Starting phenix.real_space_refine on Fri Jun 6 17:04:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ftk_29439/06_2025/8ftk_29439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ftk_29439/06_2025/8ftk_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/cci-nas-00/data/ceres_data/8ftk_29439/06_2025/8ftk_29439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ftk_29439/06_2025/8ftk_29439.map" model { file = "/net/cci-nas-00/data/ceres_data/8ftk_29439/06_2025/8ftk_29439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ftk_29439/06_2025/8ftk_29439.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.50, 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.3 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: 1.38 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: 3.10 Time building geometry restraints manager: 2.72 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: 0.00 - 1.17: 10351 1.17 - 2.33: 473 2.33 - 3.50: 71 3.50 - 4.66: 9 4.66 - 5.83: 3 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 3.120 nonbonded pdb=" O PHE A1149 " pdb=" N LEU A1153 " model vdw 2.199 3.120 nonbonded pdb=" O ASP A1663 " pdb=" N LEU A1667 " model vdw 2.270 3.120 nonbonded pdb=" O ILE A1478 " pdb=" N LEU A1482 " model vdw 2.295 3.120 nonbonded pdb=" O ASN A 111 " pdb=" N TYR A 115 " model vdw 2.333 3.120 ... (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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.100 ------------------------------------------------------------------------------- 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= 0.145 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 Details of bonding type rmsd hydrogen bonds : bond 0.15376 ( 734) hydrogen bonds : angle 6.92869 ( 2154) covalent geometry : bond 0.00192 ( 7833) covalent geometry : angle 0.57528 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.869 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0661 time to fit residues: 7.1876 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 20.0000 chunk 119 optimal weight: 30.0000 chunk 66 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 143 optimal weight: 0.4980 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.041205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.030893 restraints weight = 112328.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.031154 restraints weight = 97267.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.031363 restraints weight = 87294.978| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7833 Z= 0.150 Angle : 0.413 5.529 10907 Z= 0.269 Chirality : 0.039 0.143 1504 Planarity : 0.003 0.018 1577 Dihedral : 4.443 37.952 1577 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % 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: 0.79 (0.23), residues: 1570 helix: 1.91 (0.17), residues: 952 sheet: -1.93 (0.57), residues: 77 loop : -1.70 (0.28), residues: 541 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 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 734) hydrogen bonds : angle 5.76874 ( 2154) covalent geometry : bond 0.00199 ( 7833) covalent geometry : angle 0.41275 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.825 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0732 time to fit residues: 7.9771 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 109 optimal weight: 0.2980 chunk 4 optimal weight: 10.0000 chunk 116 optimal weight: 40.0000 chunk 157 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- 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 = 0.3081 r_free = 0.3081 target = 0.039384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.029243 restraints weight = 118305.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.029460 restraints weight = 102391.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.029710 restraints weight = 91453.952| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7833 Z= 0.253 Angle : 0.539 7.298 10907 Z= 0.358 Chirality : 0.041 0.166 1504 Planarity : 0.003 0.026 1577 Dihedral : 5.346 36.135 1577 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % 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: -0.40 (0.22), residues: 1570 helix: 0.86 (0.17), residues: 959 sheet: -1.94 (0.62), residues: 72 loop : -2.11 (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 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 734) hydrogen bonds : angle 6.16433 ( 2154) covalent geometry : bond 0.00344 ( 7833) covalent geometry : angle 0.53884 (10907) *********************** 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 to be fit. 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: 0.0729 time to fit residues: 8.0620 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 157 optimal weight: 0.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- 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 = 0.3112 r_free = 0.3112 target = 0.040144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.029804 restraints weight = 114931.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030072 restraints weight = 99019.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.030256 restraints weight = 88437.295| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 7833 Z= 0.106 Angle : 0.384 5.715 10907 Z= 0.246 Chirality : 0.039 0.157 1504 Planarity : 0.002 0.023 1577 Dihedral : 4.547 31.208 1577 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.84 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 : 0.07 % 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: 0.62 (0.23), residues: 1570 helix: 1.88 (0.17), residues: 952 sheet: -1.97 (0.60), residues: 72 loop : -2.01 (0.27), residues: 546 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 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 734) hydrogen bonds : angle 5.26942 ( 2154) covalent geometry : bond 0.00139 ( 7833) covalent geometry : angle 0.38441 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.882 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0766 time to fit residues: 8.3079 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 chunk 127 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.039547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.029296 restraints weight = 115648.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.029504 restraints weight = 100495.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.029733 restraints weight = 90450.931| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7833 Z= 0.164 Angle : 0.419 6.381 10907 Z= 0.273 Chirality : 0.039 0.159 1504 Planarity : 0.002 0.019 1577 Dihedral : 4.388 32.134 1577 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % 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: 0.93 (0.23), residues: 1570 helix: 2.14 (0.17), residues: 960 sheet: -1.65 (0.60), residues: 71 loop : -2.01 (0.27), 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 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 734) hydrogen bonds : angle 5.08388 ( 2154) covalent geometry : bond 0.00222 ( 7833) covalent geometry : angle 0.41949 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.917 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0743 time to fit residues: 8.0849 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 30.0000 chunk 120 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 12 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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 = 0.3078 r_free = 0.3078 target = 0.039166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.029777 restraints weight = 116979.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.029722 restraints weight = 97457.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.029664 restraints weight = 90347.843| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7833 Z= 0.220 Angle : 0.458 5.117 10907 Z= 0.307 Chirality : 0.039 0.154 1504 Planarity : 0.003 0.016 1577 Dihedral : 4.725 31.074 1577 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: 0.46 (0.22), residues: 1570 helix: 1.68 (0.17), residues: 962 sheet: -1.84 (0.59), residues: 71 loop : -2.02 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 734) hydrogen bonds : angle 5.33420 ( 2154) covalent geometry : bond 0.00296 ( 7833) covalent geometry : angle 0.45756 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.950 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0805 time to fit residues: 8.8548 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 113 optimal weight: 0.0870 chunk 145 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 3 optimal weight: 50.0000 chunk 152 optimal weight: 30.0000 chunk 75 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 overall best weight: 3.6164 ------------------------------------------------------------------------------- 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 = 0.3079 r_free = 0.3079 target = 0.039257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.029559 restraints weight = 117289.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.029544 restraints weight = 103393.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.029561 restraints weight = 91857.526| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7833 Z= 0.166 Angle : 0.411 5.586 10907 Z= 0.270 Chirality : 0.039 0.159 1504 Planarity : 0.002 0.015 1577 Dihedral : 4.381 29.809 1577 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % 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: 0.90 (0.23), residues: 1570 helix: 2.14 (0.17), residues: 962 sheet: -1.99 (0.58), residues: 71 loop : -2.05 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 734) hydrogen bonds : angle 5.00525 ( 2154) covalent geometry : bond 0.00225 ( 7833) covalent geometry : angle 0.41087 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.785 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0723 time to fit residues: 7.9009 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 0.0570 chunk 71 optimal weight: 0.0060 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.8118 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.039464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.029292 restraints weight = 115775.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.029547 restraints weight = 100264.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029715 restraints weight = 90269.507| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4450 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= 0.139 Angle : 0.381 5.040 10907 Z= 0.249 Chirality : 0.039 0.148 1504 Planarity : 0.002 0.014 1577 Dihedral : 4.194 28.614 1577 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: 1.32 (0.23), residues: 1570 helix: 2.48 (0.17), residues: 964 sheet: -1.98 (0.58), residues: 71 loop : -1.88 (0.28), residues: 535 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 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 734) hydrogen bonds : angle 4.73841 ( 2154) covalent geometry : bond 0.00187 ( 7833) covalent geometry : angle 0.38069 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.790 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0761 time to fit residues: 8.2100 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 119 optimal weight: 0.0770 chunk 109 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 154 optimal weight: 40.0000 chunk 142 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.5344 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.039110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.028954 restraints weight = 117921.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.029210 restraints weight = 102307.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.029351 restraints weight = 91430.049| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4810 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= 0.173 Angle : 0.408 5.313 10907 Z= 0.270 Chirality : 0.039 0.150 1504 Planarity : 0.002 0.014 1577 Dihedral : 4.277 28.713 1577 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % 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: 1.23 (0.23), residues: 1570 helix: 2.42 (0.17), residues: 958 sheet: -1.97 (0.58), residues: 71 loop : -1.89 (0.28), residues: 541 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 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 734) hydrogen bonds : angle 4.87704 ( 2154) covalent geometry : bond 0.00232 ( 7833) covalent geometry : angle 0.40829 (10907) *********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.822 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0723 time to fit residues: 7.8700 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 21.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 123 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 139 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 = 0.3074 r_free = 0.3074 target = 0.039074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.028939 restraints weight = 117205.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.029182 restraints weight = 100766.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.029397 restraints weight = 90195.127| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7833 Z= 0.159 Angle : 0.394 5.070 10907 Z= 0.260 Chirality : 0.039 0.142 1504 Planarity : 0.002 0.012 1577 Dihedral : 4.231 27.896 1577 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % 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: 1.33 (0.23), residues: 1570 helix: 2.48 (0.17), residues: 965 sheet: -2.03 (0.58), residues: 71 loop : -1.84 (0.28), residues: 534 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 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 734) hydrogen bonds : angle 4.76714 ( 2154) covalent geometry : bond 0.00213 ( 7833) covalent geometry : angle 0.39414 (10907) ********************** 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 to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.909 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0718 time to fit residues: 7.8867 Evaluate side-chains 50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 36 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 112 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.038236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.028347 restraints weight = 119669.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.028590 restraints weight = 103562.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.028715 restraints weight = 92949.634| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7833 Z= 0.257 Angle : 0.492 5.078 10907 Z= 0.336 Chirality : 0.039 0.142 1504 Planarity : 0.003 0.015 1577 Dihedral : 4.828 28.551 1577 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % 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: 0.27 (0.22), residues: 1570 helix: 1.52 (0.17), residues: 962 sheet: -2.45 (0.55), residues: 76 loop : -1.99 (0.28), residues: 532 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 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 734) hydrogen bonds : angle 5.47585 ( 2154) covalent geometry : bond 0.00346 ( 7833) covalent geometry : angle 0.49218 (10907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2959.43 seconds wall clock time: 51 minutes 28.31 seconds (3088.31 seconds total)