG D1162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: -0.1405 (tpp) cc_final: -0.1835 (ptt) REVERT: A 445 GLU cc_start: 0.7521 (pp20) cc_final: 0.7311 (pp20) REVERT: A 832 MET cc_start: 0.6369 (ttp) cc_final: 0.5924 (ttp) REVERT: A 1049 LEU cc_start: 0.7336 (pp) cc_final: 0.6975 (tp) REVERT: A 1173 MET cc_start: 0.6946 (ttp) cc_final: 0.6629 (ttm) REVERT: B 171 ILE cc_start: 0.8943 (mm) cc_final: 0.8434 (tt) REVERT: B 1143 MET cc_start: 0.8801 (mmm) cc_final: 0.8376 (mmp) REVERT: B 1252 MET cc_start: 0.7107 (mtm) cc_final: 0.6609 (pmm) REVERT: B 1290 GLN cc_start: 0.6913 (mm110) cc_final: 0.6215 (pt0) REVERT: B 1305 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7569 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3723 (m100) cc_final: 0.2656 (m100) REVERT: B 1356 TRP cc_start: 0.5544 (m-90) cc_final: 0.5263 (m100) REVERT: C 445 GLU cc_start: 0.7571 (pp20) cc_final: 0.7332 (pp20) REVERT: C 1049 LEU cc_start: 0.7194 (pp) cc_final: 0.6884 (tp) REVERT: C 1173 MET cc_start: 0.6959 (ttp) cc_final: 0.6634 (ttm) REVERT: D 171 ILE cc_start: 0.8950 (mm) cc_final: 0.8453 (tt) REVERT: D 1045 CYS cc_start: 0.8198 (m) cc_final: 0.7952 (p) REVERT: D 1143 MET cc_start: 0.8831 (mmm) cc_final: 0.8374 (mmp) REVERT: D 1252 MET cc_start: 0.7105 (mtm) cc_final: 0.6717 (pmm) REVERT: D 1290 GLN cc_start: 0.6865 (mm110) cc_final: 0.6192 (pt0) REVERT: D 1305 ARG cc_start: 0.8239 (mtm180) cc_final: 0.7567 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3776 (m100) cc_final: 0.2692 (m100) REVERT: D 1356 TRP cc_start: 0.5552 (m-90) cc_final: 0.5270 (m100) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.3368 time to fit residues: 263.3898 Evaluate side-chains 333 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 433 optimal weight: 5.9990 chunk 329 optimal weight: 8.9990 chunk 227 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 209 optimal weight: 30.0000 chunk 294 optimal weight: 5.9990 chunk 440 optimal weight: 7.9990 chunk 465 optimal weight: 4.9990 chunk 229 optimal weight: 0.0870 chunk 417 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 660 GLN B1325 ASN B1405 ASN ** B1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D1325 ASN D1405 ASN ** D1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33190 Z= 0.310 Angle : 0.658 9.077 45714 Z= 0.342 Chirality : 0.042 0.301 5584 Planarity : 0.004 0.043 5844 Dihedral : 5.579 80.592 5086 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.98 (0.13), residues: 4640 helix: 0.77 (0.10), residues: 2528 sheet: -2.12 (0.26), residues: 336 loop : -2.49 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 592 HIS 0.008 0.001 HIS B 259 PHE 0.026 0.002 PHE A 922 TYR 0.026 0.002 TYR D1083 ARG 0.003 0.001 ARG D 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: -0.0539 (tpp) cc_final: -0.1956 (ptt) REVERT: A 445 GLU cc_start: 0.7724 (pp20) cc_final: 0.7452 (pp20) REVERT: A 1049 LEU cc_start: 0.7177 (pp) cc_final: 0.6710 (tp) REVERT: A 1173 MET cc_start: 0.7019 (ttp) cc_final: 0.6609 (ttm) REVERT: A 1305 ARG cc_start: 0.5409 (mmp-170) cc_final: 0.4819 (tpp80) REVERT: B 410 LEU cc_start: 0.9301 (mt) cc_final: 0.9081 (tp) REVERT: B 1305 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7621 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3719 (m100) cc_final: 0.2725 (m100) REVERT: C 445 GLU cc_start: 0.7658 (pp20) cc_final: 0.7403 (pp20) REVERT: C 832 MET cc_start: 0.6951 (ttp) cc_final: 0.6411 (ttp) REVERT: C 1173 MET cc_start: 0.7012 (ttp) cc_final: 0.6607 (ttm) REVERT: C 1305 ARG cc_start: 0.5631 (mmp-170) cc_final: 0.4880 (tpp80) REVERT: D 171 ILE cc_start: 0.9098 (mm) cc_final: 0.8521 (tt) REVERT: D 410 LEU cc_start: 0.9315 (mt) cc_final: 0.9103 (tp) REVERT: D 1045 CYS cc_start: 0.8331 (m) cc_final: 0.8040 (p) REVERT: D 1252 MET cc_start: 0.7636 (mtm) cc_final: 0.6894 (pmm) REVERT: D 1305 ARG cc_start: 0.8333 (mtm180) cc_final: 0.7616 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3870 (m100) cc_final: 0.2900 (m100) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.3437 time to fit residues: 219.5972 Evaluate side-chains 301 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 388 optimal weight: 4.9990 chunk 264 optimal weight: 40.0000 chunk 6 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 397 optimal weight: 0.0980 chunk 322 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 237 optimal weight: 40.0000 chunk 418 optimal weight: 0.0020 chunk 117 optimal weight: 0.0040 overall best weight: 1.6204 ------------------------------------------------------------------------------- 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** A1431 ASN B1405 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33190 Z= 0.180 Angle : 0.548 7.113 45714 Z= 0.284 Chirality : 0.039 0.232 5584 Planarity : 0.004 0.039 5844 Dihedral : 5.191 80.420 5086 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.57 (0.13), residues: 4640 helix: 1.15 (0.11), residues: 2532 sheet: -2.06 (0.26), residues: 336 loop : -2.38 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 592 HIS 0.003 0.001 HIS A 231 PHE 0.021 0.001 PHE A 922 TYR 0.017 0.001 TYR D1083 ARG 0.002 0.000 ARG D1162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: -0.0544 (tpp) cc_final: -0.2084 (ptt) REVERT: A 445 GLU cc_start: 0.7897 (pp20) cc_final: 0.7630 (pp20) REVERT: A 1173 MET cc_start: 0.6942 (ttp) cc_final: 0.6588 (ttm) REVERT: A 1305 ARG cc_start: 0.5576 (mmp-170) cc_final: 0.5194 (tpp80) REVERT: B 657 TYR cc_start: 0.8405 (m-80) cc_final: 0.8157 (m-10) REVERT: B 1305 ARG cc_start: 0.8334 (mtm180) cc_final: 0.7614 (mtm-85) REVERT: B 1335 TRP cc_start: 0.3888 (m100) cc_final: 0.2784 (m100) REVERT: C 445 GLU cc_start: 0.7885 (pp20) cc_final: 0.7609 (pp20) REVERT: C 832 MET cc_start: 0.7179 (ttp) cc_final: 0.6596 (ttp) REVERT: C 1049 LEU cc_start: 0.7190 (pp) cc_final: 0.6774 (tp) REVERT: C 1173 MET cc_start: 0.6943 (ttp) cc_final: 0.6585 (ttm) REVERT: C 1305 ARG cc_start: 0.5515 (mmp-170) cc_final: 0.5143 (tpp80) REVERT: D 657 TYR cc_start: 0.8405 (m-80) cc_final: 0.8139 (m-10) REVERT: D 1045 CYS cc_start: 0.8273 (m) cc_final: 0.8035 (p) REVERT: D 1252 MET cc_start: 0.7420 (mtm) cc_final: 0.6925 (pmm) REVERT: D 1305 ARG cc_start: 0.8326 (mtm180) cc_final: 0.7610 (mtm-85) REVERT: D 1335 TRP cc_start: 0.3902 (m100) cc_final: 0.2811 (m100) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.3405 time to fit residues: 233.5266 Evaluate side-chains 323 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 156 optimal weight: 5.9990 chunk 419 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 273 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 466 optimal weight: 7.9990 chunk 387 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 chunk 154 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1405 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33190 Z= 0.329 Angle : 0.649 9.045 45714 Z= 0.340 Chirality : 0.042 0.264 5584 Planarity : 0.004 0.042 5844 Dihedral : 5.555 78.710 5086 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.82 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.77 (0.13), residues: 4640 helix: 0.92 (0.10), residues: 2532 sheet: -2.08 (0.27), residues: 324 loop : -2.37 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 849 HIS 0.005 0.001 HIS B 728 PHE 0.033 0.002 PHE A 922 TYR 0.026 0.002 TYR B1083 ARG 0.003 0.000 ARG D 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: -0.0121 (tpp) cc_final: -0.2140 (ptt) REVERT: A 445 GLU cc_start: 0.7879 (pp20) cc_final: 0.7592 (pp20) REVERT: A 1173 MET cc_start: 0.6778 (ttp) cc_final: 0.6341 (ttm) REVERT: A 1305 ARG cc_start: 0.5301 (mmp-170) cc_final: 0.4960 (tpp80) REVERT: B 1124 PHE cc_start: 0.8294 (m-80) cc_final: 0.8084 (m-10) REVERT: B 1335 TRP cc_start: 0.3997 (m100) cc_final: 0.2918 (m100) REVERT: C 445 GLU cc_start: 0.7871 (pp20) cc_final: 0.7589 (pp20) REVERT: C 1173 MET cc_start: 0.6774 (ttp) cc_final: 0.6338 (ttm) REVERT: C 1305 ARG cc_start: 0.5292 (mmp-170) cc_final: 0.4925 (tpp80) REVERT: D 1026 MET cc_start: 0.7724 (tpt) cc_final: 0.7517 (tpp) REVERT: D 1045 CYS cc_start: 0.8266 (m) cc_final: 0.8023 (t) REVERT: D 1124 PHE cc_start: 0.8304 (m-80) cc_final: 0.8062 (m-10) REVERT: D 1335 TRP cc_start: 0.4008 (m100) cc_final: 0.2933 (m100) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3387 time to fit residues: 216.5489 Evaluate side-chains 285 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 449 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 340 optimal weight: 50.0000 chunk 263 optimal weight: 1.9990 chunk 392 optimal weight: 0.9990 chunk 260 optimal weight: 40.0000 chunk 464 optimal weight: 7.9990 chunk 290 optimal weight: 0.6980 chunk 283 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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** B 270 HIS B1123 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33190 Z= 0.253 Angle : 0.596 7.723 45714 Z= 0.310 Chirality : 0.040 0.242 5584 Planarity : 0.004 0.073 5844 Dihedral : 5.399 76.802 5086 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.66 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.13), residues: 4640 helix: 1.10 (0.11), residues: 2524 sheet: -2.01 (0.27), residues: 314 loop : -2.27 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 592 HIS 0.004 0.001 HIS B 259 PHE 0.029 0.002 PHE A 922 TYR 0.036 0.002 TYR B 118 ARG 0.003 0.000 ARG C1255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: -0.0440 (tpp) cc_final: -0.2143 (ptt) REVERT: A 445 GLU cc_start: 0.7943 (pp20) cc_final: 0.7661 (pp20) REVERT: A 1173 MET cc_start: 0.6985 (ttp) cc_final: 0.6600 (ttm) REVERT: A 1305 ARG cc_start: 0.5219 (mmp-170) cc_final: 0.4976 (tpp80) REVERT: B 1124 PHE cc_start: 0.8386 (m-80) cc_final: 0.8161 (m-80) REVERT: B 1335 TRP cc_start: 0.4134 (m100) cc_final: 0.2944 (m100) REVERT: C 445 GLU cc_start: 0.7938 (pp20) cc_final: 0.7656 (pp20) REVERT: C 1173 MET cc_start: 0.6977 (ttp) cc_final: 0.6598 (ttm) REVERT: C 1305 ARG cc_start: 0.5016 (mmp-170) cc_final: 0.4756 (tpp80) REVERT: D 410 LEU cc_start: 0.9173 (tp) cc_final: 0.8937 (tp) REVERT: D 1026 MET cc_start: 0.7723 (tpt) cc_final: 0.7497 (tpp) REVERT: D 1045 CYS cc_start: 0.8226 (m) cc_final: 0.7930 (p) REVERT: D 1124 PHE cc_start: 0.8272 (m-80) cc_final: 0.8046 (m-10) REVERT: D 1335 TRP cc_start: 0.4141 (m100) cc_final: 0.2957 (m100) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3398 time to fit residues: 226.9715 Evaluate side-chains 297 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 287 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 295 optimal weight: 0.6980 chunk 316 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 365 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** B 270 HIS B 656 HIS ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS D 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 33190 Z= 0.173 Angle : 0.556 10.049 45714 Z= 0.285 Chirality : 0.039 0.217 5584 Planarity : 0.004 0.053 5844 Dihedral : 5.166 77.174 5086 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.13 (0.13), residues: 4640 helix: 1.49 (0.11), residues: 2522 sheet: -1.90 (0.28), residues: 312 loop : -2.12 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP D 592 HIS 0.002 0.000 HIS D 259 PHE 0.030 0.001 PHE A 922 TYR 0.023 0.001 TYR B 118 ARG 0.003 0.000 ARG A1255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: -0.0458 (tpp) cc_final: -0.2144 (ptt) REVERT: A 445 GLU cc_start: 0.7884 (pp20) cc_final: 0.7537 (pp20) REVERT: A 635 LEU cc_start: 0.9338 (tp) cc_final: 0.9061 (tp) REVERT: A 1049 LEU cc_start: 0.7178 (pp) cc_final: 0.6841 (tp) REVERT: A 1173 MET cc_start: 0.6929 (ttp) cc_final: 0.6575 (ttm) REVERT: A 1305 ARG cc_start: 0.5387 (mmp-170) cc_final: 0.5074 (tpp80) REVERT: B 1124 PHE cc_start: 0.8324 (m-80) cc_final: 0.8118 (m-80) REVERT: B 1335 TRP cc_start: 0.4036 (m100) cc_final: 0.2904 (m100) REVERT: C 445 GLU cc_start: 0.7886 (pp20) cc_final: 0.7557 (pp20) REVERT: C 1049 LEU cc_start: 0.7216 (pp) cc_final: 0.6872 (tp) REVERT: C 1173 MET cc_start: 0.6925 (ttp) cc_final: 0.6569 (ttm) REVERT: D 1026 MET cc_start: 0.7746 (tpt) cc_final: 0.7502 (tpp) REVERT: D 1045 CYS cc_start: 0.8050 (m) cc_final: 0.7829 (p) REVERT: D 1124 PHE cc_start: 0.8221 (m-80) cc_final: 0.7981 (m-10) REVERT: D 1335 TRP cc_start: 0.4072 (m100) cc_final: 0.2935 (m100) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.3491 time to fit residues: 242.3844 Evaluate side-chains 302 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 422 optimal weight: 9.9990 chunk 445 optimal weight: 0.8980 chunk 406 optimal weight: 1.9990 chunk 432 optimal weight: 0.9980 chunk 444 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 339 optimal weight: 0.1980 chunk 132 optimal weight: 0.2980 chunk 391 optimal weight: 0.9980 chunk 409 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 33190 Z= 0.149 Angle : 0.541 11.000 45714 Z= 0.275 Chirality : 0.038 0.252 5584 Planarity : 0.004 0.042 5844 Dihedral : 4.980 78.264 5086 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.04 (0.13), residues: 4640 helix: 1.60 (0.11), residues: 2550 sheet: -1.81 (0.27), residues: 322 loop : -2.05 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 849 HIS 0.014 0.000 HIS C 257 PHE 0.029 0.001 PHE A 922 TYR 0.017 0.001 TYR B1065 ARG 0.004 0.000 ARG B 633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6505 (mmp) cc_final: 0.5639 (tpp) REVERT: A 196 MET cc_start: -0.0424 (tpp) cc_final: -0.2126 (ptt) REVERT: A 445 GLU cc_start: 0.7748 (pp20) cc_final: 0.7468 (pp20) REVERT: A 635 LEU cc_start: 0.9380 (tp) cc_final: 0.9044 (tp) REVERT: A 832 MET cc_start: 0.7424 (tmm) cc_final: 0.6946 (tmm) REVERT: A 1049 LEU cc_start: 0.7214 (pp) cc_final: 0.6837 (tp) REVERT: A 1133 GLU cc_start: 0.8341 (tp30) cc_final: 0.8099 (tp30) REVERT: A 1173 MET cc_start: 0.6912 (ttp) cc_final: 0.6540 (ttm) REVERT: A 1305 ARG cc_start: 0.5509 (mmp-170) cc_final: 0.5130 (tpp80) REVERT: B 1335 TRP cc_start: 0.3977 (m100) cc_final: 0.2890 (m100) REVERT: C 445 GLU cc_start: 0.7816 (pp20) cc_final: 0.7510 (pp20) REVERT: C 635 LEU cc_start: 0.9288 (tp) cc_final: 0.9010 (tp) REVERT: C 832 MET cc_start: 0.7273 (tmm) cc_final: 0.6743 (tmm) REVERT: C 1049 LEU cc_start: 0.7253 (pp) cc_final: 0.6855 (tp) REVERT: C 1133 GLU cc_start: 0.8338 (tp30) cc_final: 0.8097 (tp30) REVERT: C 1173 MET cc_start: 0.6893 (ttp) cc_final: 0.6551 (ttm) REVERT: D 1026 MET cc_start: 0.7634 (tpt) cc_final: 0.7357 (tpp) REVERT: D 1124 PHE cc_start: 0.8138 (m-80) cc_final: 0.7934 (m-10) REVERT: D 1335 TRP cc_start: 0.3984 (m100) cc_final: 0.2907 (m100) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3456 time to fit residues: 243.5243 Evaluate side-chains 307 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 431 optimal weight: 0.4980 chunk 284 optimal weight: 9.9990 chunk 457 optimal weight: 0.8980 chunk 279 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 480 optimal weight: 30.0000 chunk 441 optimal weight: 30.0000 chunk 382 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 257 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 33190 Z= 0.239 Angle : 0.599 12.688 45714 Z= 0.307 Chirality : 0.040 0.245 5584 Planarity : 0.004 0.045 5844 Dihedral : 5.113 76.948 5086 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.90 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.01 (0.13), residues: 4640 helix: 1.61 (0.11), residues: 2522 sheet: -1.92 (0.27), residues: 322 loop : -2.05 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP B 815 HIS 0.011 0.001 HIS A 257 PHE 0.031 0.002 PHE A 922 TYR 0.021 0.001 TYR D 118 ARG 0.002 0.000 ARG A1255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6529 (mmp) cc_final: 0.4882 (tpp) REVERT: A 196 MET cc_start: -0.0492 (tpp) cc_final: -0.2229 (ptt) REVERT: A 445 GLU cc_start: 0.7977 (pp20) cc_final: 0.7673 (pp20) REVERT: A 832 MET cc_start: 0.7525 (tmm) cc_final: 0.7248 (tmm) REVERT: A 1173 MET cc_start: 0.6713 (ttp) cc_final: 0.6292 (ttm) REVERT: A 1305 ARG cc_start: 0.5553 (mmp-170) cc_final: 0.5196 (tpp80) REVERT: B 171 ILE cc_start: 0.9098 (mm) cc_final: 0.8401 (tt) REVERT: B 1335 TRP cc_start: 0.3982 (m100) cc_final: 0.2907 (m100) REVERT: C 134 MET cc_start: 0.6238 (mmp) cc_final: 0.4151 (tpt) REVERT: C 445 GLU cc_start: 0.7881 (pp20) cc_final: 0.7575 (pp20) REVERT: C 832 MET cc_start: 0.7505 (tmm) cc_final: 0.7244 (tmm) REVERT: C 1049 LEU cc_start: 0.7181 (pp) cc_final: 0.6854 (tp) REVERT: C 1173 MET cc_start: 0.6710 (ttp) cc_final: 0.6292 (ttm) REVERT: D 171 ILE cc_start: 0.9087 (mm) cc_final: 0.8532 (tt) REVERT: D 1026 MET cc_start: 0.7767 (tpt) cc_final: 0.7451 (tpp) REVERT: D 1335 TRP cc_start: 0.3849 (m100) cc_final: 0.2879 (m100) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.3280 time to fit residues: 217.1316 Evaluate side-chains 297 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 234 optimal weight: 40.0000 chunk 303 optimal weight: 3.9990 chunk 407 optimal weight: 0.9980 chunk 117 optimal weight: 40.0000 chunk 352 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 106 optimal weight: 40.0000 chunk 382 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 393 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 257 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.157589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124647 restraints weight = 83166.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122873 restraints weight = 107720.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123725 restraints weight = 94579.520| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33190 Z= 0.275 Angle : 0.622 10.427 45714 Z= 0.320 Chirality : 0.040 0.230 5584 Planarity : 0.004 0.048 5844 Dihedral : 5.315 75.774 5086 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.12 (0.13), residues: 4640 helix: 1.45 (0.11), residues: 2518 sheet: -1.87 (0.29), residues: 296 loop : -2.03 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP B 815 HIS 0.009 0.001 HIS C 257 PHE 0.031 0.002 PHE A 922 TYR 0.024 0.002 TYR B 118 ARG 0.003 0.000 ARG A1255 =============================================================================== Job complete usr+sys time: 5651.09 seconds wall clock time: 103 minutes 6.31 seconds (6186.31 seconds total)