Starting phenix.real_space_refine on Wed Mar 4 19:20:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v6c_31742/03_2026/7v6c_31742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v6c_31742/03_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_31742/03_2026/7v6c_31742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v6c_31742/03_2026/7v6c_31742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v6c_31742/03_2026/7v6c_31742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v6c_31742/03_2026/7v6c_31742.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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: {'RNA': 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, 'RNA': 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: 2 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, 'RNA': 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: 2 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: 3.01, per 1000 atoms: 0.19 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: 1.06 Conformation dependent library (CDL) restraints added in 492.7 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: 1.69 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: 3.58 Time building geometry restraints manager: 1.42 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: 16025 1.74 - 3.47: 5366 3.47 - 5.21: 522 5.21 - 6.94: 48 6.94 - 8.68: 5 Bond angle restraints: 21966 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 21961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8862 17.94 - 35.87: 637 35.87 - 53.81: 198 53.81 - 71.75: 82 71.75 - 89.69: 21 Dihedral angle restraints: 9800 sinusoidal: 4493 harmonic: 5307 Sorted by residual: 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 dihedral pdb=" C PHE B 306 " pdb=" N PHE B 306 " pdb=" CA PHE B 306 " pdb=" CB PHE B 306 " ideal model delta harmonic sigma weight residual -122.60 -132.03 9.43 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C ILE A1431 " pdb=" N ILE A1431 " pdb=" CA ILE A1431 " pdb=" CB ILE A1431 " ideal model delta harmonic sigma weight residual -122.00 -131.02 9.02 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 9797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1264 0.063 - 0.126: 881 0.126 - 0.188: 312 0.188 - 0.251: 57 0.251 - 0.314: 7 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 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.46e+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 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA PHE B 306 " pdb=" N PHE B 306 " pdb=" C PHE B 306 " pdb=" CB PHE B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.440 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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= 0.882 Angle : 1.558 8.680 21966 Z= 1.181 Chirality : 0.088 0.314 2521 Planarity : 0.006 0.064 2608 Dihedral : 15.168 89.685 6350 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 covalent geometry : bond 0.01179 (16068) covalent geometry : angle 1.55779 (21966) hydrogen bonds : bond 0.19341 ( 770) hydrogen bonds : angle 7.01532 ( 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 : 0.435 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: 0.1384 time to fit residues: 92.3909 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 : 0.592 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.158766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127589 restraints weight = 20618.035| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.52 r_work: 0.3353 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16068 Z= 0.123 Angle : 0.535 8.965 21966 Z= 0.285 Chirality : 0.039 0.232 2521 Planarity : 0.004 0.038 2608 Dihedral : 12.658 73.416 2775 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.28 % Allowed : 12.26 % 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: 0.81 (0.19), residues: 1766 helix: 1.79 (0.18), residues: 828 sheet: -0.39 (0.34), residues: 187 loop : -0.61 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 853 TYR 0.018 0.001 TYR A1000 PHE 0.016 0.002 PHE A1481 TRP 0.021 0.002 TRP A 885 HIS 0.005 0.001 HIS A1519 Details of bonding type rmsd covalent geometry : bond 0.00271 (16068) covalent geometry : angle 0.53450 (21966) hydrogen bonds : bond 0.04572 ( 770) hydrogen bonds : angle 4.40008 ( 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 321 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 0.576 Fit side-chains REVERT: A 354 ASN cc_start: 0.7265 (m-40) cc_final: 0.7036 (m-40) REVERT: A 378 PHE cc_start: 0.7659 (m-10) cc_final: 0.7436 (m-80) REVERT: A 393 GLU cc_start: 0.7898 (tt0) cc_final: 0.7571 (tt0) REVERT: A 418 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8198 (t) REVERT: A 424 MET cc_start: 0.8207 (ptm) cc_final: 0.7929 (ptp) REVERT: A 499 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6539 (mp0) REVERT: A 534 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7004 (t0) REVERT: A 572 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7623 (tp) REVERT: A 674 SER cc_start: 0.7474 (m) cc_final: 0.7252 (p) REVERT: A 675 ILE cc_start: 0.7577 (mm) cc_final: 0.7225 (pt) REVERT: A 711 LEU cc_start: 0.7840 (tt) cc_final: 0.7352 (mt) REVERT: A 728 GLU cc_start: 0.8009 (tt0) cc_final: 0.7806 (tt0) REVERT: A 744 MET cc_start: 0.8199 (tpp) cc_final: 0.7615 (mmt) REVERT: A 940 ILE cc_start: 0.7572 (mt) cc_final: 0.7313 (mm) REVERT: A 1042 ASN cc_start: 0.5755 (m-40) cc_final: 0.5499 (p0) REVERT: A 1087 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: A 1143 ASN cc_start: 0.7018 (m-40) cc_final: 0.6702 (t0) REVERT: A 1275 TYR cc_start: 0.8390 (m-80) cc_final: 0.8188 (m-80) REVERT: A 1320 LYS cc_start: 0.7404 (ttpt) cc_final: 0.7167 (ttpt) REVERT: A 1329 ASN cc_start: 0.7480 (m-40) cc_final: 0.7230 (m110) REVERT: A 1411 GLU cc_start: 0.5607 (tt0) cc_final: 0.5218 (mt-10) REVERT: A 1491 ASN cc_start: 0.8348 (m-40) cc_final: 0.8122 (m110) REVERT: A 1552 ASN cc_start: 0.8040 (t0) cc_final: 0.7796 (m110) REVERT: A 1555 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7287 (mtp-110) REVERT: A 1651 LYS cc_start: 0.8056 (tptp) cc_final: 0.7746 (mptt) REVERT: B 93 ASN cc_start: 0.6719 (m-40) cc_final: 0.6499 (m-40) REVERT: B 119 GLN cc_start: 0.7062 (mt0) cc_final: 0.6665 (mp10) REVERT: B 190 MET cc_start: 0.5780 (mtp) cc_final: 0.5578 (tpp) REVERT: B 240 GLU cc_start: 0.6503 (pt0) cc_final: 0.6198 (pt0) REVERT: B 252 ASP cc_start: 0.6551 (m-30) cc_final: 0.6348 (m-30) REVERT: B 270 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7682 (p) outliers start: 53 outliers final: 28 residues processed: 307 average time/residue: 0.1256 time to fit residues: 56.7468 Evaluate side-chains 239 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 418 VAL 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 270 VAL 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: 5.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 122 optimal weight: 0.0010 chunk 142 optimal weight: 7.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS A 865 GLN A1017 ASN A1076 ASN A1191 GLN A1490 ASN B 118 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122345 restraints weight = 21004.470| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.61 r_work: 0.3273 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16068 Z= 0.153 Angle : 0.560 9.269 21966 Z= 0.292 Chirality : 0.041 0.310 2521 Planarity : 0.004 0.040 2608 Dihedral : 12.356 73.701 2755 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.84 % Allowed : 12.69 % Favored : 83.47 % 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: 0.89 (0.19), residues: 1766 helix: 1.83 (0.18), residues: 821 sheet: -0.10 (0.33), residues: 205 loop : -0.60 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1397 TYR 0.024 0.002 TYR A1000 PHE 0.019 0.002 PHE A1001 TRP 0.019 0.002 TRP A 885 HIS 0.005 0.001 HIS A 899 Details of bonding type rmsd covalent geometry : bond 0.00359 (16068) covalent geometry : angle 0.56035 (21966) hydrogen bonds : bond 0.04679 ( 770) hydrogen bonds : angle 4.25513 ( 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 290 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 98 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7488 (p) REVERT: A 126 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7280 (p) REVERT: A 206 LYS cc_start: 0.7294 (mptt) cc_final: 0.7051 (mttm) REVERT: A 209 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6970 (pt0) REVERT: A 360 MET cc_start: 0.7971 (mmm) cc_final: 0.7752 (mmm) REVERT: A 374 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 378 PHE cc_start: 0.7727 (m-10) cc_final: 0.7455 (m-80) REVERT: A 393 GLU cc_start: 0.8159 (tt0) cc_final: 0.7748 (tt0) REVERT: A 414 GLU cc_start: 0.7102 (mp0) cc_final: 0.6661 (mp0) REVERT: A 499 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6365 (mp0) REVERT: A 534 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6879 (p0) REVERT: A 627 ARG cc_start: 0.7004 (mtm110) cc_final: 0.6714 (mtp85) REVERT: A 675 ILE cc_start: 0.7531 (mm) cc_final: 0.7080 (pt) REVERT: A 711 LEU cc_start: 0.7979 (tt) cc_final: 0.7444 (mt) REVERT: A 744 MET cc_start: 0.8257 (tpp) cc_final: 0.7897 (mmt) REVERT: A 797 GLU cc_start: 0.6957 (tp30) cc_final: 0.6750 (tp30) REVERT: A 908 MET cc_start: 0.5280 (mtt) cc_final: 0.4936 (mmm) REVERT: A 918 TYR cc_start: 0.6528 (t80) cc_final: 0.6293 (t80) REVERT: A 952 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6480 (p90) REVERT: A 1042 ASN cc_start: 0.6140 (m-40) cc_final: 0.5752 (p0) REVERT: A 1087 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: A 1143 ASN cc_start: 0.6882 (m-40) cc_final: 0.6557 (t0) REVERT: A 1329 ASN cc_start: 0.7467 (m-40) cc_final: 0.7162 (m110) REVERT: A 1348 PHE cc_start: 0.6118 (m-80) cc_final: 0.5616 (m-10) REVERT: A 1389 MET cc_start: 0.8556 (mmm) cc_final: 0.8353 (mmp) REVERT: A 1411 GLU cc_start: 0.5667 (tt0) cc_final: 0.5235 (mt-10) REVERT: A 1549 ARG cc_start: 0.7784 (ptp-170) cc_final: 0.7498 (ptt90) REVERT: A 1552 ASN cc_start: 0.7959 (t0) cc_final: 0.7718 (m110) REVERT: A 1689 MET cc_start: 0.7008 (mmm) cc_final: 0.6705 (mmt) REVERT: B 109 MET cc_start: 0.7716 (mtt) cc_final: 0.7388 (mtt) REVERT: B 119 GLN cc_start: 0.7230 (mt0) cc_final: 0.6892 (pt0) REVERT: B 163 SER cc_start: 0.6061 (t) cc_final: 0.5681 (p) REVERT: B 240 GLU cc_start: 0.6512 (pt0) cc_final: 0.6193 (pt0) REVERT: B 255 MET cc_start: 0.8539 (mmt) cc_final: 0.8025 (mmt) outliers start: 62 outliers final: 31 residues processed: 277 average time/residue: 0.1212 time to fit residues: 50.0305 Evaluate side-chains 225 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain A residue 186 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 865 GLN A1017 ASN A1287 ASN A1490 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124640 restraints weight = 20852.335| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.57 r_work: 0.3316 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3734 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= 0.116 Angle : 0.503 8.770 21966 Z= 0.260 Chirality : 0.038 0.320 2521 Planarity : 0.004 0.041 2608 Dihedral : 12.178 73.553 2752 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.34 % Allowed : 13.87 % Favored : 82.79 % 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: 1.94 (0.18), residues: 827 sheet: 0.20 (0.34), residues: 195 loop : -0.55 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1397 TYR 0.021 0.001 TYR A1000 PHE 0.013 0.001 PHE A1481 TRP 0.012 0.001 TRP A 885 HIS 0.005 0.001 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.00265 (16068) covalent geometry : angle 0.50297 (21966) hydrogen bonds : bond 0.04020 ( 770) hydrogen bonds : angle 4.08387 ( 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 256 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 0.587 Fit side-chains REVERT: A 98 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7476 (m) REVERT: A 126 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7084 (p) REVERT: A 147 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6681 (m-70) REVERT: A 206 LYS cc_start: 0.7339 (mptt) cc_final: 0.7127 (mttm) REVERT: A 303 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 344 MET cc_start: 0.7517 (ttp) cc_final: 0.7250 (ttt) REVERT: A 364 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8413 (m) REVERT: A 378 PHE cc_start: 0.7621 (m-10) cc_final: 0.7380 (m-80) REVERT: A 499 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6276 (mp0) REVERT: A 534 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6878 (p0) REVERT: A 711 LEU cc_start: 0.8035 (tt) cc_final: 0.7484 (mt) REVERT: A 744 MET cc_start: 0.8150 (tpp) cc_final: 0.7642 (mmt) REVERT: A 952 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.6573 (p90) REVERT: A 1042 ASN cc_start: 0.5937 (m-40) cc_final: 0.5653 (p0) REVERT: A 1136 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: A 1320 LYS cc_start: 0.7434 (ttpp) cc_final: 0.7017 (ttpt) REVERT: A 1411 GLU cc_start: 0.5832 (tt0) cc_final: 0.5419 (mt-10) REVERT: A 1549 ARG cc_start: 0.7800 (ptp-170) cc_final: 0.7388 (ptt90) REVERT: A 1552 ASN cc_start: 0.7960 (t0) cc_final: 0.7747 (m110) REVERT: A 1610 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7984 (mttm) REVERT: B 109 MET cc_start: 0.7661 (mtt) cc_final: 0.7366 (mtt) REVERT: B 240 GLU cc_start: 0.6581 (pt0) cc_final: 0.6249 (pt0) outliers start: 54 outliers final: 35 residues processed: 245 average time/residue: 0.1216 time to fit residues: 44.8181 Evaluate side-chains 228 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 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 952 TYR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 MET 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 1287 ASN Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1424 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 162 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 417 ASN A 456 ASN A1017 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 = 0.156072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125411 restraints weight = 20884.273| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.61 r_work: 0.3254 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16068 Z= 0.150 Angle : 0.547 10.530 21966 Z= 0.281 Chirality : 0.040 0.340 2521 Planarity : 0.004 0.042 2608 Dihedral : 12.171 73.668 2749 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.72 % Allowed : 14.30 % Favored : 81.98 % 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: 0.99 (0.19), residues: 1766 helix: 1.77 (0.18), residues: 827 sheet: 0.37 (0.35), residues: 204 loop : -0.52 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1397 TYR 0.024 0.001 TYR A1000 PHE 0.018 0.002 PHE A 423 TRP 0.012 0.001 TRP A 885 HIS 0.005 0.001 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.00356 (16068) covalent geometry : angle 0.54737 (21966) hydrogen bonds : bond 0.04485 ( 770) hydrogen bonds : angle 4.17619 ( 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 254 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 0.462 Fit side-chains REVERT: A 98 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7501 (m) REVERT: A 126 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7068 (p) REVERT: A 147 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6648 (m-70) REVERT: A 253 ASN cc_start: 0.6157 (OUTLIER) cc_final: 0.5922 (p0) REVERT: A 303 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 344 MET cc_start: 0.7594 (ttp) cc_final: 0.7325 (ttt) REVERT: A 364 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8500 (m) REVERT: A 374 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 378 PHE cc_start: 0.7668 (m-10) cc_final: 0.7436 (m-80) REVERT: A 534 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6804 (p0) REVERT: A 711 LEU cc_start: 0.8155 (tt) cc_final: 0.7456 (mt) REVERT: A 744 MET cc_start: 0.8023 (tpp) cc_final: 0.7523 (mmt) REVERT: A 873 ARG cc_start: 0.5529 (mmt180) cc_final: 0.5085 (mmm-85) REVERT: A 908 MET cc_start: 0.5556 (mtt) cc_final: 0.4847 (mmm) REVERT: A 952 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.6499 (p90) REVERT: A 1042 ASN cc_start: 0.5915 (m-40) cc_final: 0.5623 (p0) REVERT: A 1175 LEU cc_start: 0.8151 (mt) cc_final: 0.7925 (mt) REVERT: A 1320 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7087 (ttpt) REVERT: A 1348 PHE cc_start: 0.6190 (m-80) cc_final: 0.5504 (m-10) REVERT: A 1549 ARG cc_start: 0.7791 (ptp-170) cc_final: 0.7563 (ptt90) REVERT: A 1552 ASN cc_start: 0.7969 (t0) cc_final: 0.7750 (m110) REVERT: A 1610 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7979 (mttm) REVERT: A 1689 MET cc_start: 0.7141 (mmm) cc_final: 0.6871 (mmt) REVERT: B 109 MET cc_start: 0.7541 (mtt) cc_final: 0.7223 (mtt) REVERT: B 240 GLU cc_start: 0.6569 (pt0) cc_final: 0.6247 (pt0) outliers start: 60 outliers final: 44 residues processed: 243 average time/residue: 0.1217 time to fit residues: 44.3894 Evaluate side-chains 237 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU 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 193 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 253 ASN 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 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 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 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 946 THR 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 1065 MET 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 1237 GLU Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1301 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 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 42 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 679 HIS A1017 ASN A1287 ASN B 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122539 restraints weight = 20880.927| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.65 r_work: 0.3233 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16068 Z= 0.194 Angle : 0.598 11.082 21966 Z= 0.308 Chirality : 0.042 0.356 2521 Planarity : 0.005 0.043 2608 Dihedral : 12.285 73.738 2749 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.09 % Allowed : 14.24 % Favored : 81.67 % 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: 0.69 (0.19), residues: 1766 helix: 1.50 (0.18), residues: 827 sheet: 0.21 (0.35), residues: 204 loop : -0.64 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 853 TYR 0.026 0.002 TYR A1000 PHE 0.023 0.002 PHE A 423 TRP 0.016 0.002 TRP A 885 HIS 0.006 0.001 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.00468 (16068) covalent geometry : angle 0.59826 (21966) hydrogen bonds : bond 0.04980 ( 770) hydrogen bonds : angle 4.34672 ( 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 256 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 0.419 Fit side-chains REVERT: A 98 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7680 (m) REVERT: A 122 MET cc_start: 0.8228 (ttp) cc_final: 0.7988 (ttm) REVERT: A 147 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6596 (m-70) REVERT: A 303 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 317 LEU cc_start: 0.7092 (mp) cc_final: 0.6842 (tp) REVERT: A 344 MET cc_start: 0.7537 (ttp) cc_final: 0.7275 (ttt) REVERT: A 364 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8613 (m) REVERT: A 374 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 534 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6681 (p0) REVERT: A 744 MET cc_start: 0.8119 (tpp) cc_final: 0.7649 (mmt) REVERT: A 853 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7702 (mtp-110) REVERT: A 873 ARG cc_start: 0.5404 (mmt180) cc_final: 0.5112 (mmm-85) REVERT: A 908 MET cc_start: 0.5515 (mtt) cc_final: 0.4968 (mmm) REVERT: A 952 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.6182 (p90) REVERT: A 1042 ASN cc_start: 0.5904 (m-40) cc_final: 0.5686 (p0) REVERT: A 1175 LEU cc_start: 0.8151 (mt) cc_final: 0.7940 (mt) REVERT: A 1320 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7339 (ttpt) REVERT: A 1348 PHE cc_start: 0.6280 (m-80) cc_final: 0.5625 (m-10) REVERT: A 1549 ARG cc_start: 0.7589 (ptp-170) cc_final: 0.7383 (ptt90) REVERT: A 1552 ASN cc_start: 0.7977 (t0) cc_final: 0.7764 (m110) REVERT: B 109 MET cc_start: 0.7564 (mtt) cc_final: 0.7270 (mtt) REVERT: B 267 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6284 (mt) outliers start: 66 outliers final: 44 residues processed: 242 average time/residue: 0.1190 time to fit residues: 44.0038 Evaluate side-chains 232 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU 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 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 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 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 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 1065 MET 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 1237 GLU Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1301 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 25 SER Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 267 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 145 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 679 HIS A1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127453 restraints weight = 20533.603| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.62 r_work: 0.3299 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4343 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= 0.101 Angle : 0.503 11.016 21966 Z= 0.255 Chirality : 0.037 0.310 2521 Planarity : 0.004 0.044 2608 Dihedral : 12.102 73.541 2749 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.91 % Allowed : 16.16 % 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: 1.10 (0.20), residues: 1766 helix: 1.87 (0.18), residues: 827 sheet: 0.40 (0.36), residues: 204 loop : -0.46 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 853 TYR 0.022 0.001 TYR A1000 PHE 0.016 0.001 PHE A 977 TRP 0.014 0.001 TRP A1634 HIS 0.004 0.001 HIS A1286 Details of bonding type rmsd covalent geometry : bond 0.00223 (16068) covalent geometry : angle 0.50337 (21966) hydrogen bonds : bond 0.03770 ( 770) hydrogen bonds : angle 4.05406 ( 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: 47 poor density : 195 time to evaluate : 0.548 Fit side-chains REVERT: A 98 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7461 (m) REVERT: A 108 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8085 (tttm) REVERT: A 147 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6768 (m-70) REVERT: A 303 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8469 (mp) REVERT: A 344 MET cc_start: 0.7634 (ttp) cc_final: 0.7339 (ttt) REVERT: A 364 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8600 (m) REVERT: A 534 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6755 (p0) REVERT: A 744 MET cc_start: 0.8260 (tpp) cc_final: 0.7782 (mmt) REVERT: A 873 ARG cc_start: 0.5435 (mmt180) cc_final: 0.5225 (mmm160) REVERT: A 908 MET cc_start: 0.5456 (mtt) cc_final: 0.5096 (mmm) REVERT: A 952 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6506 (p90) REVERT: A 977 PHE cc_start: 0.6969 (t80) cc_final: 0.6750 (t80) REVERT: A 1136 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: A 1175 LEU cc_start: 0.8256 (mt) cc_final: 0.8040 (mt) REVERT: A 1320 LYS cc_start: 0.7569 (ttpp) cc_final: 0.6969 (ttpt) REVERT: A 1348 PHE cc_start: 0.6205 (m-80) cc_final: 0.5468 (m-10) REVERT: A 1552 ASN cc_start: 0.8041 (t0) cc_final: 0.7816 (m110) REVERT: A 1610 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8040 (mttm) REVERT: A 1689 MET cc_start: 0.7206 (mmm) cc_final: 0.6957 (mmt) REVERT: B 109 MET cc_start: 0.7665 (mtt) cc_final: 0.7380 (mtt) outliers start: 47 outliers final: 23 residues processed: 233 average time/residue: 0.1168 time to fit residues: 40.6669 Evaluate side-chains 213 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 389 LEU Chi-restraints excluded: chain A residue 400 CYS 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 596 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 1065 MET 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 1287 ASN Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 155 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 128 optimal weight: 0.0670 chunk 17 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 145 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 679 HIS A1017 ASN A1287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.159976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129893 restraints weight = 20800.162| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.63 r_work: 0.3339 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4507 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= 0.092 Angle : 0.484 12.223 21966 Z= 0.243 Chirality : 0.037 0.268 2521 Planarity : 0.004 0.045 2608 Dihedral : 11.959 73.482 2749 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.17 % Allowed : 16.97 % Favored : 80.87 % 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: 1.33 (0.20), residues: 1766 helix: 2.09 (0.18), residues: 827 sheet: 0.37 (0.35), residues: 214 loop : -0.35 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 416 TYR 0.021 0.001 TYR A1000 PHE 0.013 0.001 PHE A 977 TRP 0.015 0.001 TRP A1634 HIS 0.003 0.000 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.00202 (16068) covalent geometry : angle 0.48376 (21966) hydrogen bonds : bond 0.03371 ( 770) hydrogen bonds : angle 3.87702 ( 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 232 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.588 Fit side-chains REVERT: A 108 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8010 (tttm) REVERT: A 126 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 147 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6817 (m-70) REVERT: A 252 MET cc_start: 0.6896 (ttp) cc_final: 0.6692 (ttt) REVERT: A 303 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8416 (mp) REVERT: A 344 MET cc_start: 0.7638 (ttp) cc_final: 0.7351 (ttt) REVERT: A 356 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7158 (tt0) REVERT: A 364 THR cc_start: 0.8881 (m) cc_final: 0.8537 (m) REVERT: A 378 PHE cc_start: 0.7601 (m-10) cc_final: 0.7243 (m-80) REVERT: A 416 ARG cc_start: 0.7592 (ttm110) cc_final: 0.6606 (ttt90) REVERT: A 711 LEU cc_start: 0.8243 (tt) cc_final: 0.7646 (mt) REVERT: A 952 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.6706 (p90) REVERT: A 1136 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: A 1175 LEU cc_start: 0.8265 (mt) cc_final: 0.8046 (mt) REVERT: A 1320 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7166 (ttpt) REVERT: A 1552 ASN cc_start: 0.7974 (t0) cc_final: 0.7526 (m-40) REVERT: B 109 MET cc_start: 0.7636 (mtt) cc_final: 0.7340 (mtt) outliers start: 35 outliers final: 19 residues processed: 226 average time/residue: 0.1202 time to fit residues: 41.2839 Evaluate side-chains 204 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 HIS 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 389 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 MET 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 1356 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 679 HIS A1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126355 restraints weight = 20771.503| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.58 r_work: 0.3288 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16068 Z= 0.135 Angle : 0.539 11.765 21966 Z= 0.270 Chirality : 0.039 0.257 2521 Planarity : 0.004 0.044 2608 Dihedral : 12.056 73.679 2749 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.92 % Allowed : 17.46 % Favored : 80.62 % 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: 1.11 (0.20), residues: 1766 helix: 1.89 (0.18), residues: 834 sheet: 0.33 (0.35), residues: 214 loop : -0.47 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 853 TYR 0.023 0.001 TYR A1000 PHE 0.016 0.001 PHE A1001 TRP 0.011 0.001 TRP A1292 HIS 0.004 0.001 HIS A1519 Details of bonding type rmsd covalent geometry : bond 0.00320 (16068) covalent geometry : angle 0.53930 (21966) hydrogen bonds : bond 0.04146 ( 770) hydrogen bonds : angle 4.03229 ( 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 213 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.437 Fit side-chains REVERT: A 108 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8092 (tttm) REVERT: A 147 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6803 (m-70) REVERT: A 303 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 344 MET cc_start: 0.7628 (ttp) cc_final: 0.7233 (ttt) REVERT: A 378 PHE cc_start: 0.7687 (m-10) cc_final: 0.7329 (m-80) REVERT: A 952 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6414 (p90) REVERT: A 1136 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: A 1175 LEU cc_start: 0.8283 (mt) cc_final: 0.8044 (mt) REVERT: A 1320 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7288 (ttpt) REVERT: A 1552 ASN cc_start: 0.8033 (t0) cc_final: 0.7794 (m110) REVERT: B 109 MET cc_start: 0.7664 (mtt) cc_final: 0.7357 (mtt) outliers start: 31 outliers final: 22 residues processed: 209 average time/residue: 0.1204 time to fit residues: 37.8963 Evaluate side-chains 202 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 303 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 463 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 819 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 1356 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 94 optimal weight: 0.0270 chunk 11 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 HIS A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.160373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130576 restraints weight = 20646.149| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.56 r_work: 0.3348 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16068 Z= 0.093 Angle : 0.494 11.973 21966 Z= 0.246 Chirality : 0.037 0.187 2521 Planarity : 0.004 0.045 2608 Dihedral : 11.916 73.528 2749 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.55 % Allowed : 17.89 % Favored : 80.56 % 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: 1.27 (0.20), residues: 1766 helix: 2.02 (0.18), residues: 836 sheet: 0.34 (0.34), residues: 214 loop : -0.39 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 853 TYR 0.020 0.001 TYR A1000 PHE 0.010 0.001 PHE A 477 TRP 0.017 0.001 TRP A1634 HIS 0.003 0.000 HIS A1305 Details of bonding type rmsd covalent geometry : bond 0.00206 (16068) covalent geometry : angle 0.49368 (21966) hydrogen bonds : bond 0.03337 ( 770) hydrogen bonds : angle 3.83267 ( 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 209 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.573 Fit side-chains REVERT: A 108 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8071 (tttm) REVERT: A 126 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.6989 (p) REVERT: A 147 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6908 (m-70) REVERT: A 252 MET cc_start: 0.6875 (ttp) cc_final: 0.6647 (ttt) REVERT: A 303 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 344 MET cc_start: 0.7600 (ttp) cc_final: 0.7203 (ttt) REVERT: A 356 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7157 (tt0) REVERT: A 364 THR cc_start: 0.8865 (m) cc_final: 0.8509 (m) REVERT: A 378 PHE cc_start: 0.7510 (m-10) cc_final: 0.7137 (m-80) REVERT: A 832 VAL cc_start: 0.8971 (t) cc_final: 0.8536 (m) REVERT: A 952 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6669 (p90) REVERT: A 1136 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: A 1175 LEU cc_start: 0.8244 (mt) cc_final: 0.8014 (mt) REVERT: A 1320 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7143 (ttpt) REVERT: A 1552 ASN cc_start: 0.7891 (t0) cc_final: 0.7459 (m-40) REVERT: A 1654 ILE cc_start: 0.8418 (pt) cc_final: 0.8186 (pt) REVERT: B 109 MET cc_start: 0.7604 (mtt) cc_final: 0.7353 (mtt) REVERT: B 191 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6480 (mm-30) outliers start: 25 outliers final: 15 residues processed: 206 average time/residue: 0.1174 time to fit residues: 36.3591 Evaluate side-chains 205 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 HIS 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 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 536 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 952 TYR 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 1356 VAL Chi-restraints excluded: chain B residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 58 optimal weight: 0.0170 chunk 122 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 HIS A1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126786 restraints weight = 20529.157| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.61 r_work: 0.3299 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4604 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= 0.122 Angle : 0.524 12.430 21966 Z= 0.262 Chirality : 0.038 0.159 2521 Planarity : 0.004 0.045 2608 Dihedral : 11.988 73.638 2748 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.86 % Allowed : 17.59 % Favored : 80.56 % 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: 1.15 (0.20), residues: 1766 helix: 1.91 (0.18), residues: 835 sheet: 0.34 (0.35), residues: 207 loop : -0.44 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 853 TYR 0.023 0.001 TYR A1000 PHE 0.014 0.001 PHE A 423 TRP 0.009 0.001 TRP A1292 HIS 0.004 0.001 HIS A1519 Details of bonding type rmsd covalent geometry : bond 0.00285 (16068) covalent geometry : angle 0.52420 (21966) hydrogen bonds : bond 0.03967 ( 770) hydrogen bonds : angle 3.94963 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3798.67 seconds wall clock time: 65 minutes 39.66 seconds (3939.66 seconds total)