Starting phenix.real_space_refine on Sat Sep 12 12:22:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v6c_31742/09_2026/7v6c_31742.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 52 5.49 5 S 84 5.16 5 C 9817 2.51 5 N 2651 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15643 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 12487 Classifications: {'peptide': 1540} Link IDs: {'PTRANS': 65, 'TRANS': 1474} Chain breaks: 12 Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2057 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna3p_pyr': 7} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 435 Classifications: {'DNA': 1, 'RNAv2': 20} Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 7} Link IDs: {'rna3p': 20} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 413 Classifications: {'DNA': 1, 'RNAv2': 20} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 14} Link IDs: {'rna3p': 20} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C%5*END:plan': 1, ' C%5*END:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 3.71, per 1000 atoms: 0.24 Number of scatterers: 15643 At special positions: 0 Unit cell: (105.841, 156.764, 139.789, 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 84 16.00 P 52 15.00 O 3039 8.00 N 2651 7.00 C 9817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 538.1 milliseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 13 sheets defined 52.8% alpha, 11.1% beta 22 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 97 removed outlier: 6.638A pdb=" N VAL A 94 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 141 through 145 removed outlier: 4.238A pdb=" N THR A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 232 through 252 removed outlier: 4.160A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 313 removed outlier: 7.100A pdb=" N ILE A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 345 removed outlier: 3.543A pdb=" N MET A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.760A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 510 through 534 removed outlier: 3.614A pdb=" N GLN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582A removed outlier: 3.550A pdb=" N ALA A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 removed outlier: 3.598A pdb=" N ASP A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 657 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.577A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.633A pdb=" N GLN A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 4.093A pdb=" N LEU A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 916 through 925 removed outlier: 4.060A pdb=" N PHE A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1016 removed outlier: 4.408A pdb=" N LEU A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Proline residue: A 993C - end of helix removed outlier: 3.579A pdb=" N TYR A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1048 removed outlier: 4.122A pdb=" N ASN A1048 " --> pdb=" O PRO A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1084 removed outlier: 3.947A pdb=" N PHE A1082 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1083 " --> pdb=" O ILE A1079 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN A1084 " --> pdb=" O THR A1080 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1078 through 1084' Processing helix chain 'A' and resid 1087 through 1091 Processing helix chain 'A' and resid 1103 through 1116 removed outlier: 3.536A pdb=" N LEU A1107 " --> pdb=" O TYR A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.792A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1249 Processing helix chain 'A' and resid 1249 through 1260 Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.624A pdb=" N ALA A1299 " --> pdb=" O ASN A1295 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1295 through 1300' Processing helix chain 'A' and resid 1303 through 1309 Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 3.770A pdb=" N GLY A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1363 through 1382 removed outlier: 3.757A pdb=" N ALA A1367 " --> pdb=" O ASN A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 3.658A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 4.420A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 4.149A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.651A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1467 through 1491 removed outlier: 4.302A pdb=" N LEU A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1521 through 1525 Processing helix chain 'A' and resid 1529 through 1547 Processing helix chain 'A' and resid 1551 through 1557 Processing helix chain 'A' and resid 1610 through 1628 Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1655 through 1663 Processing helix chain 'A' and resid 1701 through 1720 Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 51 through 69 removed outlier: 3.732A pdb=" N SER B 61 " --> pdb=" O HIS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 145 through 163 Processing helix chain 'B' and resid 189 through 198 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.508A pdb=" N LEU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.503A pdb=" N ARG B 223 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS B 224 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 225 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE B 227 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 295 through 311 removed outlier: 4.268A pdb=" N TYR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.894A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 60 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY A 114 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE A 62 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER A 134 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL A 169 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 136 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 171 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 138 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY A 24 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 172 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 26 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 6.540A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768A through 772 Processing sheet with id=AA7, first strand: chain 'A' and resid 768A through 772 removed outlier: 4.549A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 753 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.549A pdb=" N LYS A 897 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1072 removed outlier: 4.010A pdb=" N LYS A1694 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 27 Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 120 removed outlier: 6.198A pdb=" N ILE B 114 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER B 133 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 131 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 270 removed outlier: 4.657A pdb=" N LEU B 278 " --> pdb=" O VAL B 270 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2452 1.30 - 1.43: 4448 1.43 - 1.57: 8936 1.57 - 1.70: 102 1.70 - 1.84: 130 Bond restraints: 16068 Sorted by residual: bond pdb=" C PRO A1496 " pdb=" O PRO A1496 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.30e-02 5.92e+03 3.21e+01 bond pdb=" C TYR A 396 " pdb=" O TYR A 396 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.32e-02 5.74e+03 2.07e+01 bond pdb=" N THR A 903 " pdb=" CA THR A 903 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.61e+01 bond pdb=" C PRO A 413 " pdb=" O PRO A 413 " ideal model delta sigma weight residual 1.235 1.186 0.050 1.30e-02 5.92e+03 1.45e+01 bond pdb=" CA SER A1467 " pdb=" CB SER A1467 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.49e-02 4.50e+03 1.45e+01 ... (remaining 16063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 15954 1.74 - 3.47: 5390 3.47 - 5.21: 562 5.21 - 6.94: 49 6.94 - 8.68: 5 Bond angle restraints: 21960 Sorted by residual: angle pdb=" N TYR A 11 " pdb=" CA TYR A 11 " pdb=" C TYR A 11 " ideal model delta sigma weight residual 111.82 103.42 8.40 1.16e+00 7.43e-01 5.24e+01 angle pdb=" C PRO A1188 " pdb=" CA PRO A1188 " pdb=" CB PRO A1188 " ideal model delta sigma weight residual 111.23 102.55 8.68 1.28e+00 6.10e-01 4.60e+01 angle pdb=" N ASP A1347 " pdb=" CA ASP A1347 " pdb=" C ASP A1347 " ideal model delta sigma weight residual 112.97 106.33 6.64 1.06e+00 8.90e-01 3.93e+01 angle pdb=" CA TYR B 204 " pdb=" C TYR B 204 " pdb=" O TYR B 204 " ideal model delta sigma weight residual 120.24 113.89 6.35 1.11e+00 8.12e-01 3.27e+01 angle pdb=" N TYR B 305 " pdb=" CA TYR B 305 " pdb=" C TYR B 305 " ideal model delta sigma weight residual 111.07 105.06 6.01 1.07e+00 8.73e-01 3.15e+01 ... (remaining 21955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8738 17.94 - 35.87: 637 35.87 - 53.81: 205 53.81 - 71.75: 27 71.75 - 89.69: 9 Dihedral angle restraints: 9616 sinusoidal: 4309 harmonic: 5307 Sorted by residual: dihedral pdb=" O5' U C 1 " pdb=" C5' U C 1 " pdb=" C4' U C 1 " pdb=" C3' U C 1 " ideal model delta sinusoidal sigma weight residual 60.00 13.40 46.60 3 6.40e+00 2.44e-02 4.59e+01 dihedral pdb=" O5' C F 15 " pdb=" C5' C F 15 " pdb=" C4' C F 15 " pdb=" C3' C F 15 " ideal model delta sinusoidal sigma weight residual 60.00 82.94 -22.94 3 6.40e+00 2.44e-02 1.66e+01 dihedral pdb=" C PRO A1496 " pdb=" N PRO A1496 " pdb=" CA PRO A1496 " pdb=" CB PRO A1496 " ideal model delta harmonic sigma weight residual -120.70 -110.87 -9.83 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 9613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1964 0.110 - 0.220: 502 0.220 - 0.331: 44 0.331 - 0.441: 0 0.441 - 0.551: 11 Chirality restraints: 2521 Sorted by residual: chirality pdb=" P G C 2 " pdb=" OP1 G C 2 " pdb=" OP2 G C 2 " pdb=" O5' G C 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.72 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" P G E 4 " pdb=" OP1 G E 4 " pdb=" OP2 G E 4 " pdb=" O5' G E 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" P G E 2 " pdb=" OP1 G E 2 " pdb=" OP2 G E 2 " pdb=" O5' G E 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.69 -0.52 2.00e-01 2.50e+01 6.72e+00 ... (remaining 2518 not shown) Planarity restraints: 2608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 412 " 0.025 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C THR A 412 " -0.080 2.00e-02 2.50e+03 pdb=" O THR A 412 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO A 413 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1000 " -0.033 2.00e-02 2.50e+03 2.11e-02 8.92e+00 pdb=" CG TYR A1000 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A1000 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A1000 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A1000 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1000 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A1000 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR A1000 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 204 " 0.014 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C TYR B 204 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR B 204 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP B 205 " 0.018 2.00e-02 2.50e+03 ... (remaining 2605 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1576 2.76 - 3.30: 15447 3.30 - 3.83: 24136 3.83 - 4.37: 33827 4.37 - 4.90: 51207 Nonbonded interactions: 126193 Sorted by model distance: nonbonded pdb=" O ASN A 253 " pdb=" OD1 ASN A 253 " model vdw 2.230 3.040 nonbonded pdb=" O SER B 124 " pdb=" O2' U C 9 " model vdw 2.306 3.040 nonbonded pdb=" NH1 ARG B 150 " pdb=" OP1 A D 2 " model vdw 2.312 3.120 nonbonded pdb=" O THR A 412 " pdb=" N GLU A 414 " model vdw 2.351 3.120 nonbonded pdb=" O PHE A1542 " pdb=" OG SER A1545 " model vdw 2.401 3.040 ... (remaining 126188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.012 0.074 16068 Z= 0.879 Angle : 1.568 8.680 21960 Z= 1.173 Chirality : 0.096 0.551 2521 Planarity : 0.006 0.064 2608 Dihedral : 13.945 89.685 6166 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.90 % Allowed : 7.37 % Favored : 88.73 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.64 (0.18), residues: 1766 helix: 0.42 (0.17), residues: 826 sheet: -0.80 (0.36), residues: 162 loop : -1.21 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1097 TYR 0.041 0.005 TYR A1000 PHE 0.033 0.005 PHE A 502 TRP 0.022 0.005 TRP A 885 HIS 0.014 0.003 HIS A1433 Details of bonding type rmsd/Z covalent geometry : bond 0.01177 / 0.88 (16068) covalent geometry : angle 1.56802 / 1.17 (21960) hydrogen bonds : bond 0.19341 / 12.81 ( 770) hydrogen bonds : angle 7.01532 / 5.00 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 424 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 9 ARG cc_start: 0.6835 (mtp180) cc_final: 0.6577 (ttt180) REVERT: A 75 MET cc_start: 0.7319 (mtt) cc_final: 0.7116 (mtm) REVERT: A 98 THR cc_start: 0.7148 (m) cc_final: 0.6743 (p) REVERT: A 105 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 126 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7154 (p) REVERT: A 222 MET cc_start: 0.7654 (tpt) cc_final: 0.7154 (tpp) REVERT: A 236 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7400 (mmm-85) REVERT: A 237 LEU cc_start: 0.7769 (tp) cc_final: 0.7389 (mt) REVERT: A 241 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 279 GLN cc_start: 0.6848 (tt0) cc_final: 0.6596 (tm-30) REVERT: A 290 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7338 (tp30) REVERT: A 310 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7229 (mmmm) REVERT: A 315 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6983 (mp0) REVERT: A 339 GLN cc_start: 0.7593 (tt0) cc_final: 0.7351 (mt0) REVERT: A 344 MET cc_start: 0.6417 (ttp) cc_final: 0.5754 (ttt) REVERT: A 356 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: A 360 MET cc_start: 0.7803 (mmm) cc_final: 0.7557 (mmm) REVERT: A 382 ASP cc_start: 0.7123 (m-30) cc_final: 0.6405 (t70) REVERT: A 393 GLU cc_start: 0.7829 (tt0) cc_final: 0.7267 (tt0) REVERT: A 410 GLN cc_start: 0.8007 (tt0) cc_final: 0.7785 (tt0) REVERT: A 412 THR cc_start: 0.7945 (p) cc_final: 0.7600 (p) REVERT: A 418 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8185 (t) REVERT: A 424 MET cc_start: 0.8223 (ptm) cc_final: 0.7994 (ptp) REVERT: A 439 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6674 (mp0) REVERT: A 444 LYS cc_start: 0.7398 (mttt) cc_final: 0.7154 (ttpp) REVERT: A 458 MET cc_start: 0.8383 (tpp) cc_final: 0.7658 (tpp) REVERT: A 469 ASP cc_start: 0.7459 (p0) cc_final: 0.7068 (p0) REVERT: A 487 MET cc_start: 0.7999 (tpt) cc_final: 0.7603 (tpt) REVERT: A 499 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6300 (mp0) REVERT: A 519 TYR cc_start: 0.7126 (m-80) cc_final: 0.6835 (t80) REVERT: A 633 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: A 664 VAL cc_start: 0.7807 (t) cc_final: 0.7493 (p) REVERT: A 675 ILE cc_start: 0.7446 (mm) cc_final: 0.7049 (pt) REVERT: A 708 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7448 (tt0) REVERT: A 711 LEU cc_start: 0.7722 (tt) cc_final: 0.7278 (mt) REVERT: A 728 GLU cc_start: 0.8594 (tt0) cc_final: 0.8355 (tt0) REVERT: A 744 MET cc_start: 0.8149 (tpp) cc_final: 0.7746 (mmt) REVERT: A 831 VAL cc_start: 0.8995 (t) cc_final: 0.8683 (m) REVERT: A 854 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7795 (ttm170) REVERT: A 931 ASP cc_start: 0.6896 (m-30) cc_final: 0.6467 (p0) REVERT: A 939 MET cc_start: 0.6347 (mmp) cc_final: 0.5926 (mmm) REVERT: A 947 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7746 (pm20) REVERT: A 948 GLN cc_start: 0.6607 (tt0) cc_final: 0.6227 (tp-100) REVERT: A 1020 LEU cc_start: 0.8617 (mt) cc_final: 0.8234 (tp) REVERT: A 1087 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: A 1090 MET cc_start: 0.8128 (mtt) cc_final: 0.7752 (mtp) REVERT: A 1108 ASP cc_start: 0.7698 (m-30) cc_final: 0.7119 (t0) REVERT: A 1183 LYS cc_start: 0.6670 (mttt) cc_final: 0.5926 (tptm) REVERT: A 1251 ARG cc_start: 0.7375 (mtp85) cc_final: 0.7159 (ttt90) REVERT: A 1287 ASN cc_start: 0.7680 (m110) cc_final: 0.7339 (m110) REVERT: A 1389 MET cc_start: 0.8406 (mmm) cc_final: 0.8190 (mmp) REVERT: A 1411 GLU cc_start: 0.5413 (tt0) cc_final: 0.4740 (mp0) REVERT: A 1520 ARG cc_start: 0.7924 (mmt180) cc_final: 0.7716 (mmt180) REVERT: A 1555 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6430 (mtp-110) REVERT: A 1559 GLU cc_start: 0.6289 (pt0) cc_final: 0.5870 (mt-10) REVERT: A 1607 ASP cc_start: 0.7440 (p0) cc_final: 0.6558 (m-30) REVERT: A 1651 LYS cc_start: 0.7989 (tptp) cc_final: 0.7361 (mptt) REVERT: A 1719 LYS cc_start: 0.6523 (ttpt) cc_final: 0.6261 (ttpp) REVERT: B 118 GLN cc_start: 0.7746 (mm110) cc_final: 0.7367 (mm110) REVERT: B 119 GLN cc_start: 0.6868 (mt0) cc_final: 0.6436 (mp10) REVERT: B 151 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7230 (mm110) REVERT: B 152 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6908 (mmt-90) REVERT: B 157 MET cc_start: 0.8267 (tpt) cc_final: 0.7786 (tpt) REVERT: B 190 MET cc_start: 0.5025 (mtp) cc_final: 0.4715 (tpt) REVERT: B 240 GLU cc_start: 0.6439 (pt0) cc_final: 0.6129 (pt0) outliers start: 63 outliers final: 11 residues processed: 466 average time/residue: 0.1466 time to fit residues: 98.2781 Evaluate side-chains 264 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 925 TYR Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 323 HIS A 335 HIS A 339 GLN A 407 ASN A 448 GLN A 456 ASN A 520 GLN A 562 ASN A 619 ASN A 623 ASN A 734 GLN A 884 GLN A 888 ASN A 899 HIS A 913 GLN A1017 ASN A1143 ASN A1191 GLN A1286 HIS A1287 ASN A1305 HIS A1384 GLN A1543 GLN B 11 GLN B 91 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127595 restraints weight = 20602.559| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.53 r_work: 0.3351 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16068 Z= 0.125 Angle : 0.570 9.027 21960 Z= 0.290 Chirality : 0.043 0.220 2521 Planarity : 0.004 0.038 2608 Dihedral : 8.246 58.885 2591 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.10 % Allowed : 12.45 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.84 (0.19), residues: 1766 helix: 1.81 (0.18), residues: 827 sheet: -0.38 (0.34), residues: 187 loop : -0.59 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 853 TYR 0.019 0.001 TYR A1000 PHE 0.015 0.002 PHE A1481 TRP 0.021 0.002 TRP A 885 HIS 0.005 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16068) covalent geometry : angle 0.57008 / 0.29 (21960) hydrogen bonds : bond 0.04454 / 2.92 ( 770) hydrogen bonds : angle 4.36859 / 3.17 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.632 Fit side-chains REVERT: A 354 ASN cc_start: 0.7256 (m-40) cc_final: 0.7027 (m-40) REVERT: A 378 PHE cc_start: 0.7653 (m-10) cc_final: 0.7400 (m-80) REVERT: A 393 GLU cc_start: 0.7925 (tt0) cc_final: 0.7612 (tt0) REVERT: A 424 MET cc_start: 0.8199 (ptm) cc_final: 0.7924 (ptp) REVERT: A 499 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6540 (mp0) REVERT: A 534 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7029 (t0) REVERT: A 572 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7611 (tp) REVERT: A 675 ILE cc_start: 0.7529 (mm) cc_final: 0.7211 (pt) REVERT: A 711 LEU cc_start: 0.7836 (tt) cc_final: 0.7343 (mt) REVERT: A 744 MET cc_start: 0.8183 (tpp) cc_final: 0.7606 (mmt) REVERT: A 940 ILE cc_start: 0.7577 (mt) cc_final: 0.7320 (mm) REVERT: A 1042 ASN cc_start: 0.5923 (m-40) cc_final: 0.5672 (p0) REVERT: A 1087 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: A 1143 ASN cc_start: 0.7003 (m-40) cc_final: 0.6709 (t0) REVERT: A 1275 TYR cc_start: 0.8391 (m-80) cc_final: 0.8188 (m-80) REVERT: A 1320 LYS cc_start: 0.7396 (ttpt) cc_final: 0.7157 (ttpt) REVERT: A 1329 ASN cc_start: 0.7479 (m-40) cc_final: 0.7236 (m110) REVERT: A 1411 GLU cc_start: 0.5599 (tt0) cc_final: 0.5213 (mt-10) REVERT: A 1491 ASN cc_start: 0.8346 (m-40) cc_final: 0.8135 (m110) REVERT: A 1552 ASN cc_start: 0.8064 (t0) cc_final: 0.7804 (m110) REVERT: A 1555 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7308 (mtp-110) REVERT: A 1610 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7877 (mttm) REVERT: A 1651 LYS cc_start: 0.8059 (tptp) cc_final: 0.7740 (mptt) REVERT: B 93 ASN cc_start: 0.6653 (m-40) cc_final: 0.6444 (m-40) REVERT: B 119 GLN cc_start: 0.7075 (mt0) cc_final: 0.6668 (mp10) REVERT: B 240 GLU cc_start: 0.6544 (pt0) cc_final: 0.6284 (pt0) REVERT: B 252 ASP cc_start: 0.6534 (m-30) cc_final: 0.6330 (m-30) outliers start: 50 outliers final: 29 residues processed: 306 average time/residue: 0.1339 time to fit residues: 60.6520 Evaluate side-chains 242 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 287 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS A 253 ASN A 323 HIS A 865 GLN A1076 ASN A1191 GLN A1490 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121836 restraints weight = 21055.721| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.59 r_work: 0.3232 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16068 Z= 0.200 Angle : 0.653 9.764 21960 Z= 0.328 Chirality : 0.047 0.334 2521 Planarity : 0.005 0.046 2608 Dihedral : 8.008 57.407 2570 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.09 % Allowed : 12.94 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.68 (0.19), residues: 1766 helix: 1.62 (0.17), residues: 823 sheet: -0.10 (0.33), residues: 205 loop : -0.69 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1518 TYR 0.026 0.002 TYR A1000 PHE 0.023 0.002 PHE A 423 TRP 0.021 0.002 TRP A 885 HIS 0.006 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (16068) covalent geometry : angle 0.65257 / 0.33 (21960) hydrogen bonds : bond 0.05229 / 3.42 ( 770) hydrogen bonds : angle 4.41997 / 3.21 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 223 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7213 (tp30) cc_final: 0.6907 (tt0) REVERT: A 98 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7750 (m) REVERT: A 126 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7323 (p) REVERT: A 209 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7130 (pt0) REVERT: A 364 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 374 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 378 PHE cc_start: 0.7706 (m-10) cc_final: 0.7451 (m-80) REVERT: A 393 GLU cc_start: 0.8202 (tt0) cc_final: 0.7997 (tt0) REVERT: A 534 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7066 (t0) REVERT: A 711 LEU cc_start: 0.8168 (tt) cc_final: 0.7555 (mt) REVERT: A 744 MET cc_start: 0.8336 (tpp) cc_final: 0.7815 (mmt) REVERT: A 908 MET cc_start: 0.5369 (mtt) cc_final: 0.4994 (mmm) REVERT: A 952 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.6330 (p90) REVERT: A 1042 ASN cc_start: 0.6071 (m-40) cc_final: 0.5696 (p0) REVERT: A 1087 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: A 1143 ASN cc_start: 0.6990 (m-40) cc_final: 0.6673 (t0) REVERT: A 1275 TYR cc_start: 0.8442 (m-80) cc_final: 0.8179 (m-80) REVERT: A 1329 ASN cc_start: 0.7474 (m-40) cc_final: 0.7145 (m110) REVERT: A 1348 PHE cc_start: 0.6200 (m-80) cc_final: 0.5712 (m-10) REVERT: A 1389 MET cc_start: 0.8622 (mmm) cc_final: 0.8412 (mmp) REVERT: A 1411 GLU cc_start: 0.5844 (tt0) cc_final: 0.5421 (mt-10) REVERT: A 1549 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.7529 (ptt90) REVERT: A 1552 ASN cc_start: 0.8010 (t0) cc_final: 0.7769 (m110) REVERT: B 93 ASN cc_start: 0.6584 (m-40) cc_final: 0.6307 (m-40) REVERT: B 109 MET cc_start: 0.7666 (mtt) cc_final: 0.7339 (mtt) REVERT: B 119 GLN cc_start: 0.7338 (mt0) cc_final: 0.6617 (mp10) REVERT: B 163 SER cc_start: 0.6125 (t) cc_final: 0.5754 (p) REVERT: B 240 GLU cc_start: 0.6559 (pt0) cc_final: 0.6265 (pt0) REVERT: B 252 ASP cc_start: 0.6492 (m-30) cc_final: 0.6261 (m-30) REVERT: B 255 MET cc_start: 0.8560 (mmt) cc_final: 0.8193 (mmt) outliers start: 66 outliers final: 36 residues processed: 277 average time/residue: 0.1243 time to fit residues: 52.4009 Evaluate side-chains 234 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 15 optimal weight: 0.0030 chunk 130 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 679 HIS A 865 GLN A1490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124495 restraints weight = 20700.022| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.68 r_work: 0.3265 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16068 Z= 0.140 Angle : 0.572 9.092 21960 Z= 0.283 Chirality : 0.043 0.268 2521 Planarity : 0.004 0.042 2608 Dihedral : 7.855 57.722 2569 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.72 % Allowed : 13.87 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.92 (0.19), residues: 1766 helix: 1.75 (0.18), residues: 827 sheet: 0.14 (0.34), residues: 205 loop : -0.55 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 853 TYR 0.023 0.001 TYR A1000 PHE 0.017 0.002 PHE B 306 TRP 0.014 0.001 TRP A 885 HIS 0.004 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (16068) covalent geometry : angle 0.57236 / 0.28 (21960) hydrogen bonds : bond 0.04331 / 2.84 ( 770) hydrogen bonds : angle 4.19431 / 3.06 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 0.594 Fit side-chains REVERT: A 98 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7644 (m) REVERT: A 126 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7148 (p) REVERT: A 147 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6613 (m-70) REVERT: A 303 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 344 MET cc_start: 0.7499 (ttp) cc_final: 0.7240 (ttt) REVERT: A 374 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 378 PHE cc_start: 0.7579 (m-10) cc_final: 0.7356 (m-80) REVERT: A 393 GLU cc_start: 0.7997 (tt0) cc_final: 0.7690 (tt0) REVERT: A 534 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6738 (p0) REVERT: A 711 LEU cc_start: 0.8134 (tt) cc_final: 0.7473 (mt) REVERT: A 744 MET cc_start: 0.8009 (tpp) cc_final: 0.7509 (mmt) REVERT: A 797 GLU cc_start: 0.6853 (tp30) cc_final: 0.6633 (tp30) REVERT: A 873 ARG cc_start: 0.5519 (mmt180) cc_final: 0.5264 (mmm160) REVERT: A 908 MET cc_start: 0.5269 (mtt) cc_final: 0.5012 (mmm) REVERT: A 952 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.6472 (p90) REVERT: A 1042 ASN cc_start: 0.5936 (m-40) cc_final: 0.5624 (p0) REVERT: A 1065 MET cc_start: 0.5578 (mtp) cc_final: 0.5361 (ptp) REVERT: A 1320 LYS cc_start: 0.7509 (ttpp) cc_final: 0.7275 (ttpt) REVERT: A 1348 PHE cc_start: 0.6186 (m-80) cc_final: 0.5560 (m-10) REVERT: A 1552 ASN cc_start: 0.7930 (t0) cc_final: 0.7722 (m110) REVERT: A 1559 GLU cc_start: 0.7235 (tt0) cc_final: 0.7020 (mt-10) REVERT: A 1610 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8018 (mttm) REVERT: B 93 ASN cc_start: 0.6391 (m-40) cc_final: 0.6099 (m-40) REVERT: B 109 MET cc_start: 0.7567 (mtt) cc_final: 0.7237 (mtt) REVERT: B 119 GLN cc_start: 0.7201 (mt0) cc_final: 0.6568 (mp10) REVERT: B 240 GLU cc_start: 0.6513 (pt0) cc_final: 0.6191 (pt0) REVERT: B 252 ASP cc_start: 0.6492 (m-30) cc_final: 0.6275 (m-30) outliers start: 60 outliers final: 37 residues processed: 250 average time/residue: 0.1281 time to fit residues: 48.1536 Evaluate side-chains 235 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1237 GLU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 194 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 162 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126079 restraints weight = 20709.531| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.57 r_work: 0.3306 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16068 Z= 0.123 Angle : 0.555 10.364 21960 Z= 0.272 Chirality : 0.042 0.326 2521 Planarity : 0.004 0.043 2608 Dihedral : 7.663 57.248 2566 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.47 % Allowed : 14.43 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.06 (0.19), residues: 1766 helix: 1.86 (0.18), residues: 827 sheet: 0.22 (0.35), residues: 205 loop : -0.46 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 853 TYR 0.023 0.001 TYR A1000 PHE 0.015 0.001 PHE A 977 TRP 0.011 0.001 TRP A 885 HIS 0.005 0.001 HIS A1305 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (16068) covalent geometry : angle 0.55466 / 0.27 (21960) hydrogen bonds : bond 0.04090 / 2.68 ( 770) hydrogen bonds : angle 4.09085 / 2.99 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 0.501 Fit side-chains REVERT: A 98 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7399 (m) REVERT: A 147 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6742 (m-70) REVERT: A 303 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 344 MET cc_start: 0.7700 (ttp) cc_final: 0.7415 (ttt) REVERT: A 364 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8521 (m) REVERT: A 374 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 378 PHE cc_start: 0.7683 (m-10) cc_final: 0.7412 (m-80) REVERT: A 534 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6813 (p0) REVERT: A 711 LEU cc_start: 0.8211 (tt) cc_final: 0.7532 (mt) REVERT: A 744 MET cc_start: 0.8202 (tpp) cc_final: 0.7703 (mmt) REVERT: A 799 LEU cc_start: 0.8500 (mt) cc_final: 0.8295 (mm) REVERT: A 873 ARG cc_start: 0.5520 (mmt180) cc_final: 0.5260 (mmm160) REVERT: A 952 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6492 (p90) REVERT: A 1042 ASN cc_start: 0.5867 (m-40) cc_final: 0.5571 (p0) REVERT: A 1136 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: A 1175 LEU cc_start: 0.8241 (mt) cc_final: 0.8017 (mt) REVERT: A 1320 LYS cc_start: 0.7490 (ttpp) cc_final: 0.7227 (ttpt) REVERT: A 1348 PHE cc_start: 0.6184 (m-80) cc_final: 0.5498 (m-10) REVERT: A 1552 ASN cc_start: 0.8015 (t0) cc_final: 0.7782 (m110) REVERT: A 1610 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7996 (mttm) REVERT: B 93 ASN cc_start: 0.6441 (m-40) cc_final: 0.6121 (m-40) REVERT: B 109 MET cc_start: 0.7654 (mtt) cc_final: 0.7311 (mtt) REVERT: B 119 GLN cc_start: 0.7183 (mt0) cc_final: 0.6598 (mp10) REVERT: B 240 GLU cc_start: 0.6586 (pt0) cc_final: 0.6253 (pt0) REVERT: B 252 ASP cc_start: 0.6523 (m-30) cc_final: 0.6300 (m-30) outliers start: 56 outliers final: 34 residues processed: 233 average time/residue: 0.1224 time to fit residues: 43.0304 Evaluate side-chains 226 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 258 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124121 restraints weight = 20793.218| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.65 r_work: 0.3242 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16068 Z= 0.158 Angle : 0.593 10.697 21960 Z= 0.293 Chirality : 0.044 0.338 2521 Planarity : 0.004 0.044 2608 Dihedral : 7.722 58.196 2566 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.72 % Allowed : 14.18 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.90 (0.19), residues: 1766 helix: 1.70 (0.18), residues: 828 sheet: 0.17 (0.34), residues: 212 loop : -0.52 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 853 TYR 0.025 0.001 TYR A1000 PHE 0.019 0.002 PHE A 423 TRP 0.013 0.001 TRP A 885 HIS 0.006 0.001 HIS A1305 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (16068) covalent geometry : angle 0.59323 / 0.29 (21960) hydrogen bonds : bond 0.04535 / 2.97 ( 770) hydrogen bonds : angle 4.18792 / 3.06 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.636 Fit side-chains REVERT: A 147 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6656 (m-70) REVERT: A 317 LEU cc_start: 0.7145 (mp) cc_final: 0.6899 (tp) REVERT: A 344 MET cc_start: 0.7539 (ttp) cc_final: 0.7268 (ttt) REVERT: A 364 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8549 (m) REVERT: A 374 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 534 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6724 (p0) REVERT: A 744 MET cc_start: 0.8017 (tpp) cc_final: 0.7539 (mmt) REVERT: A 873 ARG cc_start: 0.5434 (mmt180) cc_final: 0.5071 (mmm-85) REVERT: A 952 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.6264 (p90) REVERT: A 1175 LEU cc_start: 0.8182 (mt) cc_final: 0.7959 (mt) REVERT: A 1320 LYS cc_start: 0.7544 (ttpp) cc_final: 0.7170 (ttpt) REVERT: A 1348 PHE cc_start: 0.6248 (m-80) cc_final: 0.5583 (m-10) REVERT: A 1552 ASN cc_start: 0.7946 (t0) cc_final: 0.7733 (m110) REVERT: A 1610 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7952 (mttm) REVERT: B 93 ASN cc_start: 0.6433 (m-40) cc_final: 0.6211 (m110) REVERT: B 109 MET cc_start: 0.7583 (mtt) cc_final: 0.7276 (mtt) REVERT: B 252 ASP cc_start: 0.6579 (m-30) cc_final: 0.6295 (m-30) outliers start: 60 outliers final: 41 residues processed: 240 average time/residue: 0.1193 time to fit residues: 43.4411 Evaluate side-chains 229 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 258 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126364 restraints weight = 20472.648| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.55 r_work: 0.3305 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16068 Z= 0.124 Angle : 0.560 11.300 21960 Z= 0.273 Chirality : 0.042 0.319 2521 Planarity : 0.004 0.045 2608 Dihedral : 7.656 55.855 2566 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.41 % Allowed : 15.29 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.01 (0.20), residues: 1766 helix: 1.79 (0.18), residues: 834 sheet: 0.17 (0.34), residues: 212 loop : -0.47 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 853 TYR 0.024 0.001 TYR A1000 PHE 0.014 0.001 PHE A 423 TRP 0.012 0.001 TRP A1634 HIS 0.004 0.001 HIS A1305 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (16068) covalent geometry : angle 0.56028 / 0.27 (21960) hydrogen bonds : bond 0.04067 / 2.67 ( 770) hydrogen bonds : angle 4.08103 / 2.99 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.601 Fit side-chains REVERT: A 147 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6814 (m-70) REVERT: A 303 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 317 LEU cc_start: 0.7144 (mp) cc_final: 0.6859 (tp) REVERT: A 344 MET cc_start: 0.7651 (ttp) cc_final: 0.7376 (ttt) REVERT: A 364 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8543 (m) REVERT: A 534 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6720 (p0) REVERT: A 744 MET cc_start: 0.8173 (tpp) cc_final: 0.7698 (mmt) REVERT: A 799 LEU cc_start: 0.8493 (mt) cc_final: 0.8293 (mm) REVERT: A 952 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6281 (p90) REVERT: A 1136 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: A 1175 LEU cc_start: 0.8245 (mt) cc_final: 0.8025 (mt) REVERT: A 1320 LYS cc_start: 0.7489 (ttpp) cc_final: 0.7103 (ttpt) REVERT: A 1348 PHE cc_start: 0.6254 (m-80) cc_final: 0.5598 (m-10) REVERT: A 1552 ASN cc_start: 0.8041 (t0) cc_final: 0.7798 (m110) REVERT: A 1610 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8000 (mttm) REVERT: B 93 ASN cc_start: 0.6502 (m-40) cc_final: 0.6278 (m110) REVERT: B 109 MET cc_start: 0.7670 (mtt) cc_final: 0.7345 (mtt) REVERT: B 252 ASP cc_start: 0.6710 (m-30) cc_final: 0.6436 (m-30) outliers start: 55 outliers final: 43 residues processed: 230 average time/residue: 0.1296 time to fit residues: 45.0893 Evaluate side-chains 227 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 258 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 128 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 149 optimal weight: 0.0470 chunk 68 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129950 restraints weight = 20772.105| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.57 r_work: 0.3335 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16068 Z= 0.094 Angle : 0.524 11.654 21960 Z= 0.252 Chirality : 0.040 0.262 2521 Planarity : 0.004 0.045 2608 Dihedral : 7.494 57.125 2566 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.98 % Allowed : 16.47 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1766 helix: 2.08 (0.18), residues: 833 sheet: 0.25 (0.35), residues: 212 loop : -0.41 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 853 TYR 0.020 0.001 TYR A1000 PHE 0.017 0.001 PHE A 977 TRP 0.016 0.001 TRP A1634 HIS 0.003 0.000 HIS A1305 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (16068) covalent geometry : angle 0.52409 / 0.25 (21960) hydrogen bonds : bond 0.03345 / 2.20 ( 770) hydrogen bonds : angle 3.88204 / 2.86 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.607 Fit side-chains REVERT: A 108 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7969 (tttm) REVERT: A 126 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.6911 (p) REVERT: A 252 MET cc_start: 0.6818 (ttp) cc_final: 0.6569 (ttt) REVERT: A 287 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8296 (mm-40) REVERT: A 303 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 344 MET cc_start: 0.7595 (ttp) cc_final: 0.7323 (ttt) REVERT: A 356 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7107 (tt0) REVERT: A 364 THR cc_start: 0.8893 (m) cc_final: 0.8552 (m) REVERT: A 378 PHE cc_start: 0.7644 (m-10) cc_final: 0.7244 (m-80) REVERT: A 416 ARG cc_start: 0.7672 (ttm110) cc_final: 0.6633 (ttt90) REVERT: A 534 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6782 (p0) REVERT: A 832 VAL cc_start: 0.8945 (t) cc_final: 0.8724 (m) REVERT: A 952 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.6650 (p90) REVERT: A 1136 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: A 1175 LEU cc_start: 0.8273 (mt) cc_final: 0.8046 (mt) REVERT: A 1320 LYS cc_start: 0.7532 (ttpp) cc_final: 0.6969 (ttpt) REVERT: A 1552 ASN cc_start: 0.7986 (t0) cc_final: 0.7727 (m110) REVERT: A 1690 GLU cc_start: 0.7140 (tp30) cc_final: 0.6919 (tp30) REVERT: B 109 MET cc_start: 0.7677 (mtt) cc_final: 0.7358 (mtt) REVERT: B 252 ASP cc_start: 0.6615 (m-30) cc_final: 0.6382 (m-30) outliers start: 32 outliers final: 21 residues processed: 226 average time/residue: 0.1263 time to fit residues: 43.2405 Evaluate side-chains 211 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 258 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 0.0670 chunk 129 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 119 optimal weight: 8.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129516 restraints weight = 20668.978| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.60 r_work: 0.3334 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16068 Z= 0.094 Angle : 0.518 11.936 21960 Z= 0.248 Chirality : 0.040 0.225 2521 Planarity : 0.004 0.045 2608 Dihedral : 7.465 57.806 2566 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.73 % Allowed : 17.21 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.35 (0.20), residues: 1766 helix: 2.15 (0.18), residues: 834 sheet: 0.30 (0.35), residues: 214 loop : -0.39 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 416 TYR 0.020 0.001 TYR A1000 PHE 0.024 0.001 PHE A 920 TRP 0.013 0.001 TRP A1634 HIS 0.003 0.000 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (16068) covalent geometry : angle 0.51812 / 0.25 (21960) hydrogen bonds : bond 0.03383 / 2.23 ( 770) hydrogen bonds : angle 3.85270 / 2.84 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.582 Fit side-chains REVERT: A 108 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8041 (tttm) REVERT: A 126 THR cc_start: 0.7337 (OUTLIER) cc_final: 0.6893 (p) REVERT: A 252 MET cc_start: 0.6738 (ttp) cc_final: 0.6501 (ttt) REVERT: A 289 LYS cc_start: 0.8330 (mtmt) cc_final: 0.8077 (mmtt) REVERT: A 303 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 344 MET cc_start: 0.7639 (ttp) cc_final: 0.7231 (ttt) REVERT: A 364 THR cc_start: 0.8855 (m) cc_final: 0.8509 (m) REVERT: A 378 PHE cc_start: 0.7544 (m-10) cc_final: 0.7165 (m-80) REVERT: A 416 ARG cc_start: 0.7566 (ttm110) cc_final: 0.6622 (ttt90) REVERT: A 534 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6784 (p0) REVERT: A 711 LEU cc_start: 0.8242 (tt) cc_final: 0.7661 (mt) REVERT: A 952 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6630 (p90) REVERT: A 1136 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: A 1175 LEU cc_start: 0.8272 (mt) cc_final: 0.8037 (mt) REVERT: A 1320 LYS cc_start: 0.7657 (ttpp) cc_final: 0.7139 (ttpt) REVERT: A 1552 ASN cc_start: 0.7975 (t0) cc_final: 0.7557 (m-40) REVERT: B 109 MET cc_start: 0.7700 (mtt) cc_final: 0.7419 (mtt) REVERT: B 252 ASP cc_start: 0.6634 (m-30) cc_final: 0.6393 (m-30) outliers start: 28 outliers final: 21 residues processed: 216 average time/residue: 0.1281 time to fit residues: 41.4363 Evaluate side-chains 210 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 258 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126766 restraints weight = 20629.914| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.60 r_work: 0.3296 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16068 Z= 0.125 Angle : 0.557 12.170 21960 Z= 0.269 Chirality : 0.041 0.213 2521 Planarity : 0.004 0.045 2608 Dihedral : 7.533 58.279 2566 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 17.09 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.19 (0.20), residues: 1766 helix: 1.98 (0.18), residues: 835 sheet: 0.30 (0.35), residues: 214 loop : -0.45 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 416 TYR 0.023 0.001 TYR A1000 PHE 0.023 0.001 PHE A 920 TRP 0.010 0.001 TRP A1292 HIS 0.004 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16068) covalent geometry : angle 0.55720 / 0.27 (21960) hydrogen bonds : bond 0.03984 / 2.62 ( 770) hydrogen bonds : angle 3.95964 / 2.90 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8101 (tttm) REVERT: A 252 MET cc_start: 0.6802 (ttp) cc_final: 0.6521 (ttt) REVERT: A 303 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 342 GLN cc_start: 0.8007 (tp40) cc_final: 0.7313 (mm-40) REVERT: A 344 MET cc_start: 0.7633 (ttp) cc_final: 0.7232 (ttt) REVERT: A 364 THR cc_start: 0.8875 (m) cc_final: 0.8544 (m) REVERT: A 378 PHE cc_start: 0.7555 (m-10) cc_final: 0.7178 (m-80) REVERT: A 416 ARG cc_start: 0.7654 (ttm110) cc_final: 0.6627 (ttt90) REVERT: A 534 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6842 (p0) REVERT: A 797 GLU cc_start: 0.6915 (tp30) cc_final: 0.6711 (tp30) REVERT: A 920 PHE cc_start: 0.6755 (t80) cc_final: 0.6538 (t80) REVERT: A 952 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.6332 (p90) REVERT: A 1136 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: A 1175 LEU cc_start: 0.8284 (mt) cc_final: 0.8041 (mt) REVERT: A 1320 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7173 (ttpt) REVERT: A 1552 ASN cc_start: 0.7989 (t0) cc_final: 0.7774 (m110) REVERT: B 109 MET cc_start: 0.7682 (mtt) cc_final: 0.7371 (mtt) REVERT: B 252 ASP cc_start: 0.6764 (m-30) cc_final: 0.6519 (m-30) outliers start: 32 outliers final: 24 residues processed: 212 average time/residue: 0.1239 time to fit residues: 39.9024 Evaluate side-chains 212 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1137 PHE Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 258 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.0570 chunk 41 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 129 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124955 restraints weight = 20544.843| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.71 r_work: 0.3266 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16068 Z= 0.148 Angle : 0.587 12.454 21960 Z= 0.285 Chirality : 0.043 0.241 2521 Planarity : 0.004 0.046 2608 Dihedral : 7.668 57.704 2566 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.98 % Allowed : 17.52 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.00 (0.20), residues: 1766 helix: 1.77 (0.18), residues: 834 sheet: 0.34 (0.36), residues: 195 loop : -0.51 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 416 TYR 0.024 0.001 TYR A1000 PHE 0.021 0.002 PHE A 920 TRP 0.012 0.001 TRP A 885 HIS 0.004 0.001 HIS A1305 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16068) covalent geometry : angle 0.58673 / 0.29 (21960) hydrogen bonds : bond 0.04393 / 2.89 ( 770) hydrogen bonds : angle 4.10036 / 2.99 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.35 seconds wall clock time: 67 minutes 0.58 seconds (4020.58 seconds total)