Starting phenix.real_space_refine on Sun Dec 10 10:41:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwx_0780/12_2023/6kwx_0780_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.010 sd= 1.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 33 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 79 5.16 5 C 9117 2.51 5 N 2414 2.21 5 O 2603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 807": "NH1" <-> "NH2" Residue "A PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ARG 973": "NH1" <-> "NH2" Residue "A ARG 1243": "NH1" <-> "NH2" Residue "A ARG 1297": "NH1" <-> "NH2" Residue "A ARG 1331": "NH1" <-> "NH2" Residue "A ARG 1340": "NH1" <-> "NH2" Residue "A ARG 1350": "NH1" <-> "NH2" Residue "A ARG 1377": "NH1" <-> "NH2" Residue "A ARG 1410": "NH1" <-> "NH2" Residue "A ARG 1435": "NH1" <-> "NH2" Residue "A ARG 1485": "NH1" <-> "NH2" Residue "A ARG 1536": "NH1" <-> "NH2" Residue "A ARG 1620": "NH1" <-> "NH2" Residue "A ARG 1658": "NH1" <-> "NH2" Residue "A TYR 1659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1811": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14227 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1753, 14227 Unusual residues: {'IHP': 1, 'K0W': 1} Classifications: {'peptide': 1751, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 91, 'TRANS': 1658, None: 2} Not linked: pdbres="HIS A1813 " pdbres="K0W A1901 " Not linked: pdbres="K0W A1901 " pdbres="IHP A1902 " Chain breaks: 3 Time building chain proxies: 7.52, per 1000 atoms: 0.53 Number of scatterers: 14227 At special positions: 0 Unit cell: (133.12, 86.32, 121.68, 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 79 16.00 P 14 15.00 O 2603 8.00 N 2414 7.00 C 9117 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 2.4 seconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 0 sheets defined 56.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 43 through 64 removed outlier: 3.753A pdb=" N LEU A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 92 through 104 removed outlier: 3.715A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.521A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.780A pdb=" N THR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 186 through 192 removed outlier: 4.104A pdb=" N THR A 189 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.892A pdb=" N GLN A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.080A pdb=" N THR A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.670A pdb=" N ILE A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.939A pdb=" N ASN A 351 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 354 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 356 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 361 - end of helix Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.657A pdb=" N PHE A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLN A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.954A pdb=" N ALA A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 451 through 461 removed outlier: 3.532A pdb=" N ALA A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 477 through 487 removed outlier: 4.499A pdb=" N LEU A 482 " --> pdb=" O THR A 479 " (cutoff:3.500A) Proline residue: A 483 - end of helix removed outlier: 3.796A pdb=" N ARG A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.605A pdb=" N ILE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 removed outlier: 3.529A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.197A pdb=" N GLU A 544 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 599 through 614 removed outlier: 4.027A pdb=" N VAL A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 637 removed outlier: 3.547A pdb=" N ASP A 629 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 657 removed outlier: 4.102A pdb=" N LYS A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 671 through 682 removed outlier: 3.810A pdb=" N TRP A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 693 through 699 removed outlier: 4.698A pdb=" N GLU A 696 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN A 697 " --> pdb=" O TYR A 694 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 699 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 No H-bonds generated for 'chain 'A' and resid 702 through 705' Processing helix chain 'A' and resid 715 through 726 removed outlier: 3.876A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 774 through 785 Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 807 through 823 removed outlier: 3.504A pdb=" N GLN A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 removed outlier: 3.552A pdb=" N ILE A 868 " --> pdb=" O HIS A 864 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 874 " --> pdb=" O THR A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 900 Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 937 through 953 removed outlier: 3.617A pdb=" N VAL A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 975 removed outlier: 3.525A pdb=" N LEU A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 994 removed outlier: 3.648A pdb=" N GLN A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1008 No H-bonds generated for 'chain 'A' and resid 1005 through 1008' Processing helix chain 'A' and resid 1021 through 1032 Processing helix chain 'A' and resid 1049 through 1060 Proline residue: A1054 - end of helix removed outlier: 5.211A pdb=" N GLY A1060 " --> pdb=" O ILE A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1086 removed outlier: 3.630A pdb=" N ARG A1074 " --> pdb=" O PRO A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1127 through 1154 removed outlier: 3.565A pdb=" N ASP A1138 " --> pdb=" O GLU A1134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A1139 " --> pdb=" O LYS A1135 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1174 removed outlier: 4.091A pdb=" N LEU A1174 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1191 Processing helix chain 'A' and resid 1198 through 1214 Processing helix chain 'A' and resid 1247 through 1249 No H-bonds generated for 'chain 'A' and resid 1247 through 1249' Processing helix chain 'A' and resid 1260 through 1264 Processing helix chain 'A' and resid 1306 through 1313 Processing helix chain 'A' and resid 1316 through 1326 Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1356 through 1368 Proline residue: A1362 - end of helix removed outlier: 3.593A pdb=" N VAL A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1392 removed outlier: 4.121A pdb=" N LYS A1391 " --> pdb=" O ILE A1387 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS A1392 " --> pdb=" O ARG A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1414 Proline residue: A1407 - end of helix Processing helix chain 'A' and resid 1421 through 1431 removed outlier: 4.124A pdb=" N ALA A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1447 Processing helix chain 'A' and resid 1460 through 1474 removed outlier: 3.613A pdb=" N GLN A1469 " --> pdb=" O LEU A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1493 removed outlier: 5.882A pdb=" N ARG A1485 " --> pdb=" O GLU A1481 " (cutoff:3.500A) Proline residue: A1492 - end of helix Processing helix chain 'A' and resid 1499 through 1512 removed outlier: 3.770A pdb=" N GLU A1503 " --> pdb=" O LYS A1499 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG A1504 " --> pdb=" O ASN A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1540 removed outlier: 3.667A pdb=" N ARG A1536 " --> pdb=" O GLU A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1544 No H-bonds generated for 'chain 'A' and resid 1542 through 1544' Processing helix chain 'A' and resid 1568 through 1584 removed outlier: 3.504A pdb=" N ALA A1583 " --> pdb=" O LYS A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1604 Processing helix chain 'A' and resid 1619 through 1630 Processing helix chain 'A' and resid 1639 through 1649 removed outlier: 3.649A pdb=" N LEU A1643 " --> pdb=" O VAL A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1670 removed outlier: 3.687A pdb=" N LEU A1662 " --> pdb=" O ARG A1658 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A1670 " --> pdb=" O GLN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1677 Processing helix chain 'A' and resid 1680 through 1695 removed outlier: 3.710A pdb=" N LYS A1684 " --> pdb=" O GLU A1680 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A1695 " --> pdb=" O ILE A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1722 through 1732 Processing helix chain 'A' and resid 1756 through 1771 Processing helix chain 'A' and resid 1781 through 1791 removed outlier: 3.580A pdb=" N ASN A1787 " --> pdb=" O GLN A1783 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1788 " --> pdb=" O LEU A1784 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A1790 " --> pdb=" O MET A1786 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS A1791 " --> pdb=" O ASN A1787 " (cutoff:3.500A) Processing helix chain 'A' and resid 1798 through 1810 558 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3151 1.33 - 1.45: 3074 1.45 - 1.57: 8196 1.57 - 1.69: 17 1.69 - 1.81: 118 Bond restraints: 14556 Sorted by residual: bond pdb=" C VAL A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.337 1.376 -0.039 9.80e-03 1.04e+04 1.62e+01 bond pdb=" C GLN A 789 " pdb=" N PRO A 790 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.36e-02 5.41e+03 1.28e+01 bond pdb=" C TRP A 164 " pdb=" N PHE A 165 " ideal model delta sigma weight residual 1.331 1.281 0.050 1.48e-02 4.57e+03 1.14e+01 bond pdb=" O12 IHP A1902 " pdb=" P2 IHP A1902 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O15 IHP A1902 " pdb=" P5 IHP A1902 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 14551 not shown) Histogram of bond angle deviations from ideal: 93.21 - 101.76: 45 101.76 - 110.31: 3898 110.31 - 118.86: 8116 118.86 - 127.42: 7461 127.42 - 135.97: 245 Bond angle restraints: 19765 Sorted by residual: angle pdb=" N THR A 303 " pdb=" CA THR A 303 " pdb=" C THR A 303 " ideal model delta sigma weight residual 111.28 124.44 -13.16 1.09e+00 8.42e-01 1.46e+02 angle pdb=" N GLU A1270 " pdb=" CA GLU A1270 " pdb=" C GLU A1270 " ideal model delta sigma weight residual 111.36 122.77 -11.41 1.09e+00 8.42e-01 1.10e+02 angle pdb=" C ASN A1112 " pdb=" N PRO A1113 " pdb=" CA PRO A1113 " ideal model delta sigma weight residual 119.84 131.70 -11.86 1.25e+00 6.40e-01 9.00e+01 angle pdb=" N ILE A1125 " pdb=" CA ILE A1125 " pdb=" C ILE A1125 " ideal model delta sigma weight residual 112.83 103.93 8.90 9.90e-01 1.02e+00 8.09e+01 angle pdb=" N LEU A1673 " pdb=" CA LEU A1673 " pdb=" C LEU A1673 " ideal model delta sigma weight residual 111.28 118.95 -7.67 1.09e+00 8.42e-01 4.95e+01 ... (remaining 19760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 8465 24.77 - 49.54: 333 49.54 - 74.31: 26 74.31 - 99.07: 7 99.07 - 123.84: 6 Dihedral angle restraints: 8837 sinusoidal: 3700 harmonic: 5137 Sorted by residual: dihedral pdb=" CA ASP A 670 " pdb=" C ASP A 670 " pdb=" N LYS A 671 " pdb=" CA LYS A 671 " ideal model delta harmonic sigma weight residual 180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR A 750 " pdb=" C TYR A 750 " pdb=" N PHE A 751 " pdb=" CA PHE A 751 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLY A 713 " pdb=" C GLY A 713 " pdb=" N TYR A 714 " pdb=" CA TYR A 714 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 8834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 2241 1.005 - 2.010: 0 2.010 - 3.016: 0 3.016 - 4.021: 0 4.021 - 5.026: 2 Chirality restraints: 2243 Sorted by residual: chirality pdb=" C2 IHP A1902 " pdb=" C1 IHP A1902 " pdb=" C3 IHP A1902 " pdb=" O12 IHP A1902 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C3 IHP A1902 " pdb=" C2 IHP A1902 " pdb=" C4 IHP A1902 " pdb=" O13 IHP A1902 " both_signs ideal model delta sigma weight residual False -2.34 2.53 -4.87 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CB VAL A 463 " pdb=" CA VAL A 463 " pdb=" CG1 VAL A 463 " pdb=" CG2 VAL A 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 2240 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 373 " -0.025 2.00e-02 2.50e+03 5.20e-02 2.70e+01 pdb=" C TYR A 373 " 0.090 2.00e-02 2.50e+03 pdb=" O TYR A 373 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS A 374 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1482 " -0.024 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C LEU A1482 " 0.082 2.00e-02 2.50e+03 pdb=" O LEU A1482 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A1483 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 314 " 0.042 2.00e-02 2.50e+03 2.96e-02 2.19e+01 pdb=" CG TRP A 314 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP A 314 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 314 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 314 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 314 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 314 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 314 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 314 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 314 " 0.008 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 21 2.28 - 2.94: 5797 2.94 - 3.59: 21254 3.59 - 4.25: 35450 4.25 - 4.90: 57049 Nonbonded interactions: 119571 Sorted by model distance: nonbonded pdb=" O LYS A 324 " pdb=" N VAL A 326 " model vdw 1.627 2.520 nonbonded pdb=" OG SER A 975 " pdb=" SG CYS A1030 " model vdw 1.747 2.800 nonbonded pdb=" OH TYR A1286 " pdb=" O42 IHP A1902 " model vdw 1.874 2.440 nonbonded pdb=" NH2 ARG A 300 " pdb=" O GLN A1631 " model vdw 1.911 2.520 nonbonded pdb=" O THR A 887 " pdb=" CE1 PHE A 891 " model vdw 1.964 3.340 ... (remaining 119566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 2.540 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 37.980 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.011 0.104 14556 Z= 0.719 Angle : 1.553 19.179 19765 Z= 0.815 Chirality : 0.168 5.026 2243 Planarity : 0.009 0.070 2483 Dihedral : 13.541 123.843 5491 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.01 % Favored : 90.65 % Rotamer: Outliers : 1.69 % Allowed : 7.72 % Favored : 90.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.15), residues: 1743 helix: -3.00 (0.11), residues: 1072 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.005 TRP A 314 HIS 0.028 0.004 HIS A 227 PHE 0.048 0.004 PHE A 214 TYR 0.052 0.004 TYR A 997 ARG 0.017 0.002 ARG A1217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 620 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 7 residues processed: 637 average time/residue: 0.2889 time to fit residues: 262.7371 Evaluate side-chains 324 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 317 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1754 time to fit residues: 4.1589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 0.0060 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 51 GLN A 64 GLN A 125 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 310 HIS A 527 ASN A 596 GLN A 607 GLN A 697 GLN A 703 GLN A 722 HIS ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A 864 HIS A 907 HIS A 987 GLN A1021 GLN A1084 HIS A1109 GLN ** A1132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1250 HIS ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 HIS A1351 ASN A1363 HIS A1469 GLN A1569 GLN A1613 ASN A1631 GLN A1679 ASN A1787 ASN A1791 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14556 Z= 0.238 Angle : 0.864 12.666 19765 Z= 0.420 Chirality : 0.049 0.409 2243 Planarity : 0.006 0.064 2483 Dihedral : 8.183 88.493 1940 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 5.40 % Allowed : 16.20 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.18), residues: 1743 helix: -1.45 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : -2.76 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1402 HIS 0.008 0.001 HIS A 770 PHE 0.025 0.002 PHE A 602 TYR 0.026 0.002 TYR A 714 ARG 0.006 0.001 ARG A1478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 399 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 33 residues processed: 448 average time/residue: 0.2388 time to fit residues: 163.2086 Evaluate side-chains 340 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 307 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1335 time to fit residues: 10.4742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 0.0270 chunk 43 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 overall best weight: 1.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 GLN A 208 GLN A 246 GLN A 250 GLN A 616 HIS A 812 GLN ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 GLN ** A1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14556 Z= 0.240 Angle : 0.795 10.667 19765 Z= 0.382 Chirality : 0.047 0.273 2243 Planarity : 0.005 0.061 2483 Dihedral : 7.645 86.752 1940 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.94 % Favored : 93.00 % Rotamer: Outliers : 3.89 % Allowed : 19.21 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1743 helix: -0.68 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : -2.47 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1402 HIS 0.005 0.001 HIS A 864 PHE 0.027 0.002 PHE A1459 TYR 0.020 0.002 TYR A 714 ARG 0.007 0.001 ARG A1651 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 354 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 27 residues processed: 386 average time/residue: 0.2435 time to fit residues: 143.2855 Evaluate side-chains 332 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 305 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1370 time to fit residues: 9.1359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.0670 chunk 75 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 3.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 335 ASN A 812 GLN ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN A1109 GLN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1366 HIS A1569 GLN A1613 ASN ** A1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1666 GLN A1714 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14556 Z= 0.345 Angle : 0.852 12.247 19765 Z= 0.413 Chirality : 0.050 0.260 2243 Planarity : 0.005 0.052 2483 Dihedral : 7.346 89.546 1940 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 4.27 % Allowed : 20.40 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1743 helix: -0.35 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.27 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1424 HIS 0.009 0.002 HIS A1366 PHE 0.030 0.003 PHE A 903 TYR 0.024 0.002 TYR A 269 ARG 0.008 0.001 ARG A1651 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 344 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 31 residues processed: 385 average time/residue: 0.2262 time to fit residues: 135.7676 Evaluate side-chains 311 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 280 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1327 time to fit residues: 10.0942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 GLN A 987 GLN A1165 HIS ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1474 GLN ** A1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14556 Z= 0.300 Angle : 0.788 11.829 19765 Z= 0.379 Chirality : 0.047 0.210 2243 Planarity : 0.005 0.049 2483 Dihedral : 7.074 89.531 1940 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.57 % Favored : 92.37 % Rotamer: Outliers : 3.20 % Allowed : 23.35 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1743 helix: -0.09 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.11 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 196 HIS 0.005 0.001 HIS A 329 PHE 0.026 0.002 PHE A1728 TYR 0.022 0.002 TYR A 269 ARG 0.005 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 320 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 25 residues processed: 351 average time/residue: 0.2455 time to fit residues: 131.7681 Evaluate side-chains 294 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 269 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1542 time to fit residues: 9.1154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 88 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 HIS ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN A 818 HIS ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A1109 GLN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 ASN ** A1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1613 ASN ** A1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14556 Z= 0.202 Angle : 0.765 12.154 19765 Z= 0.362 Chirality : 0.045 0.290 2243 Planarity : 0.005 0.061 2483 Dihedral : 6.878 88.680 1940 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.66 % Rotamer: Outliers : 2.32 % Allowed : 25.05 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1743 helix: 0.08 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : -2.11 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1053 HIS 0.006 0.001 HIS A 227 PHE 0.027 0.002 PHE A 612 TYR 0.018 0.001 TYR A 269 ARG 0.005 0.000 ARG A1502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 310 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 13 residues processed: 328 average time/residue: 0.2265 time to fit residues: 116.0490 Evaluate side-chains 289 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 276 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1343 time to fit residues: 5.5775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 HIS ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 ASN ** A1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1613 ASN A1631 GLN ** A1791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14556 Z= 0.235 Angle : 0.757 11.205 19765 Z= 0.359 Chirality : 0.044 0.186 2243 Planarity : 0.005 0.062 2483 Dihedral : 6.721 88.946 1940 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 2.13 % Allowed : 26.24 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1743 helix: 0.15 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -1.99 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1053 HIS 0.004 0.001 HIS A 227 PHE 0.023 0.002 PHE A1603 TYR 0.019 0.002 TYR A 269 ARG 0.006 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 304 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 322 average time/residue: 0.2378 time to fit residues: 118.0010 Evaluate side-chains 279 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 265 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1609 time to fit residues: 6.2976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 14556 Z= 0.224 Angle : 0.779 12.220 19765 Z= 0.365 Chirality : 0.046 0.323 2243 Planarity : 0.005 0.067 2483 Dihedral : 6.626 88.572 1940 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.40 % Favored : 92.54 % Rotamer: Outliers : 1.38 % Allowed : 27.50 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1743 helix: 0.24 (0.17), residues: 1064 sheet: None (None), residues: 0 loop : -1.94 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A1053 HIS 0.005 0.001 HIS A 227 PHE 0.028 0.002 PHE A1728 TYR 0.020 0.002 TYR A 269 ARG 0.010 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 293 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 306 average time/residue: 0.2327 time to fit residues: 111.5739 Evaluate side-chains 285 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1374 time to fit residues: 5.1313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN A 480 HIS A 818 HIS ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** A1156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14556 Z= 0.483 Angle : 0.929 11.039 19765 Z= 0.454 Chirality : 0.053 0.363 2243 Planarity : 0.006 0.076 2483 Dihedral : 7.113 91.712 1940 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.80 % Rotamer: Outliers : 1.32 % Allowed : 27.87 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1743 helix: -0.05 (0.16), residues: 1054 sheet: None (None), residues: 0 loop : -2.06 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.004 TRP A1053 HIS 0.008 0.002 HIS A1273 PHE 0.044 0.003 PHE A 618 TYR 0.027 0.003 TYR A1087 ARG 0.010 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 283 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 296 average time/residue: 0.2390 time to fit residues: 109.1066 Evaluate side-chains 258 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1322 time to fit residues: 5.4103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 95 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** A1156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14556 Z= 0.224 Angle : 0.820 12.322 19765 Z= 0.390 Chirality : 0.046 0.202 2243 Planarity : 0.005 0.069 2483 Dihedral : 6.816 89.628 1940 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.63 % Favored : 92.31 % Rotamer: Outliers : 0.38 % Allowed : 29.44 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1743 helix: 0.25 (0.17), residues: 1044 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.003 TRP A1053 HIS 0.008 0.001 HIS A1312 PHE 0.026 0.002 PHE A 203 TYR 0.021 0.002 TYR A 269 ARG 0.011 0.001 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 296 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 298 average time/residue: 0.2354 time to fit residues: 109.5011 Evaluate side-chains 271 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1655 time to fit residues: 2.5592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** A1156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1666 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112793 restraints weight = 26259.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116794 restraints weight = 13094.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119453 restraints weight = 8114.101| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.8192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14556 Z= 0.232 Angle : 0.808 11.092 19765 Z= 0.387 Chirality : 0.046 0.212 2243 Planarity : 0.005 0.068 2483 Dihedral : 6.742 89.483 1940 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.44 % Allowed : 30.70 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1743 helix: 0.33 (0.17), residues: 1051 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.002 TRP A1053 HIS 0.006 0.001 HIS A 227 PHE 0.036 0.002 PHE A1670 TYR 0.020 0.002 TYR A 269 ARG 0.011 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.39 seconds wall clock time: 60 minutes 51.33 seconds (3651.33 seconds total)