Starting phenix.real_space_refine on Mon Mar 11 09:29:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftk_29439/03_2024/8ftk_29439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftk_29439/03_2024/8ftk_29439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftk_29439/03_2024/8ftk_29439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftk_29439/03_2024/8ftk_29439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftk_29439/03_2024/8ftk_29439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftk_29439/03_2024/8ftk_29439.pdb" } resolution = 4.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 3 Type Number sf(0) Gaussians C 4672 2.51 5 N 1584 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1584, 7840 Classifications: {'peptide': 1584} Incomplete info: {'truncation_to_alanine': 1377} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1516} Chain breaks: 6 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 5043 Unresolved non-hydrogen angles: 6424 Unresolved non-hydrogen dihedrals: 4199 Unresolved non-hydrogen chiralities: 442 Planarities with less than four sites: {'GLN:plan1': 85, 'HIS:plan': 28, 'TYR:plan': 41, 'ASN:plan1': 51, 'TRP:plan': 25, 'ASP:plan': 103, 'PHE:plan': 58, 'GLU:plan': 112, 'ARG:plan': 101} Unresolved non-hydrogen planarities: 2755 Time building chain proxies: 5.45, per 1000 atoms: 0.70 Number of scatterers: 7840 At special positions: 0 Unit cell: (91.504, 90.44, 205.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1584 8.00 N 1584 7.00 C 4672 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=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 2.3 seconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 5 sheets defined 67.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 1 through 19 Processing helix chain 'A' and resid 51 through 72 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 84 through 98 removed outlier: 4.185A pdb=" N ASP A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 removed outlier: 3.801A pdb=" N ASP A 113 " --> pdb=" O HIS A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 156 Processing helix chain 'A' and resid 159 through 180 removed outlier: 7.526A pdb=" N SER A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 170 " --> pdb=" O HIS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.609A pdb=" N ARG A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 4.292A pdb=" N THR A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 321 through 339 removed outlier: 3.522A pdb=" N SER A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.952A pdb=" N LEU A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 374 " --> pdb=" O ASN A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.895A pdb=" N ALA A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 417 removed outlier: 4.079A pdb=" N SER A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 451 Processing helix chain 'A' and resid 459 through 474 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 493 through 523 removed outlier: 3.544A pdb=" N ALA A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 removed outlier: 4.014A pdb=" N MET A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 removed outlier: 3.853A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.200A pdb=" N SER A 568 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 607 Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 655 through 684 removed outlier: 3.505A pdb=" N PHE A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 694 through 710 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 723 through 751 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 756 through 785 removed outlier: 4.541A pdb=" N GLY A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 808 Proline residue: A 804 - end of helix Processing helix chain 'A' and resid 808 through 816 Processing helix chain 'A' and resid 820 through 841 Processing helix chain 'A' and resid 846 through 858 Processing helix chain 'A' and resid 876 through 888 removed outlier: 3.738A pdb=" N LEU A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 1107 through 1117 Processing helix chain 'A' and resid 1141 through 1166 removed outlier: 3.998A pdb=" N LYS A1146 " --> pdb=" O PRO A1142 " (cutoff:3.500A) Proline residue: A1151 - end of helix removed outlier: 3.781A pdb=" N ASP A1166 " --> pdb=" O VAL A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1202 Processing helix chain 'A' and resid 1216 through 1220 removed outlier: 3.563A pdb=" N GLN A1220 " --> pdb=" O PRO A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1284 Processing helix chain 'A' and resid 1285 through 1287 No H-bonds generated for 'chain 'A' and resid 1285 through 1287' Processing helix chain 'A' and resid 1289 through 1294 Processing helix chain 'A' and resid 1308 through 1317 Processing helix chain 'A' and resid 1319 through 1330 removed outlier: 3.829A pdb=" N ALA A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A1326 " --> pdb=" O GLN A1322 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A1328 " --> pdb=" O ARG A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1344 Processing helix chain 'A' and resid 1345 through 1362 Processing helix chain 'A' and resid 1395 through 1408 Processing helix chain 'A' and resid 1432 through 1439 removed outlier: 3.938A pdb=" N VAL A1435 " --> pdb=" O ASN A1432 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A1437 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A1439 " --> pdb=" O LYS A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1462 through 1487 Proline residue: A1480 - end of helix removed outlier: 3.964A pdb=" N LEU A1487 " --> pdb=" O ASP A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1543 removed outlier: 3.879A pdb=" N GLY A1522 " --> pdb=" O ASP A1518 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR A1524 " --> pdb=" O ALA A1520 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A1543 " --> pdb=" O GLU A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1556 removed outlier: 3.731A pdb=" N HIS A1556 " --> pdb=" O GLY A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1562 removed outlier: 4.018A pdb=" N ASN A1561 " --> pdb=" O GLU A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1577 removed outlier: 3.692A pdb=" N CYS A1577 " --> pdb=" O ALA A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1583 removed outlier: 3.610A pdb=" N LEU A1583 " --> pdb=" O GLU A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1587 Processing helix chain 'A' and resid 1620 through 1628 Processing helix chain 'A' and resid 1642 through 1653 removed outlier: 4.265A pdb=" N PHE A1648 " --> pdb=" O GLU A1644 " (cutoff:3.500A) Proline residue: A1649 - end of helix Processing helix chain 'A' and resid 1670 through 1675 Processing helix chain 'A' and resid 1701 through 1717 Processing helix chain 'A' and resid 1734 through 1749 Processing helix chain 'A' and resid 1750 through 1755 removed outlier: 3.816A pdb=" N GLU A1755 " --> pdb=" O SER A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1802 Processing helix chain 'A' and resid 1818 through 1832 removed outlier: 3.757A pdb=" N ALA A1822 " --> pdb=" O GLY A1818 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1844 removed outlier: 4.234A pdb=" N LEU A1842 " --> pdb=" O ASN A1838 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 379 through 381 Processing sheet with id=AA2, first strand: chain 'A' and resid 859 through 861 Processing sheet with id=AA3, first strand: chain 'A' and resid 1186 through 1193 Processing sheet with id=AA4, first strand: chain 'A' and resid 1225 through 1229 removed outlier: 6.906A pdb=" N ILE A1208 " --> pdb=" O ILE A1268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1422 through 1424 removed outlier: 6.494A pdb=" N LEU A1423 " --> pdb=" O CYS A1548 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A1389 " --> pdb=" O LEU A1547 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA A1549 " --> pdb=" O LEU A1389 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A1391 " --> pdb=" O ALA A1549 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A1390 " --> pdb=" O ILE A1570 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A1334 " --> pdb=" O CYS A1593 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A1595 " --> pdb=" O GLY A1334 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A1336 " --> pdb=" O LEU A1595 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N HIS A1633 " --> pdb=" O LEU A1337 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A1339 " --> pdb=" O HIS A1633 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2154 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: 3.35 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1584 1.29 - 1.36: 1577 1.36 - 1.42: 0 1.42 - 1.49: 1584 1.49 - 1.55: 3088 Bond restraints: 7833 Sorted by residual: bond pdb=" N ILE A1773 " pdb=" CA ILE A1773 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.29e+00 bond pdb=" N VAL A1430 " pdb=" CA VAL A1430 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.22e+00 bond pdb=" N TYR A1139 " pdb=" CA TYR A1139 " ideal model delta sigma weight residual 1.454 1.464 -0.010 1.29e-02 6.01e+03 6.44e-01 bond pdb=" CA LYS A1411 " pdb=" CB LYS A1411 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.35e-02 5.49e+03 6.28e-01 bond pdb=" CA LEU A1678 " pdb=" C LEU A1678 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.14e-02 7.69e+03 6.11e-01 ... (remaining 7828 not shown) Histogram of bond angle deviations from ideal: 102.61 - 107.58: 86 107.58 - 112.55: 4234 112.55 - 117.52: 1348 117.52 - 122.49: 4522 122.49 - 127.46: 717 Bond angle restraints: 10907 Sorted by residual: angle pdb=" N VAL A1135 " pdb=" CA VAL A1135 " pdb=" C VAL A1135 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 angle pdb=" C LEU A1294 " pdb=" N LYS A1295 " pdb=" CA LYS A1295 " ideal model delta sigma weight residual 121.90 116.44 5.46 1.26e+00 6.30e-01 1.88e+01 angle pdb=" C TYR A1639 " pdb=" N ARG A1640 " pdb=" CA ARG A1640 " ideal model delta sigma weight residual 122.74 127.38 -4.64 1.44e+00 4.82e-01 1.04e+01 angle pdb=" N GLY A 779 " pdb=" CA GLY A 779 " pdb=" C GLY A 779 " ideal model delta sigma weight residual 112.77 108.79 3.98 1.28e+00 6.10e-01 9.67e+00 angle pdb=" C LYS A1146 " pdb=" N GLN A1147 " pdb=" CA GLN A1147 " ideal model delta sigma weight residual 120.38 124.89 -4.51 1.46e+00 4.69e-01 9.53e+00 ... (remaining 10902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.14: 4478 8.14 - 16.29: 100 16.29 - 24.43: 3 24.43 - 32.57: 3 32.57 - 40.71: 1 Dihedral angle restraints: 4585 sinusoidal: 0 harmonic: 4585 Sorted by residual: dihedral pdb=" CA VAL A1700 " pdb=" C VAL A1700 " pdb=" N ASN A1701 " pdb=" CA ASN A1701 " ideal model delta harmonic sigma weight residual 180.00 139.29 40.71 0 5.00e+00 4.00e-02 6.63e+01 dihedral pdb=" CA ARG A 480 " pdb=" C ARG A 480 " pdb=" N ALA A 481 " pdb=" CA ALA A 481 " ideal model delta harmonic sigma weight residual 180.00 148.17 31.83 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA ASP A1718 " pdb=" C ASP A1718 " pdb=" N TYR A1719 " pdb=" CA TYR A1719 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 4582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 950 0.030 - 0.060: 381 0.060 - 0.091: 109 0.091 - 0.121: 62 0.121 - 0.151: 2 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA ILE A1431 " pdb=" N ILE A1431 " pdb=" C ILE A1431 " pdb=" CB ILE A1431 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE A1420 " pdb=" N ILE A1420 " pdb=" C ILE A1420 " pdb=" CB ILE A1420 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PRO A1140 " pdb=" N PRO A1140 " pdb=" C PRO A1140 " pdb=" CB PRO A1140 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 1501 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 476 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLU A 476 " -0.032 2.00e-02 2.50e+03 pdb=" O GLU A 476 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 477 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1146 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C LYS A1146 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS A1146 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A1147 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1745 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C PHE A1745 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A1745 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A1746 " 0.008 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 101 2.68 - 3.24: 8355 3.24 - 3.79: 12356 3.79 - 4.35: 13071 4.35 - 4.90: 20921 Nonbonded interactions: 54804 Sorted by model distance: nonbonded pdb=" O LEU A 802 " pdb=" N ARG A 806 " model vdw 2.125 2.520 nonbonded pdb=" O PHE A1149 " pdb=" N LEU A1153 " model vdw 2.199 2.520 nonbonded pdb=" O ASP A1663 " pdb=" N LEU A1667 " model vdw 2.270 2.520 nonbonded pdb=" O ILE A1478 " pdb=" N LEU A1482 " model vdw 2.295 2.520 nonbonded pdb=" O ASN A 111 " pdb=" N TYR A 115 " model vdw 2.333 2.520 ... (remaining 54799 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: 2.340 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: 7.110 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.550 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.002 0.018 7833 Z= 0.141 Angle : 0.575 5.830 10907 Z= 0.404 Chirality : 0.039 0.151 1504 Planarity : 0.002 0.018 1577 Dihedral : 4.661 40.713 1577 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.74 (0.23), residues: 1570 helix: 1.83 (0.18), residues: 929 sheet: -1.80 (0.62), residues: 66 loop : -1.52 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.918 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0842 time to fit residues: 9.1111 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 30.0000 chunk 143 optimal weight: 0.0470 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7833 Z= 0.164 Angle : 0.430 5.718 10907 Z= 0.282 Chirality : 0.039 0.148 1504 Planarity : 0.003 0.022 1577 Dihedral : 4.577 35.442 1577 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.64 (0.23), residues: 1570 helix: 1.77 (0.17), residues: 960 sheet: -1.38 (0.63), residues: 68 loop : -1.89 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.866 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0700 time to fit residues: 7.7426 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 50.0000 chunk 155 optimal weight: 0.0870 chunk 128 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 115 optimal weight: 0.3980 overall best weight: 2.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7833 Z= 0.141 Angle : 0.409 6.565 10907 Z= 0.265 Chirality : 0.039 0.187 1504 Planarity : 0.002 0.028 1577 Dihedral : 4.420 29.702 1577 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 1.04 (0.23), residues: 1570 helix: 2.15 (0.18), residues: 944 sheet: -1.69 (0.57), residues: 77 loop : -1.64 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.880 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0759 time to fit residues: 8.2188 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.3980 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 144 optimal weight: 8.9990 chunk 152 optimal weight: 50.0000 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 0.0030 chunk 41 optimal weight: 7.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 7833 Z= 0.092 Angle : 0.355 4.533 10907 Z= 0.226 Chirality : 0.038 0.147 1504 Planarity : 0.002 0.019 1577 Dihedral : 3.985 26.544 1577 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 1.63 (0.23), residues: 1570 helix: 2.71 (0.18), residues: 937 sheet: -1.32 (0.63), residues: 71 loop : -1.55 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.961 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0780 time to fit residues: 8.5978 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 113 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7833 Z= 0.219 Angle : 0.457 6.795 10907 Z= 0.304 Chirality : 0.040 0.179 1504 Planarity : 0.003 0.023 1577 Dihedral : 4.516 28.739 1577 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.97 (0.23), residues: 1570 helix: 2.06 (0.17), residues: 962 sheet: -1.20 (0.65), residues: 69 loop : -1.85 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.865 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0760 time to fit residues: 8.2998 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 152 optimal weight: 50.0000 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7833 Z= 0.171 Angle : 0.418 4.517 10907 Z= 0.275 Chirality : 0.039 0.143 1504 Planarity : 0.002 0.018 1577 Dihedral : 4.372 26.396 1577 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 1.08 (0.23), residues: 1570 helix: 2.20 (0.17), residues: 962 sheet: -1.23 (0.63), residues: 70 loop : -1.90 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.894 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0714 time to fit residues: 7.9594 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7833 Z= 0.150 Angle : 0.398 5.272 10907 Z= 0.259 Chirality : 0.039 0.149 1504 Planarity : 0.002 0.018 1577 Dihedral : 4.244 25.839 1577 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 1.39 (0.23), residues: 1570 helix: 2.48 (0.17), residues: 963 sheet: -1.27 (0.63), residues: 70 loop : -1.85 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.872 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0719 time to fit residues: 7.8460 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 40.0000 chunk 138 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7833 Z= 0.138 Angle : 0.385 4.729 10907 Z= 0.251 Chirality : 0.039 0.144 1504 Planarity : 0.002 0.017 1577 Dihedral : 4.099 23.995 1577 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 1.56 (0.23), residues: 1570 helix: 2.63 (0.17), residues: 962 sheet: -1.18 (0.62), residues: 70 loop : -1.80 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.913 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0721 time to fit residues: 8.0037 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.0030 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7833 Z= 0.127 Angle : 0.369 4.709 10907 Z= 0.240 Chirality : 0.039 0.147 1504 Planarity : 0.002 0.016 1577 Dihedral : 3.955 22.941 1577 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 1.84 (0.23), residues: 1570 helix: 2.87 (0.17), residues: 964 sheet: -1.26 (0.63), residues: 70 loop : -1.71 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.893 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0744 time to fit residues: 8.1481 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7833 Z= 0.267 Angle : 0.514 5.321 10907 Z= 0.346 Chirality : 0.040 0.139 1504 Planarity : 0.003 0.017 1577 Dihedral : 4.925 24.279 1577 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.28 (0.22), residues: 1570 helix: 1.50 (0.17), residues: 955 sheet: -1.58 (0.61), residues: 71 loop : -2.02 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.899 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0751 time to fit residues: 8.1910 Evaluate side-chains 50 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.028788 restraints weight = 117562.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.029031 restraints weight = 101323.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.029227 restraints weight = 90907.802| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7833 Z= 0.190 Angle : 0.427 4.805 10907 Z= 0.285 Chirality : 0.039 0.139 1504 Planarity : 0.002 0.016 1577 Dihedral : 4.490 22.139 1577 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1570 helix: 1.95 (0.17), residues: 963 sheet: -1.69 (0.60), residues: 70 loop : -2.00 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 13 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.41 seconds wall clock time: 26 minutes 36.44 seconds (1596.44 seconds total)