Starting phenix.real_space_refine on Mon Aug 25 18:38:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psl_17855/08_2025/8psl_17855.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psl_17855/08_2025/8psl_17855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8psl_17855/08_2025/8psl_17855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psl_17855/08_2025/8psl_17855.map" model { file = "/net/cci-nas-00/data/ceres_data/8psl_17855/08_2025/8psl_17855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psl_17855/08_2025/8psl_17855.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 106 5.16 5 C 18870 2.51 5 N 4955 2.21 5 O 5678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29610 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 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: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2035, 16010 Classifications: {'peptide': 2035} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1925} Chain breaks: 1 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.48, per 1000 atoms: 0.22 Number of scatterers: 29610 At special positions: 0 Unit cell: (181.46, 181.46, 174.075, 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 106 16.00 P 1 15.00 O 5678 8.00 N 4955 7.00 C 18870 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=2.10 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: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7028 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 31 sheets defined 50.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 4.669A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 4.657A pdb=" N VAL A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 4.389A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.586A pdb=" N LYS A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 4.281A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.563A pdb=" N TRP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.451A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 463 through 483 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.536A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 669 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.921A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 725 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 839 through 845 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.511A pdb=" N PHE A 850 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 removed outlier: 4.441A pdb=" N ASN A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 935 through 956 removed outlier: 4.350A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 4.066A pdb=" N GLU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.526A pdb=" N VAL A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 4.014A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 removed outlier: 3.574A pdb=" N TRP A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 4.431A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.848A 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 1115 through 1118 Processing helix chain 'A' and resid 1137 through 1149 removed outlier: 3.719A pdb=" N GLN A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 3.940A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'A' and resid 1239 through 1243 removed outlier: 4.239A pdb=" N VAL A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1262 removed outlier: 3.755A pdb=" N LEU A1257 " --> pdb=" O GLY A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1279 removed outlier: 3.848A pdb=" N GLU A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1291 removed outlier: 4.483A pdb=" N SER A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1347 Processing helix chain 'A' and resid 1351 through 1358 removed outlier: 3.540A pdb=" N GLU A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1365 removed outlier: 3.579A pdb=" N MET A1365 " --> pdb=" O PRO A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1424 through 1430 removed outlier: 3.622A pdb=" N ALA A1429 " --> pdb=" O LEU A1426 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A1430 " --> pdb=" O THR A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1475 removed outlier: 3.599A pdb=" N LYS A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1510 removed outlier: 4.048A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.544A pdb=" N ASP A1550 " --> pdb=" O THR A1546 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1564 " --> pdb=" O MET A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.748A 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 removed outlier: 3.519A pdb=" N TRP A1591 " --> pdb=" O ALA A1587 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A1601 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1621 Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 3.981A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A1663 " --> pdb=" O ASP A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1663' Processing helix chain 'A' and resid 1666 through 1694 Processing helix chain 'A' and resid 1710 through 1717 removed outlier: 3.610A pdb=" N ASP A1717 " --> pdb=" O ASP A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1738 removed outlier: 3.574A pdb=" N ILE A1738 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.962A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (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: 3.644A pdb=" N ARG A1789 " --> pdb=" O THR A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1800 Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1833 through 1835 No H-bonds generated for 'chain 'A' and resid 1833 through 1835' Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.834A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.889A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.617A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.797A pdb=" N GLU B 203 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.028A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.592A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.596A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 72 removed outlier: 3.888A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 96 removed outlier: 4.436A pdb=" N VAL G 83 " --> pdb=" O GLN G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 115 through 133 removed outlier: 3.639A pdb=" N THR G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 122 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS G 124 " --> pdb=" O LYS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 168 through 180 removed outlier: 4.367A pdb=" N GLU G 172 " --> pdb=" O ASP G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 6.807A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 removed outlier: 4.253A pdb=" N VAL G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.669A pdb=" N SER G 233 " --> pdb=" O ASP G 229 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.917A pdb=" N GLU G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 314 removed outlier: 3.576A pdb=" N LYS G 298 " --> pdb=" O VAL G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.923A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.689A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 433 removed outlier: 3.519A pdb=" N LEU G 432 " --> pdb=" O SER G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 446 removed outlier: 4.427A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 507 through 510 Processing helix chain 'G' and resid 511 through 520 removed outlier: 3.719A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 549 removed outlier: 4.219A pdb=" N ILE G 547 " --> pdb=" O PHE G 543 " (cutoff:3.500A) removed outlier: 3.779A 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 581 through 588 removed outlier: 3.531A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 614 removed outlier: 3.622A pdb=" N ALA G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 624 No H-bonds generated for 'chain 'G' and resid 622 through 624' Processing helix chain 'G' and resid 626 through 639 removed outlier: 3.682A pdb=" N MET G 630 " --> pdb=" O SER G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 672 removed outlier: 3.538A pdb=" N LEU G 659 " --> pdb=" O ASN G 655 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.582A pdb=" N GLU G 693 " --> pdb=" O GLU G 689 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 759 removed outlier: 5.458A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 777 through 783 Processing helix chain 'G' and resid 785 through 790 removed outlier: 3.642A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP G 790 " --> pdb=" O THR G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 806 removed outlier: 3.650A pdb=" N MET G 806 " --> pdb=" O SER G 803 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 Processing helix chain 'G' and resid 831 through 835 removed outlier: 3.520A pdb=" N THR G 835 " --> pdb=" O TRP G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 859 through 872 removed outlier: 4.026A pdb=" N TRP G 865 " --> pdb=" O GLY G 861 " (cutoff:3.500A) Processing helix chain 'G' and resid 876 through 887 removed outlier: 4.191A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix Processing helix chain 'G' and resid 887 through 899 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 Processing helix chain 'G' and resid 969 through 975 removed outlier: 3.757A pdb=" N LYS G 975 " --> pdb=" O LEU G 972 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 987 removed outlier: 3.754A pdb=" N GLU G 981 " --> pdb=" O ASP G 977 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS G 982 " --> pdb=" O GLU G 978 " (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 removed outlier: 3.583A pdb=" N LYS G1030 " --> pdb=" O GLU G1026 " (cutoff:3.500A) Processing helix chain 'G' and resid 1034 through 1039 Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1063 removed outlier: 3.604A pdb=" N GLN G1061 " --> pdb=" O VAL G1058 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR G1063 " --> pdb=" O ALA G1060 " (cutoff:3.500A) Processing helix chain 'G' and resid 1069 through 1089 Processing helix chain 'G' and resid 1093 through 1097 Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 removed outlier: 3.543A pdb=" N PHE G1154 " --> pdb=" O ARG G1150 " (cutoff:3.500A) Processing helix chain 'G' and resid 1168 through 1174 removed outlier: 3.622A pdb=" N LYS G1172 " --> pdb=" O ASN G1168 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1271 removed outlier: 3.558A pdb=" N LYS G1268 " --> pdb=" O GLU G1264 " (cutoff:3.500A) Processing helix chain 'G' and resid 1293 through 1304 Processing helix chain 'G' and resid 1308 through 1312 Processing helix chain 'G' and resid 1325 through 1337 removed outlier: 3.577A pdb=" N VAL G1329 " --> pdb=" O PHE G1325 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS G1336 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1346 through 1348 No H-bonds generated for 'chain 'G' and resid 1346 through 1348' Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.806A pdb=" N ILE G1441 " --> pdb=" O THR G1437 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1523 Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.814A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 removed outlier: 3.660A pdb=" N ALA G1570 " --> pdb=" O SER G1566 " (cutoff:3.500A) Processing helix chain 'G' and resid 1581 through 1597 Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.636A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1702 removed outlier: 3.581A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1723 through 1736 removed outlier: 3.588A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (cutoff:3.500A) removed outlier: 3.729A 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: 3.804A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1841 removed outlier: 3.695A pdb=" N GLU G1829 " --> pdb=" O GLU G1825 " (cutoff:3.500A) Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.969A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1883 removed outlier: 3.523A pdb=" N TYR G1873 " --> pdb=" O GLU G1869 " (cutoff:3.500A) Processing helix chain 'G' and resid 1905 through 1921 removed outlier: 3.830A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1923 through 1930 removed outlier: 3.857A pdb=" N LEU G1927 " --> pdb=" O ASP G1923 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1949 removed outlier: 4.114A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1978 through 1983 removed outlier: 4.664A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 4.083A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 removed outlier: 3.618A pdb=" N VAL G2001 " --> pdb=" O LYS G1998 " (cutoff:3.500A) Processing helix chain 'G' and resid 2022 through 2033 Processing helix chain 'G' and resid 2036 through 2044 Processing helix chain 'G' and resid 2045 through 2047 No H-bonds generated for 'chain 'G' and resid 2045 through 2047' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.191A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN G1897 " --> pdb=" O ASN G1892 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.191A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN G1897 " --> pdb=" O ASN G1892 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.022A pdb=" N VAL A 44 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 402 removed outlier: 7.021A pdb=" N VAL A 703 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 735 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 705 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.906A pdb=" N VAL A 671 " --> pdb=" O TYR A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 500 through 503 Processing sheet with id=AA7, first strand: chain 'A' and resid 649 through 651 Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA9, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AB1, first strand: chain 'A' and resid 1326 through 1333 removed outlier: 6.646A pdb=" N ALA A1382 " --> pdb=" O GLU A1026 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A1026 " --> pdb=" O ALA A1382 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A1384 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A1024 " --> pdb=" O ILE A1384 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A1386 " --> pdb=" O THR A1022 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A1539 " --> pdb=" O VAL A1575 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id=AB3, first strand: chain 'A' and resid 1119 through 1126 removed outlier: 3.982A pdb=" N MET A1121 " --> pdb=" O LYS A1177 " (cutoff:3.500A) 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 removed outlier: 3.540A pdb=" N THR A1732 " --> pdb=" O SER A1723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB8, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB9, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.586A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 269 through 272 removed outlier: 3.880A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 157 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 418 through 420 removed outlier: 6.400A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 592 through 594 removed outlier: 6.657A pdb=" N LEU G 592 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N GLU G 618 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL G 594 " --> pdb=" O GLU G 618 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA G 620 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE G 766 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU G 730 " --> pdb=" O ILE G 766 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY G 768 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TRP G 732 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 800 " --> pdb=" O PHE G 767 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.897A 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 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 1126 through 1128 removed outlier: 3.685A pdb=" N VAL G1209 " --> pdb=" O LEU G1197 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 4.437A 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 removed outlier: 3.637A pdb=" N MET G1164 " --> pdb=" O GLN G1161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 3.740A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP G1289 " --> pdb=" O VAL G1372 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G1372 " --> pdb=" O ASP G1289 " (cutoff:3.500A) removed outlier: 13.203A pdb=" N VAL G1377 " --> pdb=" O VAL G1427 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL G1427 " --> pdb=" O VAL G1377 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU G1379 " --> pdb=" O LYS G1425 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 3.740A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP G1289 " --> pdb=" O VAL G1372 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G1372 " --> pdb=" O ASP G1289 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 14.558A pdb=" N LYS G1623 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 12.340A pdb=" N ILE G1539 " --> pdb=" O LYS G1623 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N SER G1625 " --> pdb=" O ILE G1537 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N ILE G1537 " --> pdb=" O SER G1625 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLN G1627 " --> pdb=" O ASN G1535 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N ASN G1535 " --> pdb=" O GLN G1627 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL G1629 " --> pdb=" O LEU G1533 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1432 through 1435 removed outlier: 3.514A pdb=" N ILE G1435 " --> pdb=" O LYS G1462 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY G1487 " --> pdb=" O ILE G1503 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE G1503 " --> pdb=" O GLY G1487 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE G1489 " --> pdb=" O ILE G1501 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD4, first strand: chain 'G' and resid 1737 through 1741 1373 hydrogen bonds defined for protein. 3861 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: 8.89 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6547 1.33 - 1.49: 8383 1.49 - 1.64: 15111 1.64 - 1.79: 70 1.79 - 1.95: 117 Bond restraints: 30228 Sorted by residual: bond pdb=" CG MET A1121 " pdb=" SD MET A1121 " ideal model delta sigma weight residual 1.803 1.948 -0.145 2.50e-02 1.60e+03 3.38e+01 bond pdb=" N THR G 56 " pdb=" CA THR G 56 " ideal model delta sigma weight residual 1.455 1.495 -0.040 7.00e-03 2.04e+04 3.32e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.458 1.496 -0.038 7.70e-03 1.69e+04 2.46e+01 bond pdb=" N VAL A 957 " pdb=" CA VAL A 957 " ideal model delta sigma weight residual 1.460 1.502 -0.042 8.60e-03 1.35e+04 2.34e+01 bond pdb=" C TYR A 725 " pdb=" O TYR A 725 " ideal model delta sigma weight residual 1.235 1.288 -0.053 1.10e-02 8.26e+03 2.32e+01 ... (remaining 30223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 38575 3.59 - 7.19: 2345 7.19 - 10.78: 19 10.78 - 14.38: 4 14.38 - 17.97: 1 Bond angle restraints: 40944 Sorted by residual: angle pdb=" CB GLU A 381 " pdb=" CG GLU A 381 " pdb=" CD GLU A 381 " ideal model delta sigma weight residual 112.60 130.57 -17.97 1.70e+00 3.46e-01 1.12e+02 angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 124.21 -11.61 1.70e+00 3.46e-01 4.67e+01 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 124.00 -11.40 1.70e+00 3.46e-01 4.50e+01 angle pdb=" CA GLY A1582 " pdb=" C GLY A1582 " pdb=" O GLY A1582 " ideal model delta sigma weight residual 122.52 117.24 5.28 7.90e-01 1.60e+00 4.46e+01 angle pdb=" C GLU B 272 " pdb=" N PRO B 273 " pdb=" CA PRO B 273 " ideal model delta sigma weight residual 119.87 113.04 6.83 1.04e+00 9.25e-01 4.32e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 16500 18.09 - 36.18: 1404 36.18 - 54.26: 242 54.26 - 72.35: 75 72.35 - 90.44: 31 Dihedral angle restraints: 18252 sinusoidal: 7340 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ALA G 897 " pdb=" C ALA G 897 " pdb=" N ASP G 898 " pdb=" CA ASP G 898 " ideal model delta harmonic sigma weight residual -180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+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 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY A1565 " pdb=" C GLY A1565 " pdb=" N ARG A1566 " pdb=" CA ARG A1566 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 18249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2092 0.060 - 0.120: 1744 0.120 - 0.181: 648 0.181 - 0.241: 113 0.241 - 0.301: 6 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ILE G 652 " pdb=" N ILE G 652 " pdb=" C ILE G 652 " pdb=" CB ILE G 652 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+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 2.69 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 4600 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1401 " -0.059 2.00e-02 2.50e+03 2.98e-02 1.77e+01 pdb=" CG TYR A1401 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A1401 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A1401 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A1401 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A1401 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1401 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1376 " 0.035 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A1376 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A1376 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A1376 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A1376 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1376 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1376 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 718 " -0.043 2.00e-02 2.50e+03 2.15e-02 9.28e+00 pdb=" CG TYR A 718 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 718 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 718 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 718 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 718 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 718 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 718 " -0.021 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 654 2.68 - 3.23: 28707 3.23 - 3.79: 46102 3.79 - 4.34: 64685 4.34 - 4.90: 104553 Nonbonded interactions: 244701 Sorted by model distance: nonbonded pdb=" O GLY B 222 " pdb=" OG SER B 226 " model vdw 2.124 3.040 nonbonded pdb=" O VAL G1443 " pdb=" OG SER G1446 " model vdw 2.202 3.040 nonbonded pdb=" O GLN G 456 " pdb=" NH1 ARG G 469 " model vdw 2.204 3.120 nonbonded pdb=" O PHE G1419 " pdb=" OG1 THR G1422 " model vdw 2.205 3.040 nonbonded pdb=" OE1 GLU A1107 " pdb=" OG1 THR A1191 " model vdw 2.207 3.040 ... (remaining 244696 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 29.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.015 0.792 30230 Z= 1.141 Angle : 1.891 17.974 40946 Z= 1.380 Chirality : 0.086 0.301 4603 Planarity : 0.006 0.030 5286 Dihedral : 14.701 90.442 11221 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.29 % Favored : 92.24 % Rotamer: Outliers : 0.22 % Allowed : 3.70 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.11), residues: 3761 helix: -2.57 (0.10), residues: 1628 sheet: -2.36 (0.21), residues: 460 loop : -1.93 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1430 TYR 0.059 0.005 TYR A1401 PHE 0.050 0.004 PHE A1376 TRP 0.039 0.006 TRP A1286 HIS 0.015 0.003 HIS G1697 Details of bonding type rmsd covalent geometry : bond 0.01388 (30228) covalent geometry : angle 1.88982 (40944) SS BOND : bond 0.07042 ( 1) SS BOND : angle 9.40645 ( 2) hydrogen bonds : bond 0.21659 ( 1365) hydrogen bonds : angle 9.26226 ( 3861) Misc. bond : bond 0.79174 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 309 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8767 (ttm) cc_final: 0.8557 (tpp) REVERT: A 384 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8936 (pt0) REVERT: A 419 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8952 (mt-10) REVERT: A 440 MET cc_start: 0.9522 (mmm) cc_final: 0.9283 (mmm) REVERT: A 847 GLU cc_start: 0.9146 (mp0) cc_final: 0.8873 (mp0) REVERT: A 952 GLU cc_start: 0.9043 (pp20) cc_final: 0.8837 (pp20) REVERT: A 991 ASP cc_start: 0.9180 (t0) cc_final: 0.8961 (t0) REVERT: A 1268 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8830 (tt0) REVERT: A 1273 ASP cc_start: 0.9187 (p0) cc_final: 0.8896 (p0) REVERT: A 1338 GLU cc_start: 0.8694 (mp0) cc_final: 0.8071 (mt-10) REVERT: A 1430 ARG cc_start: 0.4923 (tmt-80) cc_final: 0.4315 (tpt170) REVERT: A 1646 PHE cc_start: 0.9128 (m-10) cc_final: 0.8925 (m-10) REVERT: A 1649 LYS cc_start: 0.4656 (mmtt) cc_final: 0.4040 (mmtt) REVERT: A 1690 ASN cc_start: 0.9580 (t0) cc_final: 0.9330 (t0) REVERT: A 1819 VAL cc_start: 0.8493 (t) cc_final: 0.8267 (m) REVERT: B 185 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8749 (mt-10) REVERT: B 211 GLU cc_start: 0.8926 (mp0) cc_final: 0.8685 (mp0) REVERT: B 292 GLN cc_start: 0.9198 (mp10) cc_final: 0.8833 (mp10) REVERT: B 301 ASP cc_start: 0.8556 (t0) cc_final: 0.8201 (t0) REVERT: G 764 MET cc_start: 0.9038 (ttm) cc_final: 0.8834 (ttm) REVERT: G 863 MET cc_start: 0.9164 (mmm) cc_final: 0.8833 (mmm) REVERT: G 870 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9088 (pt0) REVERT: G 1221 MET cc_start: 0.8830 (tmm) cc_final: 0.8557 (tmm) REVERT: G 1229 MET cc_start: 0.4974 (tpt) cc_final: 0.4685 (tpt) REVERT: G 1323 MET cc_start: 0.6898 (ptp) cc_final: 0.6463 (ptp) REVERT: G 1359 MET cc_start: 0.6497 (tpp) cc_final: 0.5625 (tpt) REVERT: G 1784 MET cc_start: 0.8140 (tmm) cc_final: 0.7308 (tmm) REVERT: G 1829 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8950 (mm-30) REVERT: G 1838 MET cc_start: 0.9001 (tmm) cc_final: 0.8736 (tmm) REVERT: G 1876 GLU cc_start: 0.7583 (tp30) cc_final: 0.7318 (tp30) REVERT: G 2005 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7982 (mtp180) outliers start: 7 outliers final: 0 residues processed: 311 average time/residue: 0.1737 time to fit residues: 85.6362 Evaluate side-chains 218 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 344 GLN A 379 ASN A 506 ASN A 527 GLN A 669 ASN A 777 GLN A 983 GLN A 987 ASN A 989 GLN A1000 GLN A1380 GLN A1542 HIS A1648 GLN A1652 GLN A1783 ASN A1854 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 79 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 HIS G 330 ASN G 354 ASN G 372 ASN G 440 ASN G 747 HIS ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1078 HIS G1217 ASN G1595 ASN G1619 ASN G1697 HIS G1896 GLN G1912 ASN ** G2044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.076468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058698 restraints weight = 125175.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.059688 restraints weight = 61048.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060003 restraints weight = 35140.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060223 restraints weight = 33444.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060294 restraints weight = 29597.547| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30230 Z= 0.141 Angle : 0.581 9.011 40946 Z= 0.305 Chirality : 0.042 0.196 4603 Planarity : 0.004 0.038 5286 Dihedral : 4.746 52.778 4030 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.69 % Favored : 97.18 % Rotamer: Outliers : 0.74 % Allowed : 7.03 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.13), residues: 3761 helix: 0.04 (0.12), residues: 1663 sheet: -1.75 (0.22), residues: 511 loop : -0.84 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1956 TYR 0.017 0.002 TYR G1891 PHE 0.017 0.001 PHE G 209 TRP 0.013 0.001 TRP A1813 HIS 0.012 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00315 (30228) covalent geometry : angle 0.58025 (40944) SS BOND : bond 0.00532 ( 1) SS BOND : angle 4.39867 ( 2) hydrogen bonds : bond 0.04349 ( 1365) hydrogen bonds : angle 5.14983 ( 3861) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8146 (mp) cc_final: 0.7885 (mp) REVERT: A 923 MET cc_start: 0.6949 (ttp) cc_final: 0.6697 (ttp) REVERT: A 1040 GLU cc_start: 0.8412 (tt0) cc_final: 0.8189 (tt0) REVERT: A 1128 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7453 (mp0) REVERT: A 1162 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 1273 ASP cc_start: 0.8014 (p0) cc_final: 0.7808 (p0) REVERT: A 1338 GLU cc_start: 0.7394 (mp0) cc_final: 0.7018 (mt-10) REVERT: A 1649 LYS cc_start: 0.4667 (mmtt) cc_final: 0.4200 (mmtt) REVERT: A 1759 MET cc_start: 0.7216 (tmm) cc_final: 0.6566 (tmm) REVERT: B 185 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 207 GLU cc_start: 0.8743 (pp20) cc_final: 0.8319 (tp30) REVERT: B 229 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9246 (mm) REVERT: B 301 ASP cc_start: 0.7656 (t0) cc_final: 0.7354 (t0) REVERT: G 447 ASN cc_start: 0.8577 (m-40) cc_final: 0.8338 (p0) REVERT: G 764 MET cc_start: 0.8777 (ttm) cc_final: 0.8536 (ttm) REVERT: G 794 MET cc_start: 0.8816 (tpp) cc_final: 0.8209 (mmt) REVERT: G 870 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7919 (pt0) REVERT: G 1359 MET cc_start: 0.5620 (tpp) cc_final: 0.5072 (tpt) REVERT: G 1680 LEU cc_start: 0.9188 (mp) cc_final: 0.8874 (mt) REVERT: G 1784 MET cc_start: 0.8048 (tmm) cc_final: 0.7389 (tmm) REVERT: G 1822 MET cc_start: 0.8217 (ptp) cc_final: 0.7661 (ptp) REVERT: G 1838 MET cc_start: 0.8909 (tmm) cc_final: 0.8647 (tmm) REVERT: G 1982 MET cc_start: 0.8532 (mtp) cc_final: 0.8290 (mtp) outliers start: 24 outliers final: 14 residues processed: 276 average time/residue: 0.1809 time to fit residues: 79.8937 Evaluate side-chains 229 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1939 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 93 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 361 optimal weight: 30.0000 chunk 305 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 338 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 500 HIS ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.076032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058238 restraints weight = 126129.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059500 restraints weight = 59268.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059578 restraints weight = 32729.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059806 restraints weight = 34582.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059874 restraints weight = 28460.455| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30230 Z= 0.188 Angle : 0.574 9.201 40946 Z= 0.296 Chirality : 0.042 0.167 4603 Planarity : 0.004 0.045 5286 Dihedral : 4.587 53.560 4030 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.46 % Rotamer: Outliers : 1.05 % Allowed : 9.00 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.14), residues: 3761 helix: 0.69 (0.13), residues: 1667 sheet: -1.61 (0.22), residues: 505 loop : -0.56 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.017 0.001 TYR G2048 PHE 0.017 0.001 PHE A1809 TRP 0.013 0.001 TRP A1030 HIS 0.010 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00422 (30228) covalent geometry : angle 0.57288 (40944) SS BOND : bond 0.00316 ( 1) SS BOND : angle 4.26115 ( 2) hydrogen bonds : bond 0.03928 ( 1365) hydrogen bonds : angle 4.86527 ( 3861) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 826 MET cc_start: 0.8793 (mmm) cc_final: 0.8166 (mtp) REVERT: A 1040 GLU cc_start: 0.8463 (tt0) cc_final: 0.8237 (tt0) REVERT: A 1128 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7486 (mp0) REVERT: A 1273 ASP cc_start: 0.8074 (p0) cc_final: 0.7814 (p0) REVERT: A 1333 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: A 1338 GLU cc_start: 0.7476 (mp0) cc_final: 0.6836 (mt-10) REVERT: A 1649 LYS cc_start: 0.4426 (mmtt) cc_final: 0.4002 (mmtt) REVERT: A 1759 MET cc_start: 0.7346 (tmm) cc_final: 0.7034 (tmm) REVERT: A 1783 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.7044 (m110) REVERT: B 185 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 216 THR cc_start: 0.8230 (p) cc_final: 0.7888 (p) REVERT: B 229 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9258 (mm) REVERT: B 248 LYS cc_start: 0.8801 (tppt) cc_final: 0.8566 (tppt) REVERT: B 290 MET cc_start: 0.8889 (mmt) cc_final: 0.8676 (mmt) REVERT: B 301 ASP cc_start: 0.7741 (t0) cc_final: 0.7449 (t0) REVERT: G 325 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8777 (mt-10) REVERT: G 447 ASN cc_start: 0.8633 (m-40) cc_final: 0.8309 (p0) REVERT: G 870 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8016 (pt0) REVERT: G 1164 MET cc_start: 0.8033 (mmm) cc_final: 0.7821 (tpp) REVERT: G 1359 MET cc_start: 0.5436 (tpp) cc_final: 0.4934 (tpt) REVERT: G 1413 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8519 (mmm-85) REVERT: G 1639 LYS cc_start: 0.9220 (pttp) cc_final: 0.8952 (ptpp) REVERT: G 1680 LEU cc_start: 0.9173 (mp) cc_final: 0.8876 (mt) REVERT: G 1784 MET cc_start: 0.8138 (tmm) cc_final: 0.7485 (tmm) REVERT: G 1822 MET cc_start: 0.8255 (ptp) cc_final: 0.7733 (ptp) REVERT: G 1838 MET cc_start: 0.8959 (tmm) cc_final: 0.8630 (tmm) outliers start: 34 outliers final: 21 residues processed: 254 average time/residue: 0.1766 time to fit residues: 72.8255 Evaluate side-chains 231 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1662 THR Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 250 optimal weight: 5.9990 chunk 322 optimal weight: 40.0000 chunk 69 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 364 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 136 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1482 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1161 GLN G1226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.076138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.057796 restraints weight = 126007.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059624 restraints weight = 59306.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.059770 restraints weight = 28540.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060026 restraints weight = 28389.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060031 restraints weight = 24469.089| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30230 Z= 0.164 Angle : 0.546 8.916 40946 Z= 0.280 Chirality : 0.042 0.165 4603 Planarity : 0.004 0.044 5286 Dihedral : 4.448 53.572 4030 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 1.36 % Allowed : 9.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.14), residues: 3761 helix: 0.93 (0.13), residues: 1662 sheet: -1.44 (0.22), residues: 516 loop : -0.40 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 709 TYR 0.018 0.001 TYR G2048 PHE 0.027 0.001 PHE A 35 TRP 0.012 0.001 TRP A1030 HIS 0.009 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00367 (30228) covalent geometry : angle 0.54508 (40944) SS BOND : bond 0.00246 ( 1) SS BOND : angle 4.04819 ( 2) hydrogen bonds : bond 0.03635 ( 1365) hydrogen bonds : angle 4.68627 ( 3861) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 MET cc_start: 0.8643 (mmm) cc_final: 0.8293 (mtp) REVERT: A 1040 GLU cc_start: 0.8322 (tt0) cc_final: 0.8117 (tt0) REVERT: A 1128 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7418 (mp0) REVERT: A 1273 ASP cc_start: 0.7899 (p0) cc_final: 0.7682 (p0) REVERT: A 1338 GLU cc_start: 0.7294 (mp0) cc_final: 0.6773 (mt-10) REVERT: A 1649 LYS cc_start: 0.4391 (mmtt) cc_final: 0.3864 (mmtt) REVERT: A 1798 TYR cc_start: 0.8501 (t80) cc_final: 0.8241 (t80) REVERT: B 185 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 216 THR cc_start: 0.8142 (p) cc_final: 0.7827 (p) REVERT: B 229 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9245 (mm) REVERT: B 248 LYS cc_start: 0.8875 (tppt) cc_final: 0.8592 (tppt) REVERT: B 301 ASP cc_start: 0.7687 (t0) cc_final: 0.7400 (t0) REVERT: G 245 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: G 447 ASN cc_start: 0.8567 (m-40) cc_final: 0.8302 (p0) REVERT: G 1359 MET cc_start: 0.5529 (tpp) cc_final: 0.5027 (tpt) REVERT: G 1680 LEU cc_start: 0.9158 (mp) cc_final: 0.8856 (mt) REVERT: G 1784 MET cc_start: 0.8130 (tmm) cc_final: 0.7475 (tmm) REVERT: G 1822 MET cc_start: 0.8189 (ptp) cc_final: 0.7657 (ptp) REVERT: G 1838 MET cc_start: 0.8979 (tmm) cc_final: 0.8646 (tmm) outliers start: 44 outliers final: 21 residues processed: 253 average time/residue: 0.1733 time to fit residues: 72.5239 Evaluate side-chains 224 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 1161 GLN Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 351 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1433 HIS B 261 GLN G 330 ASN G 517 HIS G 677 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.076056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.057917 restraints weight = 127344.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059637 restraints weight = 61373.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.059827 restraints weight = 30408.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060059 restraints weight = 29864.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060074 restraints weight = 25601.652| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30230 Z= 0.171 Angle : 0.551 11.601 40946 Z= 0.281 Chirality : 0.042 0.171 4603 Planarity : 0.004 0.043 5286 Dihedral : 4.423 53.613 4030 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.39 % Allowed : 10.57 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.14), residues: 3761 helix: 1.01 (0.13), residues: 1661 sheet: -1.35 (0.22), residues: 516 loop : -0.31 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 709 TYR 0.017 0.001 TYR G2048 PHE 0.025 0.001 PHE A 35 TRP 0.012 0.001 TRP A1030 HIS 0.011 0.001 HIS A1703 Details of bonding type rmsd covalent geometry : bond 0.00383 (30228) covalent geometry : angle 0.55048 (40944) SS BOND : bond 0.00251 ( 1) SS BOND : angle 4.01422 ( 2) hydrogen bonds : bond 0.03622 ( 1365) hydrogen bonds : angle 4.63235 ( 3861) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 MET cc_start: 0.8685 (mmm) cc_final: 0.7876 (mtp) REVERT: A 1040 GLU cc_start: 0.8346 (tt0) cc_final: 0.8131 (tt0) REVERT: A 1128 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7399 (mp0) REVERT: A 1273 ASP cc_start: 0.7889 (p0) cc_final: 0.7666 (p0) REVERT: A 1333 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: A 1338 GLU cc_start: 0.7352 (mp0) cc_final: 0.6812 (mt-10) REVERT: A 1507 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: A 1649 LYS cc_start: 0.4399 (mmtt) cc_final: 0.3920 (mmtt) REVERT: A 1759 MET cc_start: 0.7306 (tmm) cc_final: 0.6780 (tmm) REVERT: A 1798 TYR cc_start: 0.8506 (t80) cc_final: 0.8247 (t80) REVERT: B 185 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 229 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9235 (mm) REVERT: B 248 LYS cc_start: 0.8883 (tppt) cc_final: 0.8675 (tppt) REVERT: B 301 ASP cc_start: 0.7674 (t0) cc_final: 0.7393 (t0) REVERT: G 245 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8471 (mm-40) REVERT: G 1359 MET cc_start: 0.5573 (tpp) cc_final: 0.5065 (tpt) REVERT: G 1680 LEU cc_start: 0.9158 (mp) cc_final: 0.8865 (mt) REVERT: G 1736 MET cc_start: 0.8255 (mpp) cc_final: 0.7958 (mpp) REVERT: G 1784 MET cc_start: 0.8167 (tmm) cc_final: 0.7505 (tmm) REVERT: G 1822 MET cc_start: 0.8243 (ptp) cc_final: 0.7661 (ptp) REVERT: G 1838 MET cc_start: 0.8971 (tmm) cc_final: 0.8621 (tmm) REVERT: G 1982 MET cc_start: 0.8353 (mtp) cc_final: 0.8128 (mpp) outliers start: 45 outliers final: 30 residues processed: 251 average time/residue: 0.1603 time to fit residues: 66.0552 Evaluate side-chains 234 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 326 optimal weight: 0.2980 chunk 204 optimal weight: 4.9990 chunk 299 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 321 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1689 HIS A1854 ASN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1161 GLN G1241 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.077386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059154 restraints weight = 125967.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060998 restraints weight = 58944.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.061161 restraints weight = 28369.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061404 restraints weight = 28175.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061408 restraints weight = 24508.084| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30230 Z= 0.101 Angle : 0.510 10.883 40946 Z= 0.259 Chirality : 0.041 0.158 4603 Planarity : 0.003 0.040 5286 Dihedral : 4.193 54.186 4030 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.45 % Rotamer: Outliers : 0.99 % Allowed : 11.96 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.14), residues: 3761 helix: 1.18 (0.13), residues: 1676 sheet: -1.20 (0.22), residues: 532 loop : -0.16 (0.17), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 709 TYR 0.018 0.001 TYR G 67 PHE 0.014 0.001 PHE A1820 TRP 0.009 0.001 TRP G 865 HIS 0.007 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00225 (30228) covalent geometry : angle 0.50962 (40944) SS BOND : bond 0.00141 ( 1) SS BOND : angle 3.39529 ( 2) hydrogen bonds : bond 0.03313 ( 1365) hydrogen bonds : angle 4.43888 ( 3861) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 MET cc_start: 0.8476 (mmm) cc_final: 0.8160 (mtp) REVERT: A 1124 GLU cc_start: 0.8135 (tt0) cc_final: 0.7908 (tt0) REVERT: A 1128 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7340 (mp0) REVERT: A 1273 ASP cc_start: 0.7844 (p0) cc_final: 0.7631 (p0) REVERT: A 1333 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: A 1338 GLU cc_start: 0.7242 (mp0) cc_final: 0.6995 (mt-10) REVERT: A 1377 MET cc_start: 0.8511 (tpp) cc_final: 0.8149 (tpp) REVERT: A 1649 LYS cc_start: 0.4448 (mmtt) cc_final: 0.3975 (mmtt) REVERT: A 1755 MET cc_start: 0.7319 (mtp) cc_final: 0.7105 (mtp) REVERT: A 1798 TYR cc_start: 0.8466 (t80) cc_final: 0.8223 (t80) REVERT: B 185 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 229 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9275 (mm) REVERT: B 248 LYS cc_start: 0.8938 (tppt) cc_final: 0.8685 (tppt) REVERT: B 301 ASP cc_start: 0.7654 (t0) cc_final: 0.7355 (t0) REVERT: G 245 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8480 (mm-40) REVERT: G 1164 MET cc_start: 0.7807 (mmm) cc_final: 0.7541 (mmm) REVERT: G 1359 MET cc_start: 0.5534 (tpp) cc_final: 0.5014 (tpt) REVERT: G 1680 LEU cc_start: 0.9131 (mp) cc_final: 0.8907 (mm) REVERT: G 1736 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7888 (mpp) REVERT: G 1784 MET cc_start: 0.8182 (tmm) cc_final: 0.7655 (tmm) REVERT: G 1838 MET cc_start: 0.8991 (tmm) cc_final: 0.8662 (tmm) outliers start: 32 outliers final: 15 residues processed: 247 average time/residue: 0.1620 time to fit residues: 65.8311 Evaluate side-chains 220 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 267 optimal weight: 0.8980 chunk 176 optimal weight: 0.0970 chunk 242 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 204 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 212 optimal weight: 0.0980 chunk 271 optimal weight: 5.9990 chunk 363 optimal weight: 30.0000 overall best weight: 2.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1854 ASN ** G1055 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 = 0.3545 r_free = 0.3545 target = 0.077128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059813 restraints weight = 125004.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060704 restraints weight = 59254.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061123 restraints weight = 33953.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061264 restraints weight = 32563.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061292 restraints weight = 28473.791| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30230 Z= 0.122 Angle : 0.521 10.444 40946 Z= 0.263 Chirality : 0.041 0.326 4603 Planarity : 0.003 0.042 5286 Dihedral : 4.164 54.008 4030 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 1.39 % Allowed : 12.05 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.14), residues: 3761 helix: 1.23 (0.13), residues: 1676 sheet: -1.07 (0.22), residues: 526 loop : -0.12 (0.17), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G2005 TYR 0.020 0.001 TYR G 180 PHE 0.023 0.001 PHE A 35 TRP 0.010 0.001 TRP A1030 HIS 0.007 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00275 (30228) covalent geometry : angle 0.51994 (40944) SS BOND : bond 0.00200 ( 1) SS BOND : angle 3.50824 ( 2) hydrogen bonds : bond 0.03333 ( 1365) hydrogen bonds : angle 4.40286 ( 3861) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8014 (m) cc_final: 0.7683 (p) REVERT: A 826 MET cc_start: 0.8428 (mmm) cc_final: 0.8097 (mtp) REVERT: A 1124 GLU cc_start: 0.8102 (tt0) cc_final: 0.7895 (tt0) REVERT: A 1333 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7338 (m-30) REVERT: A 1335 PHE cc_start: 0.8714 (t80) cc_final: 0.8493 (t80) REVERT: A 1338 GLU cc_start: 0.7305 (mp0) cc_final: 0.6983 (mt-10) REVERT: A 1507 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: A 1649 LYS cc_start: 0.4277 (mmtt) cc_final: 0.3760 (mmtt) REVERT: A 1759 MET cc_start: 0.7158 (tmm) cc_final: 0.6855 (tmm) REVERT: A 1798 TYR cc_start: 0.8427 (t80) cc_final: 0.8200 (t80) REVERT: B 185 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 229 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9240 (mm) REVERT: B 248 LYS cc_start: 0.8967 (tppt) cc_final: 0.8734 (tppt) REVERT: B 290 MET cc_start: 0.9072 (mmt) cc_final: 0.8618 (mmt) REVERT: B 301 ASP cc_start: 0.7669 (t0) cc_final: 0.7361 (t0) REVERT: G 245 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8488 (mm-40) REVERT: G 764 MET cc_start: 0.8539 (ttm) cc_final: 0.8258 (ttm) REVERT: G 930 MET cc_start: 0.8780 (mtt) cc_final: 0.8534 (mtt) REVERT: G 1323 MET cc_start: 0.7326 (ptp) cc_final: 0.6945 (ptp) REVERT: G 1359 MET cc_start: 0.5549 (tpp) cc_final: 0.4997 (tpt) REVERT: G 1680 LEU cc_start: 0.9136 (mp) cc_final: 0.8926 (mm) REVERT: G 1736 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: G 1784 MET cc_start: 0.8211 (tmm) cc_final: 0.7558 (tmm) REVERT: G 1838 MET cc_start: 0.8967 (tmm) cc_final: 0.8653 (tmm) outliers start: 45 outliers final: 28 residues processed: 253 average time/residue: 0.1572 time to fit residues: 65.3723 Evaluate side-chains 234 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1712 ASN Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 0 optimal weight: 30.0000 chunk 225 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1854 ASN ** G1055 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 = 0.3534 r_free = 0.3534 target = 0.076632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059351 restraints weight = 126510.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060242 restraints weight = 59865.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060640 restraints weight = 34135.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060802 restraints weight = 33036.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060834 restraints weight = 28714.599| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30230 Z= 0.156 Angle : 0.550 10.312 40946 Z= 0.278 Chirality : 0.042 0.327 4603 Planarity : 0.004 0.070 5286 Dihedral : 4.236 53.701 4030 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 1.20 % Allowed : 12.70 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.14), residues: 3761 helix: 1.26 (0.13), residues: 1663 sheet: -1.00 (0.23), residues: 509 loop : -0.15 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G2005 TYR 0.020 0.001 TYR G 67 PHE 0.016 0.001 PHE A1376 TRP 0.011 0.001 TRP A1030 HIS 0.008 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00349 (30228) covalent geometry : angle 0.54898 (40944) SS BOND : bond 0.00263 ( 1) SS BOND : angle 3.78457 ( 2) hydrogen bonds : bond 0.03445 ( 1365) hydrogen bonds : angle 4.42762 ( 3861) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5767 (mtt) cc_final: 0.5459 (mtt) REVERT: A 31 THR cc_start: 0.8001 (m) cc_final: 0.7691 (p) REVERT: A 826 MET cc_start: 0.8422 (mmm) cc_final: 0.8148 (mtp) REVERT: A 1040 GLU cc_start: 0.8350 (tt0) cc_final: 0.8133 (tt0) REVERT: A 1124 GLU cc_start: 0.8108 (tt0) cc_final: 0.7873 (tt0) REVERT: A 1333 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: A 1335 PHE cc_start: 0.8875 (t80) cc_final: 0.8539 (t80) REVERT: A 1338 GLU cc_start: 0.7316 (mp0) cc_final: 0.6883 (mt-10) REVERT: A 1507 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8727 (tp40) REVERT: A 1649 LYS cc_start: 0.4319 (mmtt) cc_final: 0.3682 (mmtt) REVERT: A 1759 MET cc_start: 0.7105 (tmm) cc_final: 0.6779 (tmm) REVERT: A 1798 TYR cc_start: 0.8443 (t80) cc_final: 0.8209 (t80) REVERT: B 229 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9217 (mm) REVERT: B 248 LYS cc_start: 0.8964 (tppt) cc_final: 0.8735 (tppt) REVERT: B 290 MET cc_start: 0.9028 (mmt) cc_final: 0.8547 (mmt) REVERT: B 301 ASP cc_start: 0.7714 (t0) cc_final: 0.7427 (t0) REVERT: G 245 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8509 (mm-40) REVERT: G 930 MET cc_start: 0.8826 (mtt) cc_final: 0.8581 (mtt) REVERT: G 1359 MET cc_start: 0.5589 (tpp) cc_final: 0.5060 (tpt) REVERT: G 1643 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8340 (tpp80) REVERT: G 1680 LEU cc_start: 0.9135 (mp) cc_final: 0.8924 (mm) REVERT: G 1736 MET cc_start: 0.8129 (mpp) cc_final: 0.7902 (mpp) REVERT: G 1784 MET cc_start: 0.8227 (tmm) cc_final: 0.7568 (tmm) REVERT: G 1838 MET cc_start: 0.8959 (tmm) cc_final: 0.8661 (tmm) outliers start: 39 outliers final: 32 residues processed: 238 average time/residue: 0.1616 time to fit residues: 63.4643 Evaluate side-chains 234 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1643 ARG Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1712 ASN Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 288 optimal weight: 6.9990 chunk 374 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1854 ASN ** G1055 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 = 0.3528 r_free = 0.3528 target = 0.076401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.059089 restraints weight = 125626.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059914 restraints weight = 60826.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060373 restraints weight = 34909.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060529 restraints weight = 33933.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060504 restraints weight = 29106.308| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30230 Z= 0.167 Angle : 0.559 11.181 40946 Z= 0.282 Chirality : 0.042 0.297 4603 Planarity : 0.004 0.062 5286 Dihedral : 4.287 53.422 4030 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.36 % Allowed : 12.79 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.14), residues: 3761 helix: 1.24 (0.13), residues: 1663 sheet: -1.07 (0.23), residues: 518 loop : -0.14 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 709 TYR 0.021 0.001 TYR G 67 PHE 0.019 0.001 PHE A 35 TRP 0.012 0.001 TRP A1030 HIS 0.008 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00375 (30228) covalent geometry : angle 0.55875 (40944) SS BOND : bond 0.00296 ( 1) SS BOND : angle 3.86785 ( 2) hydrogen bonds : bond 0.03484 ( 1365) hydrogen bonds : angle 4.44876 ( 3861) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5890 (mtt) cc_final: 0.5620 (mtt) REVERT: A 31 THR cc_start: 0.7923 (m) cc_final: 0.7584 (p) REVERT: A 826 MET cc_start: 0.8470 (mmm) cc_final: 0.8228 (mtp) REVERT: A 1124 GLU cc_start: 0.8190 (tt0) cc_final: 0.7916 (tt0) REVERT: A 1333 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: A 1335 PHE cc_start: 0.8995 (t80) cc_final: 0.8675 (t80) REVERT: A 1338 GLU cc_start: 0.7440 (mp0) cc_final: 0.6846 (mt-10) REVERT: A 1507 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8734 (tp40) REVERT: A 1649 LYS cc_start: 0.4125 (mmtt) cc_final: 0.3472 (mmtt) REVERT: A 1759 MET cc_start: 0.7031 (tmm) cc_final: 0.6695 (tmm) REVERT: B 229 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9208 (mm) REVERT: B 248 LYS cc_start: 0.8981 (tppt) cc_final: 0.8740 (tppt) REVERT: B 290 MET cc_start: 0.9031 (mmt) cc_final: 0.8535 (mmt) REVERT: B 301 ASP cc_start: 0.7667 (t0) cc_final: 0.7368 (t0) REVERT: G 245 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8476 (mm-40) REVERT: G 764 MET cc_start: 0.8632 (ttm) cc_final: 0.8388 (ttm) REVERT: G 930 MET cc_start: 0.8906 (mtt) cc_final: 0.8653 (mtt) REVERT: G 1164 MET cc_start: 0.7756 (tpp) cc_final: 0.7378 (tpp) REVERT: G 1323 MET cc_start: 0.7451 (ptp) cc_final: 0.7132 (ptp) REVERT: G 1359 MET cc_start: 0.5557 (tpp) cc_final: 0.4996 (tpt) REVERT: G 1643 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8366 (tpp80) REVERT: G 1680 LEU cc_start: 0.9139 (mp) cc_final: 0.8935 (mm) REVERT: G 1736 MET cc_start: 0.8194 (mpp) cc_final: 0.7930 (mpp) REVERT: G 1784 MET cc_start: 0.8256 (tmm) cc_final: 0.7604 (tmm) REVERT: G 1838 MET cc_start: 0.8976 (tmm) cc_final: 0.8665 (tmm) REVERT: G 2005 ARG cc_start: 0.7319 (tpp-160) cc_final: 0.6961 (tpp-160) outliers start: 44 outliers final: 36 residues processed: 244 average time/residue: 0.1673 time to fit residues: 67.1999 Evaluate side-chains 239 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1643 ARG Chi-restraints excluded: chain G residue 1690 VAL Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1712 ASN Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 198 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 154 optimal weight: 40.0000 chunk 302 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 142 optimal weight: 0.2980 chunk 266 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN ** A1748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1854 ASN ** G1055 HIS ** 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 = 0.3542 r_free = 0.3542 target = 0.076990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059650 restraints weight = 125167.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060473 restraints weight = 60101.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060915 restraints weight = 34776.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061121 restraints weight = 33301.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061082 restraints weight = 28499.456| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30230 Z= 0.130 Angle : 0.544 11.734 40946 Z= 0.274 Chirality : 0.042 0.272 4603 Planarity : 0.004 0.055 5286 Dihedral : 4.221 53.794 4030 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.23 % Allowed : 13.22 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.14), residues: 3761 helix: 1.30 (0.13), residues: 1661 sheet: -1.04 (0.22), residues: 528 loop : -0.10 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 709 TYR 0.022 0.001 TYR G 67 PHE 0.020 0.001 PHE G2026 TRP 0.011 0.001 TRP A1030 HIS 0.007 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00293 (30228) covalent geometry : angle 0.54365 (40944) SS BOND : bond 0.00214 ( 1) SS BOND : angle 3.61384 ( 2) hydrogen bonds : bond 0.03377 ( 1365) hydrogen bonds : angle 4.39411 ( 3861) Misc. bond : bond 0.00009 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5921 (mtt) cc_final: 0.5602 (mtt) REVERT: A 31 THR cc_start: 0.7940 (m) cc_final: 0.7615 (p) REVERT: A 342 GLN cc_start: 0.9161 (mt0) cc_final: 0.8826 (mt0) REVERT: A 826 MET cc_start: 0.8370 (mmm) cc_final: 0.8072 (mtp) REVERT: A 1333 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: A 1335 PHE cc_start: 0.8913 (t80) cc_final: 0.8568 (t80) REVERT: A 1338 GLU cc_start: 0.7284 (mp0) cc_final: 0.6823 (mt-10) REVERT: A 1507 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8702 (tp40) REVERT: A 1649 LYS cc_start: 0.4541 (mmtt) cc_final: 0.3911 (mmtt) REVERT: A 1759 MET cc_start: 0.7084 (tmm) cc_final: 0.6742 (tmm) REVERT: B 229 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9202 (mm) REVERT: B 248 LYS cc_start: 0.8957 (tppt) cc_final: 0.8738 (tppt) REVERT: B 290 MET cc_start: 0.9006 (mmt) cc_final: 0.8485 (mmt) REVERT: B 301 ASP cc_start: 0.7645 (t0) cc_final: 0.7348 (t0) REVERT: G 245 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8482 (mm-40) REVERT: G 764 MET cc_start: 0.8605 (ttm) cc_final: 0.8367 (ttm) REVERT: G 930 MET cc_start: 0.8799 (mtt) cc_final: 0.8555 (mtt) REVERT: G 1323 MET cc_start: 0.7400 (ptp) cc_final: 0.7104 (ptp) REVERT: G 1359 MET cc_start: 0.5588 (tpp) cc_final: 0.5026 (tpt) REVERT: G 1643 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8266 (tpp80) REVERT: G 1680 LEU cc_start: 0.9133 (mp) cc_final: 0.8927 (mm) REVERT: G 1736 MET cc_start: 0.8149 (mpp) cc_final: 0.7910 (mpp) REVERT: G 1784 MET cc_start: 0.8196 (tmm) cc_final: 0.7551 (tmm) REVERT: G 1838 MET cc_start: 0.8956 (tmm) cc_final: 0.8645 (tmm) outliers start: 40 outliers final: 34 residues processed: 240 average time/residue: 0.1622 time to fit residues: 64.1862 Evaluate side-chains 241 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1643 ARG Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1712 ASN Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 319 optimal weight: 10.0000 chunk 95 optimal weight: 0.2980 chunk 162 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 357 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 363 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 304 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1854 ASN A1873 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.078642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061425 restraints weight = 125982.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.062497 restraints weight = 63333.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.062688 restraints weight = 35189.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062796 restraints weight = 34747.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062919 restraints weight = 30748.850| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30230 Z= 0.094 Angle : 0.525 12.556 40946 Z= 0.262 Chirality : 0.041 0.245 4603 Planarity : 0.004 0.053 5286 Dihedral : 4.013 54.589 4030 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.96 % Allowed : 13.47 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.14), residues: 3761 helix: 1.43 (0.13), residues: 1664 sheet: -0.87 (0.23), residues: 511 loop : -0.01 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 709 TYR 0.027 0.001 TYR A 725 PHE 0.023 0.001 PHE A 450 TRP 0.009 0.001 TRP G 865 HIS 0.005 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00203 (30228) covalent geometry : angle 0.52465 (40944) SS BOND : bond 0.00071 ( 1) SS BOND : angle 2.98034 ( 2) hydrogen bonds : bond 0.03123 ( 1365) hydrogen bonds : angle 4.24783 ( 3861) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3848.34 seconds wall clock time: 67 minutes 56.66 seconds (4076.66 seconds total)