Starting phenix.real_space_refine on Tue Aug 26 17:30:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tgc_10498/08_2025/6tgc_10498.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tgc_10498/08_2025/6tgc_10498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tgc_10498/08_2025/6tgc_10498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tgc_10498/08_2025/6tgc_10498.map" model { file = "/net/cci-nas-00/data/ceres_data/6tgc_10498/08_2025/6tgc_10498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tgc_10498/08_2025/6tgc_10498.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6546 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 21243 2.51 5 N 5721 2.21 5 O 6138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "B GLU 90": not complete - not flipped Residue "B GLU 134": not complete - not flipped Residue "B GLU 206": not complete - not flipped Residue "B GLU 289": not complete - not flipped Residue "B ASP 355": not complete - not flipped Residue "B GLU 419": not complete - not flipped Residue "E GLU 90": not complete - not flipped Residue "E GLU 134": not complete - not flipped Residue "E GLU 206": not complete - not flipped Residue "E GLU 289": not complete - not flipped Residue "E ASP 355": not complete - not flipped Residue "E GLU 419": not complete - not flipped Time to flip 158 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33282 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1466 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 180} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2115 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 7, 'TRANS': 311} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 133, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 251 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'TRANS': 48} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 17, 'GLU:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 6371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 6371 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 866} Chain breaks: 6 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1026 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UNK:plan-1': 254, 'ASP:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 401 Chain: "B" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5054 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 650} Chain breaks: 3 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 614 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 30, 'GLU:plan': 35, 'TYR:plan': 1, 'HIS:plan': 4, 'GLN:plan1': 14, 'ASN:plan1': 9, 'ARG:plan': 8, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 295 Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "D" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1466 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 180} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2115 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 7, 'TRANS': 311} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 133, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 251 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'TRANS': 48} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 17, 'GLU:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 6371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 6371 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 866} Chain breaks: 6 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1026 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UNK:plan-1': 254, 'ASP:plan': 8, 'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 401 Chain: "E" Number of atoms: 5056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5056 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 651} Chain breaks: 3 Unresolved non-hydrogen bonds: 459 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 30, 'GLU:plan': 35, 'TYR:plan': 1, 'HIS:plan': 4, 'GLN:plan1': 14, 'ASN:plan1': 9, 'ARG:plan': 8, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 295 Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 11, 'TRANS': 165} Time building chain proxies: 8.66, per 1000 atoms: 0.26 Number of scatterers: 33282 At special positions: 0 Unit cell: (298.87, 261.69, 141.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6138 8.00 N 5721 7.00 C 21243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8908 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 21 sheets defined 68.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 83 through 108 Processing helix chain 'A' and resid 110 through 132 removed outlier: 3.900A pdb=" N PHE A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 removed outlier: 3.567A pdb=" N THR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 572 through 576 removed outlier: 3.501A pdb=" N GLU A 576 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.755A pdb=" N UNK A 634 " --> pdb=" O UNK A 630 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK A 635 " --> pdb=" O UNK A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 removed outlier: 4.222A pdb=" N HIS A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 690 through 701 removed outlier: 4.596A pdb=" N UNK A 697 " --> pdb=" O UNK A 693 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N UNK A 698 " --> pdb=" O UNK A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 708 through 719 removed outlier: 3.826A pdb=" N UNK A 712 " --> pdb=" O UNK A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 736 removed outlier: 3.975A pdb=" N UNK A 733 " --> pdb=" O UNK A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 761 Processing helix chain 'A' and resid 765 through 783 removed outlier: 4.100A pdb=" N UNK A 769 " --> pdb=" O UNK A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 5.438A pdb=" N UNK A 795 " --> pdb=" O UNK A 791 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK A 796 " --> pdb=" O UNK A 792 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK A 797 " --> pdb=" O UNK A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.868A pdb=" N UNK A 807 " --> pdb=" O UNK A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 824 Processing helix chain 'A' and resid 830 through 846 removed outlier: 3.868A pdb=" N UNK A 834 " --> pdb=" O UNK A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 870 Processing helix chain 'A' and resid 873 through 891 removed outlier: 4.767A pdb=" N UNK A 877 " --> pdb=" O UNK A 873 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK A 884 " --> pdb=" O UNK A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 911 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 935 through 949 Processing helix chain 'A' and resid 950 through 959 Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.522A pdb=" N LEU A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1014 Processing helix chain 'A' and resid 1023 through 1039 removed outlier: 3.800A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1059 Processing helix chain 'A' and resid 1061 through 1076 removed outlier: 3.795A pdb=" N LEU A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 4.074A pdb=" N VAL A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A1090 " --> pdb=" O PRO A1086 " (cutoff:3.500A) Proline residue: A1091 - end of helix Processing helix chain 'A' and resid 1098 through 1104 removed outlier: 3.592A pdb=" N GLU A1102 " --> pdb=" O ILE A1098 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1104 " --> pdb=" O GLU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1117 removed outlier: 3.961A pdb=" N ILE A1110 " --> pdb=" O ALA A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1140 removed outlier: 4.095A pdb=" N LEU A1134 " --> pdb=" O ASN A1130 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A1135 " --> pdb=" O GLU A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1162 removed outlier: 4.529A pdb=" N GLN A1151 " --> pdb=" O GLU A1147 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A1155 " --> pdb=" O GLN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1192 removed outlier: 3.825A pdb=" N ASP A1187 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1214 Processing helix chain 'A' and resid 1216 through 1235 removed outlier: 3.951A pdb=" N TYR A1220 " --> pdb=" O ARG A1216 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG A1222 " --> pdb=" O GLU A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1250 removed outlier: 3.599A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1291 Processing helix chain 'A' and resid 1293 through 1311 removed outlier: 4.207A pdb=" N ALA A1297 " --> pdb=" O MET A1293 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A1298 " --> pdb=" O TRP A1294 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1330 removed outlier: 3.719A pdb=" N GLN A1320 " --> pdb=" O GLU A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1382 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1418 through 1423 Processing helix chain 'A' and resid 1430 through 1434 Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1493 through 1519 Processing helix chain 'A' and resid 1524 through 1536 removed outlier: 3.739A pdb=" N SER A1528 " --> pdb=" O ILE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1550 Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 4.129A pdb=" N VAL A1556 " --> pdb=" O THR A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1589 Proline residue: A1578 - end of helix removed outlier: 3.747A pdb=" N LYS A1589 " --> pdb=" O LYS A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1618 removed outlier: 4.190A pdb=" N PHE A1598 " --> pdb=" O ASN A1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.514A pdb=" N ILE B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.829A pdb=" N GLU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.677A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.535A pdb=" N GLY B 234 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 253 removed outlier: 3.517A pdb=" N GLN B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 4.157A pdb=" N GLN B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 287 through 304 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 317 through 333 removed outlier: 3.844A pdb=" N ALA B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.748A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.836A pdb=" N HIS B 448 " --> pdb=" O PHE B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 471 Processing helix chain 'B' and resid 476 through 489 Processing helix chain 'B' and resid 490 through 495 removed outlier: 4.581A pdb=" N THR B 493 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 509 Processing helix chain 'B' and resid 512 through 529 removed outlier: 3.705A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 Processing helix chain 'B' and resid 535 through 540 removed outlier: 3.829A pdb=" N LYS B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 535 through 540' Processing helix chain 'B' and resid 540 through 559 removed outlier: 3.760A pdb=" N GLN B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.576A pdb=" N GLU B 639 " --> pdb=" O LYS B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.597A pdb=" N THR B 666 " --> pdb=" O TYR B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.702A pdb=" N MET B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.653A pdb=" N LEU C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.899A pdb=" N TYR C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 65' Processing helix chain 'C' and resid 87 through 96 removed outlier: 5.356A pdb=" N ARG C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.350A pdb=" N GLU C 171 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 108 Processing helix chain 'D' and resid 110 through 132 removed outlier: 3.899A pdb=" N PHE D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 159 removed outlier: 3.567A pdb=" N THR D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 498 through 504 Processing helix chain 'D' and resid 572 through 576 removed outlier: 3.501A pdb=" N GLU D 576 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.755A pdb=" N UNK D 634 " --> pdb=" O UNK D 630 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNK D 635 " --> pdb=" O UNK D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 661 removed outlier: 4.222A pdb=" N HIS D 652 " --> pdb=" O ILE D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 690 through 701 removed outlier: 4.596A pdb=" N UNK D 697 " --> pdb=" O UNK D 693 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK D 698 " --> pdb=" O UNK D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 708 through 719 removed outlier: 3.826A pdb=" N UNK D 712 " --> pdb=" O UNK D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 736 removed outlier: 3.975A pdb=" N UNK D 733 " --> pdb=" O UNK D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 761 Processing helix chain 'D' and resid 765 through 783 removed outlier: 4.099A pdb=" N UNK D 769 " --> pdb=" O UNK D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 797 removed outlier: 5.436A pdb=" N UNK D 795 " --> pdb=" O UNK D 791 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK D 796 " --> pdb=" O UNK D 792 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK D 797 " --> pdb=" O UNK D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 807 removed outlier: 3.868A pdb=" N UNK D 807 " --> pdb=" O UNK D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 824 Processing helix chain 'D' and resid 830 through 846 removed outlier: 3.868A pdb=" N UNK D 834 " --> pdb=" O UNK D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 870 Processing helix chain 'D' and resid 873 through 891 removed outlier: 4.767A pdb=" N UNK D 877 " --> pdb=" O UNK D 873 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N UNK D 884 " --> pdb=" O UNK D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 911 Processing helix chain 'D' and resid 912 through 921 Processing helix chain 'D' and resid 935 through 949 Processing helix chain 'D' and resid 950 through 959 Processing helix chain 'D' and resid 965 through 982 removed outlier: 3.522A pdb=" N LEU D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1014 Processing helix chain 'D' and resid 1023 through 1039 removed outlier: 3.800A pdb=" N GLN D1039 " --> pdb=" O ALA D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1059 Processing helix chain 'D' and resid 1061 through 1076 removed outlier: 3.796A pdb=" N LEU D1065 " --> pdb=" O ASP D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 4.074A pdb=" N VAL D1089 " --> pdb=" O ILE D1085 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY D1090 " --> pdb=" O PRO D1086 " (cutoff:3.500A) Proline residue: D1091 - end of helix Processing helix chain 'D' and resid 1098 through 1104 removed outlier: 3.592A pdb=" N GLU D1102 " --> pdb=" O ILE D1098 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D1104 " --> pdb=" O GLU D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1117 removed outlier: 3.961A pdb=" N ILE D1110 " --> pdb=" O ALA D1106 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1140 removed outlier: 4.095A pdb=" N LEU D1134 " --> pdb=" O ASN D1130 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS D1135 " --> pdb=" O GLU D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1162 removed outlier: 4.528A pdb=" N GLN D1151 " --> pdb=" O GLU D1147 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D1155 " --> pdb=" O GLN D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1192 removed outlier: 3.825A pdb=" N ASP D1187 " --> pdb=" O GLU D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1196 through 1214 Processing helix chain 'D' and resid 1216 through 1235 removed outlier: 3.951A pdb=" N TYR D1220 " --> pdb=" O ARG D1216 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG D1222 " --> pdb=" O GLU D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1250 removed outlier: 3.598A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1272 through 1291 Processing helix chain 'D' and resid 1293 through 1311 removed outlier: 4.207A pdb=" N ALA D1297 " --> pdb=" O MET D1293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D1298 " --> pdb=" O TRP D1294 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS D1301 " --> pdb=" O ALA D1297 " (cutoff:3.500A) Processing helix chain 'D' and resid 1316 through 1330 removed outlier: 3.719A pdb=" N GLN D1320 " --> pdb=" O GLU D1316 " (cutoff:3.500A) Processing helix chain 'D' and resid 1371 through 1382 Processing helix chain 'D' and resid 1395 through 1401 Processing helix chain 'D' and resid 1418 through 1423 Processing helix chain 'D' and resid 1430 through 1434 Processing helix chain 'D' and resid 1457 through 1462 Processing helix chain 'D' and resid 1493 through 1519 Processing helix chain 'D' and resid 1524 through 1536 removed outlier: 3.738A pdb=" N SER D1528 " --> pdb=" O ILE D1524 " (cutoff:3.500A) Processing helix chain 'D' and resid 1542 through 1550 Processing helix chain 'D' and resid 1552 through 1559 removed outlier: 4.129A pdb=" N VAL D1556 " --> pdb=" O THR D1552 " (cutoff:3.500A) Processing helix chain 'D' and resid 1562 through 1589 Proline residue: D1578 - end of helix removed outlier: 3.746A pdb=" N LYS D1589 " --> pdb=" O LYS D1585 " (cutoff:3.500A) Processing helix chain 'D' and resid 1594 through 1618 removed outlier: 4.190A pdb=" N PHE D1598 " --> pdb=" O ASN D1594 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 41 removed outlier: 3.502A pdb=" N ILE E 33 " --> pdb=" O PRO E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 80 through 92 Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.631A pdb=" N GLU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 136 Processing helix chain 'E' and resid 154 through 167 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 194 through 212 Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.651A pdb=" N GLN E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 230 through 234 removed outlier: 3.534A pdb=" N GLY E 234 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 254 Processing helix chain 'E' and resid 255 through 269 removed outlier: 4.028A pdb=" N GLN E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 279 Processing helix chain 'E' and resid 287 through 304 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 317 through 333 removed outlier: 3.664A pdb=" N ILE E 324 " --> pdb=" O GLN E 320 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.634A pdb=" N LEU E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 404 removed outlier: 3.540A pdb=" N ASN E 402 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 442 through 447 Processing helix chain 'E' and resid 450 through 471 Processing helix chain 'E' and resid 476 through 492 removed outlier: 4.003A pdb=" N ARG E 490 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 495 No H-bonds generated for 'chain 'E' and resid 493 through 495' Processing helix chain 'E' and resid 498 through 508 Processing helix chain 'E' and resid 513 through 522 removed outlier: 5.008A pdb=" N GLN E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER E 520 " --> pdb=" O LYS E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 529 removed outlier: 4.147A pdb=" N PHE E 528 " --> pdb=" O ASN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 540 removed outlier: 3.566A pdb=" N ILE E 540 " --> pdb=" O LEU E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 559 removed outlier: 3.841A pdb=" N GLY E 559 " --> pdb=" O ARG E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 658 through 672 Processing helix chain 'E' and resid 680 through 701 removed outlier: 4.120A pdb=" N MET E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 699 " --> pdb=" O LYS E 695 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP E 700 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 701 " --> pdb=" O ARG E 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.653A pdb=" N LEU F 19 " --> pdb=" O GLY F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.899A pdb=" N TYR F 64 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 65 " --> pdb=" O GLU F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 65' Processing helix chain 'F' and resid 87 through 96 removed outlier: 5.357A pdb=" N ARG F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 122 through 131 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.349A pdb=" N GLU F 171 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 172 " --> pdb=" O VAL F 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.016A pdb=" N TYR A 48 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 37 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 12 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 67 " --> pdb=" O HIS A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 460 removed outlier: 3.622A pdb=" N VAL A 452 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1361 through 1363 Processing sheet with id=AA5, first strand: chain 'A' and resid 1386 through 1387 removed outlier: 4.772A pdb=" N GLU A1386 " --> pdb=" O ILE A1406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1412 through 1414 removed outlier: 4.560A pdb=" N ARG A1441 " --> pdb=" O VAL A1414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1447 through 1448 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 25 removed outlier: 10.395A pdb=" N THR B 73 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LYS B 9 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 75 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA B 11 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 77 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU B 13 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N THR B 79 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 589 through 590 removed outlier: 4.343A pdb=" N HIS B 601 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 615 through 618 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.567A pdb=" N VAL C 46 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 6 " --> pdb=" O TRP C 56 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL C 77 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 7 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE C 82 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C 112 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 56 through 57 removed outlier: 6.017A pdb=" N TYR D 48 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE D 37 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS D 12 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D 67 " --> pdb=" O HIS D 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 427 through 430 Processing sheet with id=AB5, first strand: chain 'D' and resid 458 through 460 removed outlier: 3.623A pdb=" N VAL D 452 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1361 through 1363 Processing sheet with id=AB7, first strand: chain 'D' and resid 1386 through 1387 removed outlier: 4.772A pdb=" N GLU D1386 " --> pdb=" O ILE D1406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 1412 through 1414 removed outlier: 4.560A pdb=" N ARG D1441 " --> pdb=" O VAL D1414 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1447 through 1448 Processing sheet with id=AC1, first strand: chain 'E' and resid 20 through 25 removed outlier: 10.361A pdb=" N THR E 73 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS E 9 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU E 75 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA E 11 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU E 77 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU E 13 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR E 79 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU E 51 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 615 through 618 Processing sheet with id=AC3, first strand: chain 'F' and resid 41 through 46 removed outlier: 3.566A pdb=" N VAL F 46 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL F 77 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 7 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL F 113 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 80 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE F 82 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5268 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: 7.81 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6766 1.32 - 1.45: 8946 1.45 - 1.58: 17843 1.58 - 1.71: 17 1.71 - 1.84: 304 Bond restraints: 33876 Sorted by residual: bond pdb=" N LEU E 608 " pdb=" CA LEU E 608 " ideal model delta sigma weight residual 1.457 1.328 0.129 1.41e-02 5.03e+03 8.35e+01 bond pdb=" C LYS D1474 " pdb=" N LEU D1475 " ideal model delta sigma weight residual 1.331 1.256 0.075 9.80e-03 1.04e+04 5.79e+01 bond pdb=" C LYS A1474 " pdb=" N LEU A1475 " ideal model delta sigma weight residual 1.331 1.256 0.074 9.80e-03 1.04e+04 5.75e+01 bond pdb=" CB TRP A1294 " pdb=" CG TRP A1294 " ideal model delta sigma weight residual 1.498 1.314 0.184 3.10e-02 1.04e+03 3.53e+01 bond pdb=" N LYS A1327 " pdb=" CA LYS A1327 " ideal model delta sigma weight residual 1.458 1.391 0.066 1.12e-02 7.97e+03 3.51e+01 ... (remaining 33871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 45625 7.50 - 15.01: 345 15.01 - 22.51: 36 22.51 - 30.02: 4 30.02 - 37.52: 4 Bond angle restraints: 46014 Sorted by residual: angle pdb=" C THR D1521 " pdb=" N LEU D1522 " pdb=" CA LEU D1522 " ideal model delta sigma weight residual 121.83 152.51 -30.68 1.56e+00 4.11e-01 3.87e+02 angle pdb=" C THR A1521 " pdb=" N LEU A1522 " pdb=" CA LEU A1522 " ideal model delta sigma weight residual 121.83 152.49 -30.66 1.56e+00 4.11e-01 3.86e+02 angle pdb=" CA LEU A1300 " pdb=" CB LEU A1300 " pdb=" CG LEU A1300 " ideal model delta sigma weight residual 116.30 78.78 37.52 3.50e+00 8.16e-02 1.15e+02 angle pdb=" CA LEU D1300 " pdb=" CB LEU D1300 " pdb=" CG LEU D1300 " ideal model delta sigma weight residual 116.30 78.78 37.52 3.50e+00 8.16e-02 1.15e+02 angle pdb=" C ARG E 578 " pdb=" N LEU E 579 " pdb=" CA LEU E 579 " ideal model delta sigma weight residual 122.21 106.08 16.13 1.62e+00 3.81e-01 9.91e+01 ... (remaining 46009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 19458 35.88 - 71.76: 976 71.76 - 107.65: 32 107.65 - 143.53: 2 143.53 - 179.41: 8 Dihedral angle restraints: 20476 sinusoidal: 6856 harmonic: 13620 Sorted by residual: dihedral pdb=" CA GLU A1195 " pdb=" C GLU A1195 " pdb=" N SER A1196 " pdb=" CA SER A1196 " ideal model delta harmonic sigma weight residual 180.00 126.48 53.52 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA GLU D1195 " pdb=" C GLU D1195 " pdb=" N SER D1196 " pdb=" CA SER D1196 " ideal model delta harmonic sigma weight residual 180.00 126.53 53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASN D 445 " pdb=" C ASN D 445 " pdb=" N VAL D 446 " pdb=" CA VAL D 446 " ideal model delta harmonic sigma weight residual -180.00 -126.91 -53.09 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4694 0.105 - 0.210: 607 0.210 - 0.315: 92 0.315 - 0.419: 12 0.419 - 0.524: 7 Chirality restraints: 5412 Sorted by residual: chirality pdb=" CB ILE E 548 " pdb=" CA ILE E 548 " pdb=" CG1 ILE E 548 " pdb=" CG2 ILE E 548 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CG LEU D1300 " pdb=" CB LEU D1300 " pdb=" CD1 LEU D1300 " pdb=" CD2 LEU D1300 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CG LEU A1300 " pdb=" CB LEU A1300 " pdb=" CD1 LEU A1300 " pdb=" CD2 LEU A1300 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 5409 not shown) Planarity restraints: 5928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A1587 " 0.027 2.00e-02 2.50e+03 5.61e-02 3.14e+01 pdb=" C HIS A1587 " -0.097 2.00e-02 2.50e+03 pdb=" O HIS A1587 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1588 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D1587 " -0.027 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" C HIS D1587 " 0.097 2.00e-02 2.50e+03 pdb=" O HIS D1587 " -0.037 2.00e-02 2.50e+03 pdb=" N GLU D1588 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D1607 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C LYS D1607 " 0.079 2.00e-02 2.50e+03 pdb=" O LYS D1607 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN D1608 " -0.027 2.00e-02 2.50e+03 ... (remaining 5925 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 758 2.45 - 3.06: 31889 3.06 - 3.67: 61931 3.67 - 4.29: 89315 4.29 - 4.90: 124749 Nonbonded interactions: 308642 Sorted by model distance: nonbonded pdb=" OG SER A 109 " pdb=" NZ LYS A 110 " model vdw 1.835 3.120 nonbonded pdb=" OG SER D 109 " pdb=" NZ LYS D 110 " model vdw 1.835 3.120 nonbonded pdb=" O LEU A1152 " pdb=" OG SER A1155 " model vdw 1.881 3.040 nonbonded pdb=" O LEU D1152 " pdb=" OG SER D1155 " model vdw 1.881 3.040 nonbonded pdb=" O ILE E 548 " pdb=" NH1 ARG E 552 " model vdw 1.924 3.120 ... (remaining 308637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 5 through 583 or (resid 584 and (name N or name CA or name \ C or name O or name CB )) or resid 585 through 726)) selection = (chain 'E' and (resid 5 through 676 or (resid 677 through 678 and (name N or nam \ e CA or name C or name O or name CB )) or resid 679 through 726)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.260 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 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 : 0.016 0.184 33876 Z= 0.781 Angle : 1.861 37.523 46014 Z= 0.999 Chirality : 0.076 0.524 5412 Planarity : 0.011 0.096 5928 Dihedral : 20.202 179.409 11568 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 101.86 Ramachandran Plot: Outliers : 1.92 % Allowed : 22.03 % Favored : 76.05 % Rotamer: Outliers : 15.44 % Allowed : 11.90 % Favored : 72.66 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 2.53 % Twisted General : 1.91 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.63 (0.11), residues: 3750 helix: -3.53 (0.08), residues: 1780 sheet: -4.46 (0.23), residues: 268 loop : -3.79 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG E 683 TYR 0.057 0.007 TYR A1059 PHE 0.075 0.007 PHE A1030 TRP 0.063 0.006 TRP E 665 HIS 0.024 0.005 HIS D1587 Details of bonding type rmsd covalent geometry : bond 0.01551 (33876) covalent geometry : angle 1.86051 (46014) hydrogen bonds : bond 0.25936 ( 1812) hydrogen bonds : angle 10.06364 ( 5268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 457 poor density : 363 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: -0.0201 (mtt) cc_final: -0.2052 (tpt) REVERT: A 1066 ILE cc_start: 0.1910 (OUTLIER) cc_final: 0.1606 (mm) REVERT: A 1073 MET cc_start: -0.5479 (tmm) cc_final: -0.7044 (mmt) REVERT: A 1095 MET cc_start: 0.3441 (tpp) cc_final: 0.2738 (mmm) REVERT: A 1102 GLU cc_start: 0.4039 (OUTLIER) cc_final: 0.3702 (pm20) REVERT: A 1223 TYR cc_start: 0.7028 (m-80) cc_final: 0.6638 (m-80) REVERT: A 1242 TYR cc_start: 0.6963 (m-80) cc_final: 0.6580 (m-80) REVERT: A 1342 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: B 231 HIS cc_start: 0.6824 (m-70) cc_final: 0.6379 (m-70) REVERT: B 552 ARG cc_start: -0.1646 (mmm160) cc_final: -0.1846 (mmt90) REVERT: C 4 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.6776 (pt) REVERT: C 53 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7811 (tt) REVERT: C 76 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8069 (t0) REVERT: D 1 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5647 (tpt) REVERT: D 125 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8788 (mtp) REVERT: D 139 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7604 (p0) REVERT: D 141 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8766 (pp) REVERT: D 450 MET cc_start: 0.5299 (mtt) cc_final: 0.4788 (mtt) REVERT: D 490 MET cc_start: -0.4789 (tmt) cc_final: -0.4992 (ttt) REVERT: D 546 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8854 (p90) REVERT: D 549 LEU cc_start: 0.9081 (mt) cc_final: 0.8650 (tp) REVERT: D 556 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8121 (p) REVERT: D 975 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8570 (tpp) REVERT: D 977 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9162 (mtpt) REVERT: D 1028 ASN cc_start: 0.9633 (OUTLIER) cc_final: 0.9253 (t0) REVERT: D 1071 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8767 (tpt170) REVERT: D 1216 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7728 (ttm170) REVERT: D 1250 LEU cc_start: 0.9349 (tp) cc_final: 0.9119 (mm) REVERT: D 1444 TYR cc_start: 0.7583 (t80) cc_final: 0.7163 (t80) REVERT: D 1462 MET cc_start: -0.4561 (ttm) cc_final: -0.4798 (ttm) REVERT: D 1487 MET cc_start: 0.6577 (tpp) cc_final: 0.6045 (tpp) REVERT: D 1605 CYS cc_start: 0.8619 (t) cc_final: 0.8378 (t) REVERT: E 310 MET cc_start: 0.8369 (mmp) cc_final: 0.7869 (mmt) REVERT: E 386 TYR cc_start: 0.9036 (t80) cc_final: 0.8620 (t80) REVERT: E 391 HIS cc_start: 0.5464 (m170) cc_final: 0.5167 (m-70) REVERT: E 677 MET cc_start: 0.7243 (mtt) cc_final: 0.6892 (ptt) REVERT: E 721 ASP cc_start: 0.9008 (m-30) cc_final: 0.8589 (p0) REVERT: F 1 MET cc_start: 0.7299 (mtm) cc_final: 0.6781 (mtm) REVERT: F 145 MET cc_start: 0.3150 (tpt) cc_final: 0.2761 (tpt) REVERT: F 170 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8638 (m-30) outliers start: 457 outliers final: 185 residues processed: 759 average time/residue: 0.2438 time to fit residues: 289.6999 Evaluate side-chains 489 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 286 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 9.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 38 GLN A 89 GLN A 156 ASN B 122 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN B 366 ASN B 383 ASN B 442 HIS B 448 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 ASN C 26 ASN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 118 GLN D 146 GLN E 71 ASN ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN E 248 ASN ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN E 439 ASN ** E 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.220132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4554 r_free = 0.4554 target = 0.166135 restraints weight = 288715.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.157879 restraints weight = 269139.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.154285 restraints weight = 270161.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.154316 restraints weight = 228588.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.153999 restraints weight = 188446.403| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 33876 Z= 0.347 Angle : 1.167 16.573 46014 Z= 0.588 Chirality : 0.055 0.362 5412 Planarity : 0.009 0.177 5928 Dihedral : 8.706 56.655 4826 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 39.85 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.15 % Favored : 86.43 % Rotamer: Outliers : 1.12 % Allowed : 8.28 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.90 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.05 (0.12), residues: 3750 helix: -2.23 (0.10), residues: 1924 sheet: -3.97 (0.23), residues: 352 loop : -2.78 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 508 TYR 0.050 0.004 TYR A1347 PHE 0.054 0.004 PHE D1442 TRP 0.049 0.004 TRP E 665 HIS 0.014 0.003 HIS D1273 Details of bonding type rmsd covalent geometry : bond 0.00724 (33876) covalent geometry : angle 1.16721 (46014) hydrogen bonds : bond 0.07669 ( 1812) hydrogen bonds : angle 7.55725 ( 5268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 357 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 994 MET cc_start: -0.3933 (ppp) cc_final: -0.4159 (ppp) REVERT: A 1073 MET cc_start: -0.5766 (tmm) cc_final: -0.6908 (mmt) REVERT: A 1095 MET cc_start: 0.3021 (tpp) cc_final: 0.2682 (mmm) REVERT: A 1201 MET cc_start: 0.5788 (mtp) cc_final: 0.5546 (mtp) REVERT: A 1242 TYR cc_start: 0.8169 (m-80) cc_final: 0.7734 (m-80) REVERT: A 1287 TYR cc_start: 0.8564 (m-10) cc_final: 0.8360 (m-80) REVERT: A 1289 ASP cc_start: 0.7715 (p0) cc_final: 0.7418 (p0) REVERT: A 1347 TYR cc_start: 0.8760 (m-80) cc_final: 0.8235 (m-80) REVERT: A 1540 MET cc_start: 0.9360 (mmp) cc_final: 0.8895 (mmm) REVERT: A 1588 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: B 166 MET cc_start: 0.5514 (mmp) cc_final: 0.5031 (mmp) REVERT: B 356 TYR cc_start: 0.3743 (m-80) cc_final: 0.3315 (m-80) REVERT: B 386 TYR cc_start: -0.4642 (t80) cc_final: -0.5169 (t80) REVERT: B 692 MET cc_start: -0.8090 (mmt) cc_final: -0.8607 (ttt) REVERT: C 26 ASN cc_start: 0.7544 (t0) cc_final: 0.7101 (t0) REVERT: C 112 LEU cc_start: 0.9191 (tp) cc_final: 0.8749 (tp) REVERT: C 173 ILE cc_start: 0.8479 (mt) cc_final: 0.7385 (mt) REVERT: D 1 MET cc_start: 0.6208 (mmt) cc_final: 0.5841 (tpt) REVERT: D 121 MET cc_start: 0.8979 (mtt) cc_final: 0.8543 (tmm) REVERT: D 450 MET cc_start: 0.3944 (mtt) cc_final: 0.3710 (mtt) REVERT: D 490 MET cc_start: 0.0720 (ttt) cc_final: -0.0084 (ttm) REVERT: D 535 MET cc_start: 0.5062 (pmm) cc_final: 0.4822 (pmm) REVERT: D 1088 MET cc_start: 0.7853 (tpt) cc_final: 0.7568 (tpp) REVERT: D 1092 ILE cc_start: 0.8909 (mt) cc_final: 0.8628 (mt) REVERT: D 1379 MET cc_start: 0.3938 (tpp) cc_final: 0.3733 (tpp) REVERT: D 1479 LEU cc_start: 0.8636 (tp) cc_final: 0.8291 (tp) REVERT: D 1487 MET cc_start: 0.6892 (mmt) cc_final: 0.6300 (tpp) REVERT: D 1511 MET cc_start: 0.9098 (mtm) cc_final: 0.8825 (mtt) REVERT: E 12 ILE cc_start: 0.2234 (mm) cc_final: 0.1879 (mm) REVERT: E 208 MET cc_start: 0.5759 (ppp) cc_final: 0.5437 (ppp) REVERT: E 262 MET cc_start: 0.8059 (tmm) cc_final: 0.7739 (tmm) REVERT: E 391 HIS cc_start: 0.3749 (m170) cc_final: 0.3482 (m-70) REVERT: E 677 MET cc_start: 0.7764 (mtt) cc_final: 0.7348 (ptt) outliers start: 33 outliers final: 9 residues processed: 388 average time/residue: 0.2383 time to fit residues: 147.2762 Evaluate side-chains 286 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 137 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 81 optimal weight: 50.0000 chunk 160 optimal weight: 50.0000 chunk 78 optimal weight: 40.0000 chunk 114 optimal weight: 0.7980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN E 227 GLN E 231 HIS E 233 GLN E 240 GLN E 260 GLN E 278 HIS ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 ASN ** E 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.171528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.139082 restraints weight = 110902.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.132563 restraints weight = 117038.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.132031 restraints weight = 126315.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.131987 restraints weight = 118821.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.131912 restraints weight = 114213.879| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 33876 Z= 0.269 Angle : 0.967 15.808 46014 Z= 0.487 Chirality : 0.049 0.317 5412 Planarity : 0.007 0.113 5928 Dihedral : 7.719 50.268 4826 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 32.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.67 % Favored : 89.09 % Rotamer: Outliers : 0.61 % Allowed : 7.77 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.90 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.13), residues: 3750 helix: -1.30 (0.11), residues: 1984 sheet: -4.03 (0.22), residues: 344 loop : -2.48 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 128 TYR 0.037 0.004 TYR D1347 PHE 0.046 0.003 PHE D1210 TRP 0.046 0.003 TRP E 665 HIS 0.014 0.002 HIS D1587 Details of bonding type rmsd covalent geometry : bond 0.00572 (33876) covalent geometry : angle 0.96744 (46014) hydrogen bonds : bond 0.06215 ( 1812) hydrogen bonds : angle 6.74211 ( 5268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 339 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1 MET cc_start: -0.8265 (mpp) cc_final: -0.8493 (mpp) REVERT: A 121 MET cc_start: -0.4254 (tpt) cc_final: -0.5847 (tpt) REVERT: A 1062 MET cc_start: -0.1655 (ppp) cc_final: -0.2171 (ptt) REVERT: A 1073 MET cc_start: -0.7510 (tmm) cc_final: -0.7838 (mmt) REVERT: A 1095 MET cc_start: 0.3531 (tpp) cc_final: 0.3065 (mmm) REVERT: A 1287 TYR cc_start: 0.8820 (m-10) cc_final: 0.8381 (m-80) REVERT: A 1293 MET cc_start: 0.9305 (mpp) cc_final: 0.8786 (mpp) REVERT: A 1347 TYR cc_start: 0.9562 (m-80) cc_final: 0.9110 (m-80) REVERT: A 1487 MET cc_start: 0.9311 (mpp) cc_final: 0.8524 (tmm) REVERT: A 1529 MET cc_start: 0.8210 (tmm) cc_final: 0.7938 (tmm) REVERT: A 1608 ASN cc_start: 0.9105 (m110) cc_final: 0.8377 (m110) REVERT: B 53 HIS cc_start: 0.8056 (m-70) cc_final: 0.7805 (m-70) REVERT: B 168 HIS cc_start: 0.6113 (m170) cc_final: 0.5809 (m170) REVERT: B 231 HIS cc_start: 0.6443 (m-70) cc_final: 0.6161 (m-70) REVERT: B 675 LYS cc_start: 0.1972 (tptp) cc_final: 0.1750 (tttt) REVERT: B 692 MET cc_start: -0.7062 (mmt) cc_final: -0.8082 (ttt) REVERT: C 26 ASN cc_start: 0.8240 (t0) cc_final: 0.7514 (t0) REVERT: C 72 TYR cc_start: 0.7760 (m-80) cc_final: 0.7434 (m-80) REVERT: D 1 MET cc_start: 0.5015 (mmt) cc_final: 0.4123 (tpt) REVERT: D 114 PHE cc_start: 0.8813 (t80) cc_final: 0.8466 (t80) REVERT: D 121 MET cc_start: 0.9113 (mtt) cc_final: 0.8866 (tmm) REVERT: D 125 MET cc_start: 0.8444 (tpt) cc_final: 0.8113 (tpt) REVERT: D 1088 MET cc_start: 0.7844 (tpt) cc_final: 0.7543 (tpp) REVERT: D 1092 ILE cc_start: 0.8824 (mt) cc_final: 0.8508 (mt) REVERT: D 1250 LEU cc_start: 0.9102 (mm) cc_final: 0.8662 (tp) REVERT: D 1296 GLU cc_start: 0.8756 (pm20) cc_final: 0.8136 (pm20) REVERT: D 1303 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9003 (mm-30) REVERT: D 1444 TYR cc_start: 0.7348 (t80) cc_final: 0.6241 (t80) REVERT: D 1487 MET cc_start: 0.7213 (mmt) cc_final: 0.6603 (tpp) REVERT: D 1568 HIS cc_start: 0.9243 (t-90) cc_final: 0.9035 (t70) REVERT: D 1612 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8837 (tmtt) REVERT: E 383 ASN cc_start: 0.3895 (m110) cc_final: 0.3578 (m110) REVERT: E 391 HIS cc_start: 0.7687 (m90) cc_final: 0.7482 (m-70) REVERT: E 442 HIS cc_start: 0.9346 (m-70) cc_final: 0.9059 (m-70) REVERT: E 677 MET cc_start: 0.7693 (mtt) cc_final: 0.7245 (ptt) REVERT: F 1 MET cc_start: 0.6142 (mtt) cc_final: 0.5791 (mtt) outliers start: 18 outliers final: 8 residues processed: 357 average time/residue: 0.2386 time to fit residues: 136.2926 Evaluate side-chains 283 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 275 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 7 optimal weight: 50.0000 chunk 107 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 149 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 69 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 231 HIS E 240 GLN E 303 ASN E 391 HIS E 464 ASN ** E 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 HIS E 660 HIS F 74 GLN ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.160544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.124615 restraints weight = 143646.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.118349 restraints weight = 164718.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.118938 restraints weight = 143125.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.118416 restraints weight = 134048.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.118509 restraints weight = 128245.558| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.152 33876 Z= 0.458 Angle : 1.187 23.010 46014 Z= 0.601 Chirality : 0.056 0.445 5412 Planarity : 0.009 0.217 5928 Dihedral : 7.968 52.484 4826 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 44.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.83 % Favored : 86.83 % Rotamer: Outliers : 0.47 % Allowed : 7.84 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.27 % Twisted General : 0.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.13), residues: 3750 helix: -1.22 (0.11), residues: 1994 sheet: -4.19 (0.23), residues: 322 loop : -2.56 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1370 TYR 0.075 0.006 TYR A1347 PHE 0.057 0.004 PHE D1352 TRP 0.056 0.004 TRP E 665 HIS 0.023 0.003 HIS D1587 Details of bonding type rmsd covalent geometry : bond 0.00929 (33876) covalent geometry : angle 1.18657 (46014) hydrogen bonds : bond 0.06917 ( 1812) hydrogen bonds : angle 7.04695 ( 5268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 325 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 MET cc_start: -0.7495 (tmm) cc_final: -0.7919 (mpp) REVERT: A 1201 MET cc_start: 0.7813 (mtp) cc_final: 0.7563 (mtp) REVERT: A 1293 MET cc_start: 0.9159 (mpp) cc_final: 0.8833 (mpp) REVERT: A 1309 GLU cc_start: 0.7056 (tp30) cc_final: 0.6850 (tp30) REVERT: A 1333 MET cc_start: 0.8660 (tmm) cc_final: 0.8449 (tmm) REVERT: A 1347 TYR cc_start: 0.9381 (m-80) cc_final: 0.9174 (m-80) REVERT: A 1611 MET cc_start: 0.9702 (ptt) cc_final: 0.9475 (ppp) REVERT: B 168 HIS cc_start: 0.7027 (m170) cc_final: 0.6821 (m170) REVERT: B 231 HIS cc_start: 0.6427 (m-70) cc_final: 0.6144 (m-70) REVERT: B 242 TYR cc_start: 0.9355 (m-80) cc_final: 0.9144 (m-80) REVERT: B 290 MET cc_start: -0.7084 (tpt) cc_final: -0.7706 (ttt) REVERT: C 64 TYR cc_start: 0.7614 (m-10) cc_final: 0.7280 (m-10) REVERT: C 169 PHE cc_start: 0.8982 (m-80) cc_final: 0.8765 (m-10) REVERT: D 1 MET cc_start: 0.5113 (mmt) cc_final: 0.4182 (tpt) REVERT: D 121 MET cc_start: 0.9085 (mtt) cc_final: 0.8761 (tmm) REVERT: D 1088 MET cc_start: 0.8229 (tpt) cc_final: 0.7860 (tpp) REVERT: D 1092 ILE cc_start: 0.9115 (mt) cc_final: 0.8797 (mt) REVERT: D 1293 MET cc_start: 0.8127 (mtt) cc_final: 0.7173 (ttm) REVERT: D 1296 GLU cc_start: 0.8602 (pm20) cc_final: 0.8137 (pm20) REVERT: D 1303 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8942 (mm-30) REVERT: D 1421 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6681 (m-80) REVERT: D 1442 PHE cc_start: 0.7125 (m-80) cc_final: 0.5996 (m-80) REVERT: D 1444 TYR cc_start: 0.7951 (t80) cc_final: 0.7256 (t80) REVERT: D 1478 ILE cc_start: 0.9164 (mm) cc_final: 0.8610 (tp) REVERT: D 1496 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7988 (mm-30) REVERT: D 1507 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9087 (pp20) REVERT: D 1508 LYS cc_start: 0.9437 (ptpp) cc_final: 0.9152 (pttt) REVERT: D 1511 MET cc_start: 0.9065 (mtm) cc_final: 0.8818 (mtt) REVERT: D 1598 PHE cc_start: 0.7335 (t80) cc_final: 0.7047 (t80) REVERT: E 12 ILE cc_start: 0.0190 (mm) cc_final: -0.0124 (mm) REVERT: E 97 MET cc_start: 0.1644 (tpt) cc_final: 0.1390 (tpt) REVERT: E 262 MET cc_start: 0.5576 (tmm) cc_final: 0.5255 (tmm) REVERT: E 391 HIS cc_start: 0.7407 (m-70) cc_final: 0.7194 (m90) REVERT: F 1 MET cc_start: 0.6900 (mtt) cc_final: 0.6071 (mtm) outliers start: 14 outliers final: 10 residues processed: 339 average time/residue: 0.2355 time to fit residues: 127.6531 Evaluate side-chains 281 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 270 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 194 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 79 optimal weight: 50.0000 chunk 185 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN E 231 HIS E 240 GLN ** E 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.211273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.135116 restraints weight = 262193.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.135646 restraints weight = 202531.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.130921 restraints weight = 176271.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.130043 restraints weight = 148170.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.130147 restraints weight = 137296.231| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 33876 Z= 0.177 Angle : 0.862 20.235 46014 Z= 0.430 Chirality : 0.046 0.253 5412 Planarity : 0.006 0.082 5928 Dihedral : 6.983 48.971 4826 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.61 % Favored : 91.23 % Rotamer: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.13), residues: 3750 helix: -0.55 (0.11), residues: 1976 sheet: -3.89 (0.25), residues: 314 loop : -2.17 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1601 TYR 0.032 0.003 TYR A1348 PHE 0.054 0.003 PHE A1288 TRP 0.037 0.003 TRP E 665 HIS 0.012 0.002 HIS D1486 Details of bonding type rmsd covalent geometry : bond 0.00378 (33876) covalent geometry : angle 0.86173 (46014) hydrogen bonds : bond 0.05041 ( 1812) hydrogen bonds : angle 6.14088 ( 5268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 340 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 992 MET cc_start: -0.2353 (mpp) cc_final: -0.4823 (ptt) REVERT: A 1073 MET cc_start: -0.6541 (tmm) cc_final: -0.7411 (mtt) REVERT: A 1311 GLU cc_start: 0.8597 (tp30) cc_final: 0.8337 (mm-30) REVERT: A 1313 PHE cc_start: 0.6137 (m-80) cc_final: 0.5367 (m-80) REVERT: A 1347 TYR cc_start: 0.8807 (m-80) cc_final: 0.8397 (m-80) REVERT: A 1348 TYR cc_start: 0.8818 (m-80) cc_final: 0.8323 (m-10) REVERT: A 1443 HIS cc_start: 0.8545 (m90) cc_final: 0.8317 (m90) REVERT: A 1502 MET cc_start: 0.8819 (ttt) cc_final: 0.8445 (ttt) REVERT: A 1611 MET cc_start: 0.9573 (ptt) cc_final: 0.9371 (ppp) REVERT: B 166 MET cc_start: 0.6657 (mmp) cc_final: 0.6278 (mmp) REVERT: C 84 LEU cc_start: 0.6693 (mt) cc_final: 0.6250 (mp) REVERT: C 169 PHE cc_start: 0.9040 (m-80) cc_final: 0.8711 (m-10) REVERT: D 1 MET cc_start: 0.6329 (mmt) cc_final: 0.5594 (tpt) REVERT: D 121 MET cc_start: 0.9120 (mtt) cc_final: 0.8858 (tmm) REVERT: D 535 MET cc_start: 0.4890 (pmm) cc_final: 0.4460 (ptp) REVERT: D 1062 MET cc_start: 0.8949 (pmm) cc_final: 0.7841 (pmm) REVERT: D 1088 MET cc_start: 0.7978 (tpt) cc_final: 0.7585 (tpp) REVERT: D 1092 ILE cc_start: 0.9105 (mt) cc_final: 0.8819 (mt) REVERT: D 1184 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8244 (tptp) REVERT: D 1219 MET cc_start: 0.7962 (tpt) cc_final: 0.7433 (tpt) REVERT: D 1293 MET cc_start: 0.8024 (mtt) cc_final: 0.7494 (tpt) REVERT: D 1296 GLU cc_start: 0.8888 (pm20) cc_final: 0.8129 (pm20) REVERT: D 1301 CYS cc_start: 0.8469 (m) cc_final: 0.8111 (m) REVERT: D 1303 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8898 (mm-30) REVERT: D 1311 GLU cc_start: 0.7740 (tt0) cc_final: 0.7475 (tt0) REVERT: D 1320 GLN cc_start: 0.9167 (mp10) cc_final: 0.8923 (mp10) REVERT: D 1442 PHE cc_start: 0.6514 (m-80) cc_final: 0.5485 (m-80) REVERT: D 1444 TYR cc_start: 0.6252 (t80) cc_final: 0.5672 (t80) REVERT: D 1478 ILE cc_start: 0.8910 (mm) cc_final: 0.8476 (tp) REVERT: D 1487 MET cc_start: 0.7307 (mmt) cc_final: 0.6755 (mmm) REVERT: D 1508 LYS cc_start: 0.9129 (ptpp) cc_final: 0.8671 (pttm) REVERT: D 1527 LEU cc_start: 0.9322 (mt) cc_final: 0.8889 (mt) REVERT: D 1612 LYS cc_start: 0.9294 (mtmm) cc_final: 0.8865 (tmtt) REVERT: E 97 MET cc_start: 0.2801 (tpt) cc_final: 0.2561 (tpt) REVERT: E 208 MET cc_start: 0.6229 (ppp) cc_final: 0.5931 (ppp) REVERT: E 262 MET cc_start: 0.8153 (tmm) cc_final: 0.7823 (tmm) REVERT: F 1 MET cc_start: 0.6254 (mtt) cc_final: 0.4891 (mtt) outliers start: 4 outliers final: 4 residues processed: 344 average time/residue: 0.2374 time to fit residues: 130.0606 Evaluate side-chains 286 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 119 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 79 optimal weight: 50.0000 chunk 118 optimal weight: 5.9990 chunk 146 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS E 231 HIS E 240 GLN E 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.158802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.116450 restraints weight = 140784.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.116994 restraints weight = 99331.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.116200 restraints weight = 90369.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.115998 restraints weight = 108510.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.116037 restraints weight = 89808.097| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.149 33876 Z= 0.458 Angle : 1.152 19.110 46014 Z= 0.586 Chirality : 0.056 0.452 5412 Planarity : 0.009 0.234 5928 Dihedral : 7.523 52.444 4826 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 42.67 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.19 % Favored : 87.41 % Rotamer: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.13), residues: 3750 helix: -0.72 (0.11), residues: 1975 sheet: -3.74 (0.28), residues: 260 loop : -2.43 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 128 TYR 0.077 0.005 TYR D 985 PHE 0.053 0.004 PHE D1210 TRP 0.048 0.003 TRP E 665 HIS 0.017 0.003 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00947 (33876) covalent geometry : angle 1.15218 (46014) hydrogen bonds : bond 0.06580 ( 1812) hydrogen bonds : angle 6.75449 ( 5268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 304 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1073 MET cc_start: -0.7679 (tmm) cc_final: -0.8064 (mtt) REVERT: A 1347 TYR cc_start: 0.9469 (m-80) cc_final: 0.9269 (m-80) REVERT: A 1502 MET cc_start: 0.9293 (ttt) cc_final: 0.8790 (ttt) REVERT: A 1604 GLU cc_start: 0.9308 (mp0) cc_final: 0.8997 (pm20) REVERT: B 168 HIS cc_start: 0.7070 (m170) cc_final: 0.6769 (m170) REVERT: B 231 HIS cc_start: 0.7182 (m-70) cc_final: 0.6579 (m-70) REVERT: B 290 MET cc_start: -0.6970 (tpt) cc_final: -0.7592 (ttt) REVERT: B 356 TYR cc_start: -0.0018 (m-80) cc_final: -0.0349 (m-80) REVERT: C 169 PHE cc_start: 0.9094 (m-80) cc_final: 0.8670 (m-10) REVERT: D 1 MET cc_start: 0.5586 (mmt) cc_final: 0.4089 (tpt) REVERT: D 510 MET cc_start: 0.8890 (mmp) cc_final: 0.8057 (mmp) REVERT: D 529 MET cc_start: 0.8598 (tmm) cc_final: 0.8236 (tmm) REVERT: D 559 MET cc_start: 0.2750 (mmt) cc_final: 0.2388 (mmt) REVERT: D 992 MET cc_start: 0.8634 (ppp) cc_final: 0.8396 (ppp) REVERT: D 1088 MET cc_start: 0.8206 (tpt) cc_final: 0.7775 (tpp) REVERT: D 1092 ILE cc_start: 0.9274 (mt) cc_final: 0.8946 (mt) REVERT: D 1102 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: D 1296 GLU cc_start: 0.9023 (pm20) cc_final: 0.8325 (pm20) REVERT: D 1303 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8975 (mm-30) REVERT: D 1396 ASP cc_start: 0.9692 (m-30) cc_final: 0.9465 (m-30) REVERT: D 1444 TYR cc_start: 0.6975 (t80) cc_final: 0.6322 (t80) REVERT: D 1475 LEU cc_start: 0.9440 (mt) cc_final: 0.9166 (tp) REVERT: D 1487 MET cc_start: 0.7972 (mmt) cc_final: 0.7690 (mmt) REVERT: D 1511 MET cc_start: 0.9104 (ptt) cc_final: 0.8805 (ptt) REVERT: E 97 MET cc_start: 0.1726 (tpt) cc_final: 0.1459 (tpt) REVERT: E 262 MET cc_start: 0.5950 (tmm) cc_final: 0.5595 (tmm) REVERT: F 1 MET cc_start: 0.7045 (mtt) cc_final: 0.6718 (mtm) REVERT: F 6 CYS cc_start: 0.6616 (t) cc_final: 0.6334 (t) REVERT: F 138 THR cc_start: 0.8516 (p) cc_final: 0.8249 (p) outliers start: 7 outliers final: 5 residues processed: 311 average time/residue: 0.2118 time to fit residues: 107.0163 Evaluate side-chains 260 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 254 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 41 optimal weight: 30.0000 chunk 188 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 24 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 127 optimal weight: 50.0000 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.145498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.099623 restraints weight = 84066.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.093379 restraints weight = 114906.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.092613 restraints weight = 115980.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.092538 restraints weight = 121476.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.092554 restraints weight = 109926.226| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.8131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.146 33876 Z= 0.442 Angle : 1.138 15.555 46014 Z= 0.578 Chirality : 0.055 0.362 5412 Planarity : 0.009 0.251 5928 Dihedral : 7.613 60.578 4826 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 41.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.75 % Favored : 87.04 % Rotamer: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 1.27 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.13), residues: 3750 helix: -0.67 (0.11), residues: 1939 sheet: -3.71 (0.27), residues: 275 loop : -2.52 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG D1370 TYR 0.086 0.004 TYR D1281 PHE 0.041 0.004 PHE A1352 TRP 0.077 0.004 TRP D 102 HIS 0.019 0.003 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00911 (33876) covalent geometry : angle 1.13769 (46014) hydrogen bonds : bond 0.06459 ( 1812) hydrogen bonds : angle 6.75994 ( 5268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 300 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 MET cc_start: -0.7862 (tmm) cc_final: -0.8150 (mtt) REVERT: A 1203 CYS cc_start: 0.8910 (m) cc_final: 0.8707 (m) REVERT: A 1219 MET cc_start: 0.9412 (tpt) cc_final: 0.8875 (tpp) REVERT: A 1223 TYR cc_start: 0.8651 (m-80) cc_final: 0.7346 (m-80) REVERT: A 1313 PHE cc_start: 0.8148 (m-80) cc_final: 0.7837 (m-80) REVERT: A 1333 MET cc_start: 0.9059 (tmm) cc_final: 0.8791 (tmm) REVERT: A 1347 TYR cc_start: 0.9527 (m-80) cc_final: 0.9200 (m-80) REVERT: A 1443 HIS cc_start: 0.9426 (m90) cc_final: 0.9214 (m-70) REVERT: A 1479 LEU cc_start: 0.8208 (tp) cc_final: 0.7719 (tp) REVERT: A 1502 MET cc_start: 0.9349 (ttt) cc_final: 0.8917 (ttt) REVERT: B 168 HIS cc_start: 0.6047 (m170) cc_final: 0.5720 (m170) REVERT: B 231 HIS cc_start: 0.7184 (m-70) cc_final: 0.6617 (m-70) REVERT: B 242 TYR cc_start: 0.8940 (m-80) cc_final: 0.8713 (m-80) REVERT: B 290 MET cc_start: -0.7580 (tpt) cc_final: -0.7993 (ttt) REVERT: C 1 MET cc_start: 0.7813 (mtt) cc_final: 0.7272 (mmt) REVERT: C 169 PHE cc_start: 0.9267 (m-80) cc_final: 0.9050 (m-10) REVERT: D 1 MET cc_start: 0.5927 (mmt) cc_final: 0.5035 (tpt) REVERT: D 510 MET cc_start: 0.9052 (mmp) cc_final: 0.8706 (mmp) REVERT: D 529 MET cc_start: 0.8844 (tmm) cc_final: 0.8240 (tmm) REVERT: D 535 MET cc_start: 0.5776 (pmm) cc_final: 0.5527 (pmm) REVERT: D 559 MET cc_start: 0.3074 (mmt) cc_final: 0.2417 (mmt) REVERT: D 1088 MET cc_start: 0.8117 (tpt) cc_final: 0.7750 (tpp) REVERT: D 1092 ILE cc_start: 0.9197 (mt) cc_final: 0.8807 (mt) REVERT: D 1184 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8627 (tptp) REVERT: D 1210 PHE cc_start: 0.9177 (t80) cc_final: 0.8943 (t80) REVERT: D 1293 MET cc_start: 0.9245 (tpt) cc_final: 0.8712 (tpt) REVERT: D 1296 GLU cc_start: 0.8829 (pm20) cc_final: 0.8410 (pm20) REVERT: D 1303 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9004 (mm-30) REVERT: D 1405 TYR cc_start: 0.9419 (m-80) cc_final: 0.9173 (m-80) REVERT: D 1478 ILE cc_start: 0.9124 (mm) cc_final: 0.8906 (tp) REVERT: D 1511 MET cc_start: 0.9484 (ptt) cc_final: 0.8823 (ptt) REVERT: D 1568 HIS cc_start: 0.9373 (m-70) cc_final: 0.9073 (m-70) REVERT: E 97 MET cc_start: 0.0210 (tpt) cc_final: -0.0064 (tpt) REVERT: F 1 MET cc_start: 0.6952 (mtt) cc_final: 0.6258 (mtt) outliers start: 4 outliers final: 4 residues processed: 304 average time/residue: 0.2091 time to fit residues: 103.5222 Evaluate side-chains 270 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 142 optimal weight: 50.0000 chunk 45 optimal weight: 50.0000 chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 40.0000 chunk 92 optimal weight: 0.0470 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 50.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.149816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.098528 restraints weight = 75851.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.095842 restraints weight = 94525.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.095758 restraints weight = 85935.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.095758 restraints weight = 79744.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.095758 restraints weight = 79744.427| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.8608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 33876 Z= 0.334 Angle : 0.996 14.393 46014 Z= 0.504 Chirality : 0.050 0.346 5412 Planarity : 0.008 0.190 5928 Dihedral : 7.270 59.856 4826 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 34.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.63 % Favored : 88.16 % Rotamer: Outliers : 0.14 % Allowed : 2.10 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.14), residues: 3750 helix: -0.48 (0.12), residues: 1946 sheet: -3.66 (0.27), residues: 277 loop : -2.46 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D1370 TYR 0.057 0.003 TYR D1434 PHE 0.062 0.003 PHE D1433 TRP 0.047 0.003 TRP E 665 HIS 0.018 0.002 HIS D1273 Details of bonding type rmsd covalent geometry : bond 0.00697 (33876) covalent geometry : angle 0.99582 (46014) hydrogen bonds : bond 0.05851 ( 1812) hydrogen bonds : angle 6.42459 ( 5268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 305 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 MET cc_start: -0.7809 (tmm) cc_final: -0.8105 (mtt) REVERT: A 1203 CYS cc_start: 0.8917 (m) cc_final: 0.8692 (m) REVERT: A 1219 MET cc_start: 0.9503 (tpt) cc_final: 0.8920 (tpp) REVERT: A 1223 TYR cc_start: 0.8483 (m-80) cc_final: 0.6941 (m-80) REVERT: A 1231 HIS cc_start: 0.9552 (m170) cc_final: 0.9218 (m-70) REVERT: A 1333 MET cc_start: 0.8996 (tmm) cc_final: 0.8638 (tmm) REVERT: A 1462 MET cc_start: 0.8701 (ttt) cc_final: 0.8144 (tmm) REVERT: A 1479 LEU cc_start: 0.8299 (tp) cc_final: 0.7862 (tp) REVERT: A 1502 MET cc_start: 0.9215 (ttt) cc_final: 0.8733 (ttt) REVERT: A 1604 GLU cc_start: 0.9487 (mp0) cc_final: 0.9282 (mp0) REVERT: B 168 HIS cc_start: 0.5873 (m170) cc_final: 0.5555 (m170) REVERT: B 231 HIS cc_start: 0.7138 (m-70) cc_final: 0.6600 (m-70) REVERT: B 242 TYR cc_start: 0.9000 (m-80) cc_final: 0.8773 (m-80) REVERT: B 290 MET cc_start: -0.7639 (tpt) cc_final: -0.8053 (ttt) REVERT: B 659 LYS cc_start: 0.6511 (tptp) cc_final: 0.6296 (tptp) REVERT: C 1 MET cc_start: 0.7166 (mtt) cc_final: 0.6051 (mmt) REVERT: C 157 CYS cc_start: 0.8097 (t) cc_final: 0.7781 (t) REVERT: C 169 PHE cc_start: 0.9264 (m-80) cc_final: 0.8963 (m-10) REVERT: D 1 MET cc_start: 0.6016 (mmt) cc_final: 0.5235 (tpt) REVERT: D 510 MET cc_start: 0.8905 (mmp) cc_final: 0.8697 (mmp) REVERT: D 559 MET cc_start: 0.3316 (mmt) cc_final: 0.2710 (mmt) REVERT: D 1088 MET cc_start: 0.8178 (tpt) cc_final: 0.7823 (tpp) REVERT: D 1092 ILE cc_start: 0.9210 (mt) cc_final: 0.8833 (mt) REVERT: D 1184 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8480 (tptp) REVERT: D 1210 PHE cc_start: 0.9030 (t80) cc_final: 0.8674 (t80) REVERT: D 1293 MET cc_start: 0.9086 (tpt) cc_final: 0.8485 (tpt) REVERT: D 1296 GLU cc_start: 0.8729 (pm20) cc_final: 0.8111 (pm20) REVERT: D 1303 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9012 (mm-30) REVERT: D 1511 MET cc_start: 0.9330 (ptt) cc_final: 0.9067 (ptt) REVERT: D 1568 HIS cc_start: 0.9324 (m-70) cc_final: 0.9014 (m-70) REVERT: D 1598 PHE cc_start: 0.8192 (t80) cc_final: 0.7979 (t80) REVERT: E 97 MET cc_start: -0.0204 (tpt) cc_final: -0.0414 (tpt) REVERT: E 423 MET cc_start: 0.9090 (mpp) cc_final: 0.8768 (tmm) REVERT: F 145 MET cc_start: 0.4629 (tpt) cc_final: 0.4335 (tpt) outliers start: 4 outliers final: 4 residues processed: 309 average time/residue: 0.1844 time to fit residues: 93.8032 Evaluate side-chains 277 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 177 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 202 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 131 optimal weight: 30.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS B 448 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 52 ASN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.164920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.138313 restraints weight = 61753.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.108371 restraints weight = 68452.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.106218 restraints weight = 98306.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.106155 restraints weight = 91293.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.106279 restraints weight = 73731.319| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.8952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33876 Z= 0.181 Angle : 0.851 15.093 46014 Z= 0.428 Chirality : 0.046 0.275 5412 Planarity : 0.006 0.086 5928 Dihedral : 6.637 54.106 4826 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.15 % Favored : 90.67 % Rotamer: Outliers : 0.14 % Allowed : 1.35 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.14), residues: 3750 helix: -0.14 (0.12), residues: 1966 sheet: -3.35 (0.30), residues: 248 loop : -2.26 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1370 TYR 0.047 0.003 TYR A1348 PHE 0.041 0.002 PHE D1433 TRP 0.035 0.003 TRP E 665 HIS 0.008 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00391 (33876) covalent geometry : angle 0.85075 (46014) hydrogen bonds : bond 0.04790 ( 1812) hydrogen bonds : angle 5.91452 ( 5268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 326 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 MET cc_start: -0.7646 (tmm) cc_final: -0.7977 (mtt) REVERT: A 1203 CYS cc_start: 0.8727 (m) cc_final: 0.8444 (m) REVERT: A 1219 MET cc_start: 0.9369 (tpt) cc_final: 0.8677 (tpp) REVERT: A 1223 TYR cc_start: 0.8533 (m-80) cc_final: 0.6950 (m-80) REVERT: A 1333 MET cc_start: 0.9036 (tmm) cc_final: 0.8534 (tmm) REVERT: A 1462 MET cc_start: 0.8212 (ttt) cc_final: 0.7751 (tmm) REVERT: A 1479 LEU cc_start: 0.7785 (tp) cc_final: 0.7565 (tp) REVERT: B 168 HIS cc_start: 0.5927 (m170) cc_final: 0.5655 (m170) REVERT: B 231 HIS cc_start: 0.7143 (m-70) cc_final: 0.6602 (m-70) REVERT: B 242 TYR cc_start: 0.8913 (m-80) cc_final: 0.8680 (m-80) REVERT: C 1 MET cc_start: 0.6820 (mtt) cc_final: 0.5883 (mmt) REVERT: C 157 CYS cc_start: 0.7733 (t) cc_final: 0.7388 (t) REVERT: D 1 MET cc_start: 0.5873 (mmt) cc_final: 0.5021 (tpt) REVERT: D 510 MET cc_start: 0.8977 (mmp) cc_final: 0.8663 (mmp) REVERT: D 529 MET cc_start: 0.8723 (tmm) cc_final: 0.8516 (tmm) REVERT: D 1062 MET cc_start: 0.8809 (pmm) cc_final: 0.8166 (pmm) REVERT: D 1088 MET cc_start: 0.7799 (tpt) cc_final: 0.7414 (tpp) REVERT: D 1092 ILE cc_start: 0.8913 (mt) cc_final: 0.8593 (mt) REVERT: D 1095 MET cc_start: 0.7479 (tpp) cc_final: 0.7011 (tpp) REVERT: D 1184 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8348 (tptp) REVERT: D 1210 PHE cc_start: 0.9039 (t80) cc_final: 0.8801 (t80) REVERT: D 1219 MET cc_start: 0.7892 (tpt) cc_final: 0.7629 (tpt) REVERT: D 1293 MET cc_start: 0.9044 (tpt) cc_final: 0.8616 (tpt) REVERT: D 1296 GLU cc_start: 0.8811 (pm20) cc_final: 0.8263 (pm20) REVERT: D 1303 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8933 (mm-30) REVERT: D 1478 ILE cc_start: 0.8889 (mm) cc_final: 0.8636 (tp) REVERT: D 1511 MET cc_start: 0.9232 (ptt) cc_final: 0.9016 (ptt) REVERT: D 1568 HIS cc_start: 0.9297 (m-70) cc_final: 0.8957 (m-70) REVERT: E 97 MET cc_start: 0.0434 (tpt) cc_final: 0.0182 (tpt) REVERT: E 391 HIS cc_start: 0.7849 (m-70) cc_final: 0.7622 (m-70) REVERT: E 677 MET cc_start: 0.8143 (ptt) cc_final: 0.7291 (ppp) REVERT: F 145 MET cc_start: 0.4721 (tpt) cc_final: 0.3801 (tpt) outliers start: 4 outliers final: 4 residues processed: 330 average time/residue: 0.1862 time to fit residues: 99.6110 Evaluate side-chains 280 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 92 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 27 optimal weight: 50.0000 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.148209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.099766 restraints weight = 75642.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.096088 restraints weight = 91977.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.095630 restraints weight = 84050.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.095630 restraints weight = 80393.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.095630 restraints weight = 80393.658| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.9315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 33876 Z= 0.349 Angle : 1.008 16.633 46014 Z= 0.511 Chirality : 0.050 0.309 5412 Planarity : 0.007 0.100 5928 Dihedral : 6.961 56.819 4826 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 33.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.17 % Favored : 88.56 % Rotamer: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.14), residues: 3750 helix: -0.34 (0.12), residues: 1963 sheet: -3.51 (0.28), residues: 263 loop : -2.29 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D1370 TYR 0.071 0.004 TYR D 985 PHE 0.041 0.003 PHE D1174 TRP 0.041 0.003 TRP D 102 HIS 0.019 0.002 HIS D1273 Details of bonding type rmsd covalent geometry : bond 0.00727 (33876) covalent geometry : angle 1.00826 (46014) hydrogen bonds : bond 0.05711 ( 1812) hydrogen bonds : angle 6.23798 ( 5268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 300 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 MET cc_start: -0.7758 (tmm) cc_final: -0.8067 (mtt) REVERT: A 1095 MET cc_start: 0.3950 (mmp) cc_final: 0.3447 (tpp) REVERT: A 1219 MET cc_start: 0.9317 (tpt) cc_final: 0.8624 (tpp) REVERT: A 1223 TYR cc_start: 0.8487 (m-80) cc_final: 0.6994 (m-80) REVERT: A 1231 HIS cc_start: 0.9582 (m-70) cc_final: 0.9265 (m-70) REVERT: A 1303 GLU cc_start: 0.8440 (pp20) cc_final: 0.8088 (tm-30) REVERT: A 1310 MET cc_start: 0.8626 (ptm) cc_final: 0.8013 (ppp) REVERT: A 1333 MET cc_start: 0.8892 (tmm) cc_final: 0.8501 (tmm) REVERT: A 1462 MET cc_start: 0.8751 (ttt) cc_final: 0.8370 (tmm) REVERT: A 1479 LEU cc_start: 0.8506 (tp) cc_final: 0.8129 (tp) REVERT: A 1502 MET cc_start: 0.9236 (ttt) cc_final: 0.8738 (ttt) REVERT: B 53 HIS cc_start: 0.7040 (m-70) cc_final: 0.6829 (m-70) REVERT: B 168 HIS cc_start: 0.5425 (m170) cc_final: 0.5155 (m170) REVERT: B 231 HIS cc_start: 0.7106 (m-70) cc_final: 0.6616 (m-70) REVERT: B 242 TYR cc_start: 0.8852 (m-80) cc_final: 0.8623 (m-80) REVERT: B 290 MET cc_start: -0.7515 (tpt) cc_final: -0.7956 (ttt) REVERT: C 1 MET cc_start: 0.7164 (mtt) cc_final: 0.6328 (mmt) REVERT: C 157 CYS cc_start: 0.7966 (t) cc_final: 0.7720 (t) REVERT: C 174 ARG cc_start: 0.8039 (mmp-170) cc_final: 0.7702 (mmt180) REVERT: D 1 MET cc_start: 0.5900 (mmt) cc_final: 0.4983 (tpt) REVERT: D 510 MET cc_start: 0.8682 (mmp) cc_final: 0.8327 (mmp) REVERT: D 529 MET cc_start: 0.8879 (tmm) cc_final: 0.8621 (tmm) REVERT: D 1062 MET cc_start: 0.8762 (pmm) cc_final: 0.8187 (pmm) REVERT: D 1088 MET cc_start: 0.8039 (tpt) cc_final: 0.7748 (tpp) REVERT: D 1092 ILE cc_start: 0.9270 (mt) cc_final: 0.8926 (mt) REVERT: D 1095 MET cc_start: 0.8295 (tpp) cc_final: 0.7658 (tpp) REVERT: D 1184 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8382 (tptp) REVERT: D 1201 MET cc_start: 0.9348 (mmp) cc_final: 0.9146 (mmp) REVERT: D 1210 PHE cc_start: 0.9009 (t80) cc_final: 0.8632 (t80) REVERT: D 1293 MET cc_start: 0.9193 (tpt) cc_final: 0.8493 (tpp) REVERT: D 1296 GLU cc_start: 0.8843 (pm20) cc_final: 0.8124 (pm20) REVERT: D 1303 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9020 (mm-30) REVERT: D 1405 TYR cc_start: 0.9478 (m-80) cc_final: 0.9201 (m-80) REVERT: D 1468 SER cc_start: 0.9489 (m) cc_final: 0.9274 (t) REVERT: D 1568 HIS cc_start: 0.9363 (m-70) cc_final: 0.9024 (m-70) REVERT: D 1598 PHE cc_start: 0.8013 (t80) cc_final: 0.7806 (t80) REVERT: E 383 ASN cc_start: 0.3583 (m-40) cc_final: 0.3259 (m110) REVERT: E 677 MET cc_start: 0.8381 (ptt) cc_final: 0.7354 (ppp) REVERT: F 145 MET cc_start: 0.5607 (tpt) cc_final: 0.4472 (tpt) outliers start: 5 outliers final: 5 residues processed: 305 average time/residue: 0.2065 time to fit residues: 101.4359 Evaluate side-chains 266 residues out of total 3442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 261 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 155 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 148 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 chunk 145 optimal weight: 7.9990 chunk 152 optimal weight: 50.0000 chunk 116 optimal weight: 3.9990 chunk 160 optimal weight: 50.0000 chunk 43 optimal weight: 8.9990 chunk 131 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN B 237 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS B 448 HIS ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 240 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.145824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.098471 restraints weight = 79328.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.093479 restraints weight = 104675.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.092981 restraints weight = 93116.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.092929 restraints weight = 101997.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.092964 restraints weight = 92449.221| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.9970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 33876 Z= 0.374 Angle : 1.045 16.838 46014 Z= 0.532 Chirality : 0.052 0.330 5412 Planarity : 0.008 0.113 5928 Dihedral : 7.125 60.037 4826 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 35.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.24 % Favored : 87.57 % Rotamer: Outliers : 0.17 % Allowed : 1.25 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.03 % Twisted Proline : 0.63 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.14), residues: 3750 helix: -0.41 (0.12), residues: 1949 sheet: -3.48 (0.32), residues: 237 loop : -2.26 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1370 TYR 0.122 0.004 TYR D1368 PHE 0.050 0.003 PHE D1433 TRP 0.040 0.003 TRP E 575 HIS 0.023 0.002 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00772 (33876) covalent geometry : angle 1.04507 (46014) hydrogen bonds : bond 0.05956 ( 1812) hydrogen bonds : angle 6.40066 ( 5268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14055.99 seconds wall clock time: 240 minutes 13.53 seconds (14413.53 seconds total)