Starting phenix.real_space_refine on Wed May 28 05:12:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8prv_17839/05_2025/8prv_17839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8prv_17839/05_2025/8prv_17839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8prv_17839/05_2025/8prv_17839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8prv_17839/05_2025/8prv_17839.map" model { file = "/net/cci-nas-00/data/ceres_data/8prv_17839/05_2025/8prv_17839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8prv_17839/05_2025/8prv_17839.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 109 5.16 5 C 18968 2.51 5 N 4982 2.21 5 O 5744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29814 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1584, 12379 Classifications: {'peptide': 1584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1522} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1222 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16010 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'J8W:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'A5S': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'COA': 1, 'FMN': 1, 'NAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.70, per 1000 atoms: 0.59 Number of scatterers: 29814 At special positions: 0 Unit cell: (183.57, 181.46, 178.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 11 15.00 O 5744 8.00 N 4982 7.00 C 18968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.20 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.57 Conformation dependent library (CDL) restraints added in 3.6 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 32 sheets defined 52.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.543A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.802A pdb=" N GLY A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.647A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.197A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 4.105A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 463 through 483 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.559A pdb=" N TYR A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 652 through 669 removed outlier: 3.630A pdb=" N LEU A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.968A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 removed outlier: 3.570A pdb=" N ARG A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.468A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 880 No H-bonds generated for 'chain 'A' and resid 878 through 880' Processing helix chain 'A' and resid 881 through 889 removed outlier: 4.328A pdb=" N GLU A 886 " --> pdb=" O ASN A 882 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLY A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 892 No H-bonds generated for 'chain 'A' and resid 890 through 892' Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 935 through 970 Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.779A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 4.156A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 4.488A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1194 through 1199 Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.728A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1253 through 1262 Processing helix chain 'A' and resid 1273 through 1279 removed outlier: 3.697A pdb=" N GLU A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A1278 " --> pdb=" O ILE A1274 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1273 through 1279' Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1361 through 1366 removed outlier: 4.436A pdb=" N SER A1366 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1440 through 1443 removed outlier: 3.643A pdb=" N LEU A1443 " --> pdb=" O SER A1440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1440 through 1443' Processing helix chain 'A' and resid 1444 through 1477 removed outlier: 3.570A pdb=" N GLN A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1510 Processing helix chain 'A' and resid 1520 through 1529 removed outlier: 3.527A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1536 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.509A pdb=" N ASP A1550 " --> pdb=" O THR A1546 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.553A pdb=" N THR A1581 " --> pdb=" O GLN A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1603 Processing helix chain 'A' and resid 1615 through 1621 Processing helix chain 'A' and resid 1658 through 1665 removed outlier: 3.780A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1695 Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1734 through 1738 removed outlier: 3.649A pdb=" N ILE A1738 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1758 Processing helix chain 'A' and resid 1777 through 1779 No H-bonds generated for 'chain 'A' and resid 1777 through 1779' Processing helix chain 'A' and resid 1783 through 1791 removed outlier: 4.279A pdb=" N ARG A1789 " --> pdb=" O THR A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1801 removed outlier: 3.535A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.932A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.502A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.778A pdb=" N GLY B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.595A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.787A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 removed outlier: 3.584A pdb=" N ALA B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.781A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.530A pdb=" N THR G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.909A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 133 removed outlier: 3.816A pdb=" N THR G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.752A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.459A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 222 through 225 removed outlier: 3.517A pdb=" N THR G 225 " --> pdb=" O PRO G 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 222 through 225' Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 233 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 266 removed outlier: 3.655A pdb=" N TYR G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 285 removed outlier: 4.111A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 314 Processing helix chain 'G' and resid 320 through 327 Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.913A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 360 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 removed outlier: 3.754A pdb=" N LYS G 364 " --> pdb=" O PRO G 361 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN G 365 " --> pdb=" O ALA G 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 361 through 365' Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.584A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 433 removed outlier: 3.683A pdb=" N LEU G 432 " --> pdb=" O SER G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 446 removed outlier: 4.451A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 removed outlier: 3.550A pdb=" N ARG G 478 " --> pdb=" O SER G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 507 through 510 removed outlier: 3.633A pdb=" N SER G 510 " --> pdb=" O GLY G 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 507 through 510' Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.877A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 4.002A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 555 Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 583 through 588 Processing helix chain 'G' and resid 603 through 614 Processing helix chain 'G' and resid 626 through 641 Processing helix chain 'G' and resid 655 through 671 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.558A pdb=" N LEU G 698 " --> pdb=" O TYR G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 722 Processing helix chain 'G' and resid 747 through 759 removed outlier: 5.269A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG G 759 " --> pdb=" O SER G 755 " (cutoff:3.500A) Processing helix chain 'G' and resid 773 through 782 removed outlier: 3.696A pdb=" N THR G 777 " --> pdb=" O SER G 773 " (cutoff:3.500A) Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 783 through 789 removed outlier: 3.647A pdb=" N SER G 786 " --> pdb=" O GLY G 783 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE G 789 " --> pdb=" O SER G 786 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 808 removed outlier: 4.399A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 Processing helix chain 'G' and resid 831 through 837 Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 879 through 898 removed outlier: 3.584A pdb=" N THR G 883 " --> pdb=" O LYS G 879 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 917 Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 removed outlier: 3.526A pdb=" N ARG G 944 " --> pdb=" O ASP G 940 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU G 955 " --> pdb=" O LEU G 951 " (cutoff:3.500A) Processing helix chain 'G' and resid 969 through 974 removed outlier: 3.752A pdb=" N ASP G 974 " --> pdb=" O SER G 971 " (cutoff:3.500A) Processing helix chain 'G' and resid 975 through 987 removed outlier: 3.683A pdb=" N ALA G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1034 through 1043 removed outlier: 3.787A pdb=" N SER G1037 " --> pdb=" O LEU G1034 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1062 Processing helix chain 'G' and resid 1069 through 1090 Processing helix chain 'G' and resid 1093 through 1097 removed outlier: 3.572A pdb=" N ILE G1097 " --> pdb=" O GLU G1094 " (cutoff:3.500A) Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 Processing helix chain 'G' and resid 1168 through 1174 Processing helix chain 'G' and resid 1189 through 1192 Processing helix chain 'G' and resid 1257 through 1271 removed outlier: 3.575A pdb=" N MET G1265 " --> pdb=" O ARG G1261 " (cutoff:3.500A) Processing helix chain 'G' and resid 1293 through 1305 Processing helix chain 'G' and resid 1308 through 1312 removed outlier: 3.551A pdb=" N VAL G1312 " --> pdb=" O GLU G1309 " (cutoff:3.500A) Processing helix chain 'G' and resid 1324 through 1337 removed outlier: 4.021A pdb=" N VAL G1328 " --> pdb=" O ASP G1324 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA G1337 " --> pdb=" O ALA G1333 " (cutoff:3.500A) Processing helix chain 'G' and resid 1338 through 1339 No H-bonds generated for 'chain 'G' and resid 1338 through 1339' Processing helix chain 'G' and resid 1340 through 1344 removed outlier: 3.668A pdb=" N ASP G1344 " --> pdb=" O ASN G1341 " (cutoff:3.500A) Processing helix chain 'G' and resid 1418 through 1422 Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.500A pdb=" N ILE G1441 " --> pdb=" O THR G1437 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1524 Processing helix chain 'G' and resid 1550 through 1558 Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 removed outlier: 3.565A pdb=" N SER G1585 " --> pdb=" O HIS G1581 " (cutoff:3.500A) Processing helix chain 'G' and resid 1601 through 1603 No H-bonds generated for 'chain 'G' and resid 1601 through 1603' Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.656A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1703 Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1724 through 1736 removed outlier: 3.629A pdb=" N MET G1736 " --> pdb=" O ASN G1732 " (cutoff:3.500A) Processing helix chain 'G' and resid 1769 through 1772 Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1819 removed outlier: 4.104A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1842 removed outlier: 3.701A pdb=" N VAL G1842 " --> pdb=" O MET G1838 " (cutoff:3.500A) Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.647A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) Processing helix chain 'G' and resid 1867 through 1883 removed outlier: 3.522A pdb=" N THR G1882 " --> pdb=" O VAL G1878 " (cutoff:3.500A) Processing helix chain 'G' and resid 1904 through 1921 removed outlier: 3.562A pdb=" N ASN G1915 " --> pdb=" O THR G1911 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G1916 " --> pdb=" O ASN G1912 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1924 through 1931 removed outlier: 3.570A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G1931 " --> pdb=" O LEU G1927 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1953 removed outlier: 3.676A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G1949 " --> pdb=" O ASP G1945 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.829A pdb=" N LYS G1994 " --> pdb=" O SER G1990 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN G1995 " --> pdb=" O PHE G1991 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 Processing helix chain 'G' and resid 2022 through 2033 Processing helix chain 'G' and resid 2035 through 2044 Processing helix chain 'G' and resid 2044 through 2050 removed outlier: 3.843A pdb=" N GLN G2050 " --> pdb=" O GLU G2046 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.278A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN G1897 " --> pdb=" O ASN G1892 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.658A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.500A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR A 677 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE A 769 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 649 through 651 removed outlier: 4.158A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA7, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA8, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.505A pdb=" N TYR A1332 " --> pdb=" O GLY A1248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.577A pdb=" N ALA A1382 " --> pdb=" O GLU A1026 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A1026 " --> pdb=" O ALA A1382 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A1384 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE A1024 " --> pdb=" O ILE A1384 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A1386 " --> pdb=" O THR A1022 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1060 through 1066 removed outlier: 4.259A pdb=" N TRP A1075 " --> pdb=" O VAL A1084 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB3, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id=AB4, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB5, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB6, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB7, first strand: chain 'A' and resid 1768 through 1775 removed outlier: 3.776A pdb=" N ASP A1866 " --> pdb=" O THR A1885 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.684A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 267 through 272 removed outlier: 7.460A pdb=" N LEU G 156 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA G 270 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA G 158 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY G 272 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE G 160 " --> pdb=" O GLY G 272 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 527 " --> pdb=" O GLY G 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 417 through 420 removed outlier: 7.305A pdb=" N ASN G 376 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL G 371 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC3, first strand: chain 'G' and resid 592 through 594 removed outlier: 3.934A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE G 647 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU G 679 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE G 649 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE G 681 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU G 651 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.567A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 906 through 907 removed outlier: 3.565A pdb=" N GLN G 910 " --> pdb=" O VAL G 907 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC7, first strand: chain 'G' and resid 1127 through 1128 removed outlier: 3.504A pdb=" N THR G1196 " --> pdb=" O GLU G1183 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id=AC9, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 5.121A pdb=" N LYS G1286 " --> pdb=" O ALA G1376 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA G1376 " --> pdb=" O LYS G1286 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS G1288 " --> pdb=" O THR G1374 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N THR G1374 " --> pdb=" O LYS G1288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G1380 " --> pdb=" O ASP G1391 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL G1393 " --> pdb=" O ILE G1378 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE G1378 " --> pdb=" O VAL G1393 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 5.121A pdb=" N LYS G1286 " --> pdb=" O ALA G1376 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA G1376 " --> pdb=" O LYS G1286 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS G1288 " --> pdb=" O THR G1374 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N THR G1374 " --> pdb=" O LYS G1288 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU G1405 " --> pdb=" O TYR G1357 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR G1357 " --> pdb=" O GLU G1405 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR G1407 " --> pdb=" O ASN G1355 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN G1355 " --> pdb=" O THR G1407 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER G1409 " --> pdb=" O LEU G1353 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU G1622 " --> pdb=" O ASP G1543 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP G1543 " --> pdb=" O LEU G1622 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY G1630 " --> pdb=" O ASN G1535 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N ASN G1535 " --> pdb=" O GLY G1630 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N ILE G1632 " --> pdb=" O LEU G1533 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N LEU G1533 " --> pdb=" O ILE G1632 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 6.500A pdb=" N GLU G1469 " --> pdb=" O CYS G1485 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS G1485 " --> pdb=" O GLU G1469 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU G1471 " --> pdb=" O VAL G1483 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL G1483 " --> pdb=" O GLU G1471 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR G1473 " --> pdb=" O SER G1481 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 6.500A pdb=" N GLU G1469 " --> pdb=" O CYS G1485 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS G1485 " --> pdb=" O GLU G1469 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU G1471 " --> pdb=" O VAL G1483 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL G1483 " --> pdb=" O GLU G1471 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR G1473 " --> pdb=" O SER G1481 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD5, first strand: chain 'G' and resid 1737 through 1741 removed outlier: 3.524A pdb=" N GLU G1749 " --> pdb=" O PHE G1738 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) 1467 hydrogen bonds defined for protein. 4101 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: 14.79 Time building geometry restraints manager: 7.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.18: 10 1.18 - 1.36: 9795 1.36 - 1.53: 16528 1.53 - 1.70: 3918 1.70 - 1.88: 191 Bond restraints: 30442 Sorted by residual: bond pdb=" CG ASP G1845 " pdb=" OD1 ASP G1845 " ideal model delta sigma weight residual 1.249 1.557 -0.308 1.90e-02 2.77e+03 2.63e+02 bond pdb=" CG ASP G1845 " pdb=" OD2 ASP G1845 " ideal model delta sigma weight residual 1.249 1.012 0.237 1.90e-02 2.77e+03 1.56e+02 bond pdb=" OG J8W G1808 " pdb=" C2 J8W G1808 " ideal model delta sigma weight residual 1.331 1.463 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C VAL A 734 " pdb=" O VAL A 734 " ideal model delta sigma weight residual 1.238 1.166 0.072 1.28e-02 6.10e+03 3.15e+01 bond pdb=" C5A NAP G2102 " pdb=" C6A NAP G2102 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 30437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 39862 4.08 - 8.16: 1382 8.16 - 12.24: 15 12.24 - 16.31: 2 16.31 - 20.39: 1 Bond angle restraints: 41262 Sorted by residual: angle pdb=" CB ASP G1845 " pdb=" CG ASP G1845 " pdb=" OD1 ASP G1845 " ideal model delta sigma weight residual 118.40 98.01 20.39 2.30e+00 1.89e-01 7.86e+01 angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.24 125.02 -4.78 6.30e-01 2.52e+00 5.75e+01 angle pdb=" CA THR A1282 " pdb=" CB THR A1282 " pdb=" OG1 THR A1282 " ideal model delta sigma weight residual 109.60 98.66 10.94 1.50e+00 4.44e-01 5.31e+01 angle pdb=" OD1 ASP G1845 " pdb=" CG ASP G1845 " pdb=" OD2 ASP G1845 " ideal model delta sigma weight residual 122.90 107.57 15.33 2.40e+00 1.74e-01 4.08e+01 angle pdb=" CA GLY A 383 " pdb=" C GLY A 383 " pdb=" O GLY A 383 " ideal model delta sigma weight residual 122.23 118.05 4.18 6.90e-01 2.10e+00 3.66e+01 ... (remaining 41257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16522 17.95 - 35.90: 1531 35.90 - 53.84: 311 53.84 - 71.79: 94 71.79 - 89.74: 36 Dihedral angle restraints: 18494 sinusoidal: 7571 harmonic: 10923 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual -86.00 0.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CA CYS A1327 " pdb=" C CYS A1327 " pdb=" N ILE A1328 " pdb=" CA ILE A1328 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 18491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2042 0.058 - 0.117: 1630 0.117 - 0.175: 747 0.175 - 0.234: 183 0.234 - 0.292: 28 Chirality restraints: 4630 Sorted by residual: chirality pdb=" CA J8W G1808 " pdb=" N J8W G1808 " pdb=" C J8W G1808 " pdb=" CB J8W G1808 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL G1616 " pdb=" N VAL G1616 " pdb=" C VAL G1616 " pdb=" CB VAL G1616 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4627 not shown) Planarity restraints: 5306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP G1845 " -0.075 2.00e-02 2.50e+03 1.55e-01 2.40e+02 pdb=" CG ASP G1845 " 0.263 2.00e-02 2.50e+03 pdb=" OD1 ASP G1845 " -0.050 2.00e-02 2.50e+03 pdb=" OD2 ASP G1845 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " -0.004 2.00e-02 2.50e+03 2.45e-02 2.71e+01 pdb=" C10 FMN G2101 " 0.009 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.027 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.013 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.018 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.036 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.013 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.007 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.044 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.002 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.035 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.022 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " 0.006 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.025 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.040 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.041 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.063 2.00e-02 2.50e+03 3.23e-02 2.09e+01 pdb=" CG TYR A1529 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.033 2.00e-02 2.50e+03 ... (remaining 5303 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2475 2.76 - 3.30: 29639 3.30 - 3.83: 45715 3.83 - 4.37: 64326 4.37 - 4.90: 102860 Nonbonded interactions: 245015 Sorted by model distance: nonbonded pdb=" OD1 ASP A 376 " pdb=" NH1 ARG B 276 " model vdw 2.228 3.120 nonbonded pdb=" O ALA G1813 " pdb=" OG SER G1817 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.296 3.040 nonbonded pdb=" O TRP A1030 " pdb=" OG1 THR A1035 " model vdw 2.296 3.040 nonbonded pdb=" OE2 GLU G1811 " pdb=" OH TYR G2010 " model vdw 2.311 3.040 ... (remaining 245010 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.240 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 67.050 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.014 0.308 30444 Z= 1.039 Angle : 1.901 20.392 41264 Z= 1.373 Chirality : 0.091 0.292 4630 Planarity : 0.007 0.155 5306 Dihedral : 15.383 89.738 11457 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 0.22 % Allowed : 3.33 % Favored : 96.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.11), residues: 3764 helix: -2.66 (0.09), residues: 1650 sheet: -1.90 (0.19), residues: 511 loop : -1.22 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.010 TRP G 732 HIS 0.016 0.004 HIS G1568 PHE 0.054 0.007 PHE G 799 TYR 0.063 0.008 TYR A1529 ARG 0.040 0.001 ARG G1849 Details of bonding type rmsd hydrogen bonds : bond 0.22204 ( 1454) hydrogen bonds : angle 9.23270 ( 4101) SS BOND : bond 0.17342 ( 1) SS BOND : angle 15.86988 ( 2) covalent geometry : bond 0.01413 (30442) covalent geometry : angle 1.89781 (41262) Misc. bond : bond 0.04770 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 3.203 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9096 (mtt) cc_final: 0.8864 (mtt) REVERT: A 352 MET cc_start: 0.8699 (ttp) cc_final: 0.8480 (ttm) REVERT: A 1066 ASN cc_start: 0.7930 (m-40) cc_final: 0.7384 (m-40) REVERT: A 1692 MET cc_start: 0.9131 (ttt) cc_final: 0.8916 (ttt) REVERT: A 1840 VAL cc_start: 0.7749 (p) cc_final: 0.7425 (m) REVERT: G 46 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6991 (mp0) REVERT: G 132 MET cc_start: 0.7992 (mmp) cc_final: 0.7646 (mmp) REVERT: G 300 ILE cc_start: 0.8780 (mm) cc_final: 0.8553 (mt) REVERT: G 447 ASN cc_start: 0.8688 (m-40) cc_final: 0.8084 (p0) REVERT: G 599 PRO cc_start: 0.8882 (OUTLIER) cc_final: 0.8589 (Cg_endo) REVERT: G 794 MET cc_start: 0.9264 (mtt) cc_final: 0.9054 (mtt) REVERT: G 1265 MET cc_start: 0.9084 (tmm) cc_final: 0.8514 (tmm) REVERT: G 1838 MET cc_start: 0.8968 (mtt) cc_final: 0.8668 (mtt) REVERT: G 1939 HIS cc_start: 0.7983 (t-90) cc_final: 0.7550 (t70) REVERT: G 1964 PHE cc_start: 0.7420 (m-80) cc_final: 0.7062 (m-80) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 1.6168 time to fit residues: 286.5990 Evaluate side-chains 116 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain G residue 599 PRO Chi-restraints excluded: chain G residue 709 SER Chi-restraints excluded: chain G residue 1586 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 295 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 411 GLN A 475 GLN A 527 GLN A1380 GLN A1852 HIS B 292 GLN G 36 GLN G 79 GLN G 102 HIS G 110 GLN G 181 HIS G 221 ASN G 245 GLN G 440 ASN G 446 ASN G 495 GLN G 500 HIS G 718 ASN G 747 HIS G 760 HIS G 993 GLN G1055 HIS G1178 GLN G1217 ASN G1355 ASN G1432 GLN G1851 ASN G1890 ASN G1912 ASN G1983 ASN G2013 ASN G2020 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.045472 restraints weight = 98526.005| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.02 r_work: 0.2726 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 30444 Z= 0.219 Angle : 0.594 7.992 41264 Z= 0.317 Chirality : 0.045 0.204 4630 Planarity : 0.004 0.054 5306 Dihedral : 8.318 84.619 4269 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.77 % Allowed : 6.56 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 3764 helix: 0.09 (0.12), residues: 1700 sheet: -1.16 (0.21), residues: 478 loop : -0.45 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 661 HIS 0.009 0.001 HIS A1689 PHE 0.021 0.002 PHE A 35 TYR 0.024 0.002 TYR G1553 ARG 0.006 0.001 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 1454) hydrogen bonds : angle 5.20419 ( 4101) SS BOND : bond 0.01470 ( 1) SS BOND : angle 6.93033 ( 2) covalent geometry : bond 0.00511 (30442) covalent geometry : angle 0.59242 (41262) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 3.153 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9130 (mtt) cc_final: 0.8919 (mtt) REVERT: A 344 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: A 352 MET cc_start: 0.8788 (ttp) cc_final: 0.8582 (ttm) REVERT: A 1066 ASN cc_start: 0.7656 (m-40) cc_final: 0.6940 (m-40) REVERT: A 1794 GLN cc_start: 0.7448 (tt0) cc_final: 0.7184 (pt0) REVERT: G 794 MET cc_start: 0.9381 (mtt) cc_final: 0.9130 (mtp) REVERT: G 1939 HIS cc_start: 0.7980 (t-90) cc_final: 0.7516 (t70) REVERT: G 1964 PHE cc_start: 0.7401 (m-80) cc_final: 0.7154 (m-80) outliers start: 25 outliers final: 11 residues processed: 136 average time/residue: 1.4564 time to fit residues: 234.4179 Evaluate side-chains 120 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1845 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 226 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 329 optimal weight: 50.0000 chunk 239 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 317 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1000 GLN A1852 HIS G 752 GLN G1302 HIS G1619 ASN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.045866 restraints weight = 98335.793| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.02 r_work: 0.2743 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30444 Z= 0.195 Angle : 0.547 8.804 41264 Z= 0.288 Chirality : 0.044 0.197 4630 Planarity : 0.004 0.042 5306 Dihedral : 7.727 79.194 4262 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.05 % Allowed : 7.98 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 3764 helix: 0.95 (0.12), residues: 1706 sheet: -0.85 (0.21), residues: 475 loop : -0.19 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 661 HIS 0.009 0.001 HIS A1689 PHE 0.023 0.002 PHE A 35 TYR 0.023 0.002 TYR G1553 ARG 0.004 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 1454) hydrogen bonds : angle 4.82530 ( 4101) SS BOND : bond 0.02418 ( 1) SS BOND : angle 7.25947 ( 2) covalent geometry : bond 0.00462 (30442) covalent geometry : angle 0.54453 (41262) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 3.466 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8703 (ttp) cc_final: 0.8497 (ttm) REVERT: A 1066 ASN cc_start: 0.7509 (m-40) cc_final: 0.6807 (m-40) REVERT: G 220 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: G 447 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8384 (t0) REVERT: G 794 MET cc_start: 0.9370 (mtt) cc_final: 0.9113 (mtp) REVERT: G 1939 HIS cc_start: 0.7993 (t-90) cc_final: 0.7583 (t-170) REVERT: G 1964 PHE cc_start: 0.7414 (m-80) cc_final: 0.7186 (m-80) outliers start: 34 outliers final: 15 residues processed: 133 average time/residue: 1.4065 time to fit residues: 223.9554 Evaluate side-chains 125 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 138 optimal weight: 0.9990 chunk 325 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 268 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 244 optimal weight: 0.0370 chunk 120 optimal weight: 10.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1794 GLN G1241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046854 restraints weight = 98683.090| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.05 r_work: 0.2769 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30444 Z= 0.120 Angle : 0.483 8.736 41264 Z= 0.253 Chirality : 0.042 0.166 4630 Planarity : 0.003 0.038 5306 Dihedral : 7.165 75.555 4262 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.08 % Allowed : 8.90 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3764 helix: 1.39 (0.13), residues: 1703 sheet: -0.65 (0.22), residues: 475 loop : 0.01 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.022 0.001 PHE A 35 TYR 0.018 0.001 TYR G1553 ARG 0.002 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 1454) hydrogen bonds : angle 4.55989 ( 4101) SS BOND : bond 0.01051 ( 1) SS BOND : angle 5.65188 ( 2) covalent geometry : bond 0.00276 (30442) covalent geometry : angle 0.48100 (41262) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1066 ASN cc_start: 0.7448 (m-40) cc_final: 0.6784 (m-40) REVERT: G 86 LEU cc_start: 0.8567 (mt) cc_final: 0.8349 (mt) REVERT: G 151 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: G 447 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8332 (t0) REVERT: G 794 MET cc_start: 0.9328 (mtt) cc_final: 0.9069 (mtp) REVERT: G 995 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9012 (mm) REVERT: G 1854 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8084 (mmm) REVERT: G 1939 HIS cc_start: 0.7949 (t-90) cc_final: 0.7653 (t-170) outliers start: 35 outliers final: 14 residues processed: 136 average time/residue: 1.4198 time to fit residues: 231.8365 Evaluate side-chains 124 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1854 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 232 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 167 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 269 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047080 restraints weight = 98066.861| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.04 r_work: 0.2778 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30444 Z= 0.117 Angle : 0.470 8.014 41264 Z= 0.245 Chirality : 0.042 0.165 4630 Planarity : 0.003 0.037 5306 Dihedral : 6.786 72.305 4262 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.32 % Allowed : 9.43 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3764 helix: 1.54 (0.13), residues: 1711 sheet: -0.54 (0.22), residues: 474 loop : 0.09 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.022 0.001 PHE A 35 TYR 0.018 0.001 TYR G1553 ARG 0.002 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 1454) hydrogen bonds : angle 4.44732 ( 4101) SS BOND : bond 0.01978 ( 1) SS BOND : angle 5.74241 ( 2) covalent geometry : bond 0.00267 (30442) covalent geometry : angle 0.46807 (41262) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 3.137 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: A 1066 ASN cc_start: 0.7512 (m-40) cc_final: 0.6892 (m-40) REVERT: B 164 ASP cc_start: 0.7693 (m-30) cc_final: 0.7346 (p0) REVERT: B 232 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7814 (tp) REVERT: G 86 LEU cc_start: 0.8562 (mt) cc_final: 0.8344 (mt) REVERT: G 151 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: G 794 MET cc_start: 0.9335 (mtt) cc_final: 0.9068 (mtp) REVERT: G 995 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9009 (mm) REVERT: G 1854 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8002 (mmm) REVERT: G 1939 HIS cc_start: 0.7931 (t-90) cc_final: 0.7571 (t70) outliers start: 43 outliers final: 21 residues processed: 143 average time/residue: 1.3526 time to fit residues: 232.1139 Evaluate side-chains 133 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1854 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 184 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 376 optimal weight: 7.9990 chunk 352 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 285 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 155 GLN G 715 GLN ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046512 restraints weight = 98884.373| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.07 r_work: 0.2758 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30444 Z= 0.171 Angle : 0.509 10.013 41264 Z= 0.264 Chirality : 0.043 0.175 4630 Planarity : 0.004 0.039 5306 Dihedral : 6.726 70.176 4262 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.32 % Allowed : 9.95 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1708 sheet: -0.58 (0.22), residues: 487 loop : 0.12 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.023 0.002 PHE A 35 TYR 0.022 0.002 TYR G1553 ARG 0.003 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1454) hydrogen bonds : angle 4.53553 ( 4101) SS BOND : bond 0.01878 ( 1) SS BOND : angle 6.73657 ( 2) covalent geometry : bond 0.00402 (30442) covalent geometry : angle 0.50674 (41262) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 3.746 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: A 1066 ASN cc_start: 0.7509 (m-40) cc_final: 0.6855 (m-40) REVERT: B 164 ASP cc_start: 0.7682 (m-30) cc_final: 0.7366 (p0) REVERT: B 232 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7810 (tp) REVERT: G 86 LEU cc_start: 0.8625 (mt) cc_final: 0.8365 (mt) REVERT: G 220 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: G 794 MET cc_start: 0.9355 (mtt) cc_final: 0.9119 (mtp) REVERT: G 1854 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7935 (mmm) REVERT: G 1939 HIS cc_start: 0.7941 (t-90) cc_final: 0.7606 (t70) outliers start: 43 outliers final: 22 residues processed: 145 average time/residue: 1.3795 time to fit residues: 242.1220 Evaluate side-chains 134 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1854 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 376 optimal weight: 9.9990 chunk 369 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 300 optimal weight: 0.0370 chunk 346 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.061310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046246 restraints weight = 98489.625| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.03 r_work: 0.2754 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30444 Z= 0.201 Angle : 0.532 9.602 41264 Z= 0.276 Chirality : 0.044 0.184 4630 Planarity : 0.004 0.041 5306 Dihedral : 6.721 68.958 4262 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.17 % Allowed : 10.57 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3764 helix: 1.41 (0.13), residues: 1708 sheet: -0.58 (0.21), residues: 487 loop : 0.09 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.023 0.002 PHE A 35 TYR 0.023 0.002 TYR G1553 ARG 0.006 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 1454) hydrogen bonds : angle 4.61145 ( 4101) SS BOND : bond 0.02430 ( 1) SS BOND : angle 7.02137 ( 2) covalent geometry : bond 0.00474 (30442) covalent geometry : angle 0.52967 (41262) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 3.227 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: A 1066 ASN cc_start: 0.7507 (m-40) cc_final: 0.6819 (m-40) REVERT: A 1298 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8783 (tp) REVERT: B 164 ASP cc_start: 0.7685 (m-30) cc_final: 0.7358 (p0) REVERT: B 232 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7806 (tp) REVERT: G 86 LEU cc_start: 0.8644 (mt) cc_final: 0.8387 (mt) REVERT: G 151 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: G 220 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: G 794 MET cc_start: 0.9360 (mtt) cc_final: 0.9098 (mtp) REVERT: G 1854 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: G 1919 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7610 (mm) REVERT: G 1939 HIS cc_start: 0.8029 (t-90) cc_final: 0.7718 (t70) REVERT: G 1945 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7900 (t0) outliers start: 38 outliers final: 24 residues processed: 142 average time/residue: 1.4467 time to fit residues: 249.3558 Evaluate side-chains 139 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 1919 LEU Chi-restraints excluded: chain G residue 1945 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 297 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 251 optimal weight: 0.0970 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1512 HIS ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.062235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047321 restraints weight = 98679.159| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.06 r_work: 0.2785 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30444 Z= 0.111 Angle : 0.470 7.769 41264 Z= 0.244 Chirality : 0.042 0.153 4630 Planarity : 0.003 0.038 5306 Dihedral : 6.375 67.341 4262 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.23 % Allowed : 10.75 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1718 sheet: -0.49 (0.22), residues: 480 loop : 0.17 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.021 0.001 PHE A 35 TYR 0.016 0.001 TYR G1553 ARG 0.006 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1454) hydrogen bonds : angle 4.41586 ( 4101) SS BOND : bond 0.01895 ( 1) SS BOND : angle 5.66380 ( 2) covalent geometry : bond 0.00253 (30442) covalent geometry : angle 0.46809 (41262) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 3.194 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: A 1066 ASN cc_start: 0.7437 (m-40) cc_final: 0.6754 (m-40) REVERT: B 164 ASP cc_start: 0.7667 (m-30) cc_final: 0.7356 (p0) REVERT: B 232 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7801 (tp) REVERT: G 86 LEU cc_start: 0.8595 (mt) cc_final: 0.8384 (mt) REVERT: G 151 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: G 794 MET cc_start: 0.9340 (mtt) cc_final: 0.9067 (mtp) REVERT: G 1854 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: G 1872 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7308 (tp-100) REVERT: G 1919 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7584 (mm) REVERT: G 1939 HIS cc_start: 0.8054 (t-90) cc_final: 0.7699 (t70) outliers start: 40 outliers final: 22 residues processed: 144 average time/residue: 1.3397 time to fit residues: 233.3461 Evaluate side-chains 134 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 1919 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 61 optimal weight: 0.7980 chunk 251 optimal weight: 0.4980 chunk 203 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 322 optimal weight: 8.9990 chunk 328 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 220 optimal weight: 30.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046981 restraints weight = 98074.237| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.06 r_work: 0.2775 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30444 Z= 0.144 Angle : 0.492 9.865 41264 Z= 0.255 Chirality : 0.042 0.161 4630 Planarity : 0.003 0.039 5306 Dihedral : 6.351 67.869 4262 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.26 % Allowed : 10.78 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3764 helix: 1.56 (0.13), residues: 1719 sheet: -0.47 (0.22), residues: 480 loop : 0.17 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.022 0.001 PHE A 35 TYR 0.020 0.001 TYR G1553 ARG 0.006 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1454) hydrogen bonds : angle 4.45312 ( 4101) SS BOND : bond 0.02050 ( 1) SS BOND : angle 6.57285 ( 2) covalent geometry : bond 0.00336 (30442) covalent geometry : angle 0.49014 (41262) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 3.663 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: A 1066 ASN cc_start: 0.7431 (m-40) cc_final: 0.6749 (m-40) REVERT: A 1298 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8748 (tp) REVERT: B 164 ASP cc_start: 0.7564 (m-30) cc_final: 0.7289 (p0) REVERT: B 232 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7809 (tp) REVERT: G 80 PHE cc_start: 0.7297 (m-80) cc_final: 0.7079 (m-80) REVERT: G 86 LEU cc_start: 0.8639 (mt) cc_final: 0.8388 (mt) REVERT: G 151 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: G 714 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8609 (t) REVERT: G 794 MET cc_start: 0.9368 (mtt) cc_final: 0.9102 (mtp) REVERT: G 1854 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7915 (mmm) REVERT: G 1872 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7363 (tp-100) REVERT: G 1919 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7567 (mm) REVERT: G 1939 HIS cc_start: 0.8063 (t-90) cc_final: 0.7697 (t70) outliers start: 41 outliers final: 23 residues processed: 144 average time/residue: 1.3183 time to fit residues: 229.2148 Evaluate side-chains 140 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 1919 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 264 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 chunk 333 optimal weight: 7.9990 chunk 364 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046804 restraints weight = 98695.864| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.06 r_work: 0.2770 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30444 Z= 0.170 Angle : 0.507 8.534 41264 Z= 0.263 Chirality : 0.043 0.174 4630 Planarity : 0.004 0.039 5306 Dihedral : 6.374 67.919 4262 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.14 % Allowed : 10.91 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1720 sheet: -0.49 (0.22), residues: 480 loop : 0.15 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.022 0.002 PHE A 35 TYR 0.021 0.002 TYR G1553 ARG 0.006 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1454) hydrogen bonds : angle 4.51664 ( 4101) SS BOND : bond 0.02343 ( 1) SS BOND : angle 6.78440 ( 2) covalent geometry : bond 0.00399 (30442) covalent geometry : angle 0.50471 (41262) Misc. bond : bond 0.00018 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 3.318 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: A 1066 ASN cc_start: 0.7435 (m-40) cc_final: 0.6737 (m-40) REVERT: A 1298 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8776 (tp) REVERT: B 164 ASP cc_start: 0.7591 (m-30) cc_final: 0.7300 (p0) REVERT: B 232 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7836 (tp) REVERT: G 80 PHE cc_start: 0.7290 (m-80) cc_final: 0.7079 (m-80) REVERT: G 151 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: G 714 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8608 (t) REVERT: G 794 MET cc_start: 0.9370 (mtt) cc_final: 0.9125 (mtp) REVERT: G 1631 MET cc_start: 0.9249 (mmm) cc_final: 0.8515 (mmt) REVERT: G 1854 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7900 (mmm) REVERT: G 1872 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7379 (tp-100) REVERT: G 1919 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7556 (mm) REVERT: G 1939 HIS cc_start: 0.8070 (t-90) cc_final: 0.7749 (t70) outliers start: 37 outliers final: 23 residues processed: 142 average time/residue: 1.3804 time to fit residues: 235.7275 Evaluate side-chains 139 residues out of total 3248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 1919 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 152 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 364 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 341 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0570 chunk 272 optimal weight: 7.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1790 ASN ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046990 restraints weight = 98251.156| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.05 r_work: 0.2775 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30444 Z= 0.148 Angle : 0.499 11.275 41264 Z= 0.257 Chirality : 0.043 0.165 4630 Planarity : 0.003 0.039 5306 Dihedral : 6.293 69.775 4262 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.05 % Allowed : 11.09 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3764 helix: 1.52 (0.13), residues: 1719 sheet: -0.45 (0.22), residues: 468 loop : 0.17 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.022 0.001 PHE A 35 TYR 0.019 0.001 TYR G1553 ARG 0.008 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1454) hydrogen bonds : angle 4.47534 ( 4101) SS BOND : bond 0.02055 ( 1) SS BOND : angle 6.34939 ( 2) covalent geometry : bond 0.00345 (30442) covalent geometry : angle 0.49690 (41262) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20285.14 seconds wall clock time: 351 minutes 9.16 seconds (21069.16 seconds total)