Starting phenix.real_space_refine on Fri Aug 22 21:14:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ftk_29439/08_2025/8ftk_29439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ftk_29439/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ftk_29439/08_2025/8ftk_29439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ftk_29439/08_2025/8ftk_29439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ftk_29439/08_2025/8ftk_29439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ftk_29439/08_2025/8ftk_29439.map" } resolution = 4.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 112, 'ASN:plan1': 51, 'ASP:plan': 103, 'TYR:plan': 41, 'GLN:plan1': 85, 'TRP:plan': 25, 'ARG:plan': 101, 'PHE:plan': 58, 'HIS:plan': 28} Unresolved non-hydrogen planarities: 2755 Time building chain proxies: 2.40, per 1000 atoms: 0.31 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: 0.95 Conformation dependent library (CDL) restraints added in 461.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.43 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: 1.77 Time building geometry restraints manager: 1.18 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: 3.250 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 7833) covalent geometry : angle 0.57528 (10907) hydrogen bonds : bond 0.15376 ( 734) hydrogen bonds : angle 6.92869 ( 2154) *********************** 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 : 0.301 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0343 time to fit residues: 3.5597 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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 = 0.2988 r_free = 0.2988 target = 0.038729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.027333 restraints weight = 128545.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027563 restraints weight = 113069.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.027725 restraints weight = 101973.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.027899 restraints weight = 94097.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028027 restraints weight = 87875.550| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7833 Z= 0.188 Angle : 0.445 5.893 10907 Z= 0.293 Chirality : 0.040 0.162 1504 Planarity : 0.003 0.019 1577 Dihedral : 4.607 37.639 1577 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1570 helix: 1.67 (0.17), residues: 953 sheet: -2.00 (0.57), residues: 77 loop : -1.88 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7833) covalent geometry : angle 0.44482 (10907) hydrogen bonds : bond 0.04330 ( 734) hydrogen bonds : angle 5.87534 ( 2154) *********************** 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 : 0.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0354 time to fit residues: 3.7375 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 77 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 5.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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 = 0.2978 r_free = 0.2978 target = 0.038242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.026988 restraints weight = 128192.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.027192 restraints weight = 112624.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027369 restraints weight = 102475.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.027498 restraints weight = 94345.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.027615 restraints weight = 88429.456| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7833 Z= 0.141 Angle : 0.409 6.323 10907 Z= 0.265 Chirality : 0.039 0.172 1504 Planarity : 0.002 0.026 1577 Dihedral : 4.343 30.960 1577 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.75 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 : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.23), residues: 1570 helix: 2.10 (0.18), residues: 949 sheet: -1.85 (0.60), residues: 72 loop : -1.74 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 7833) covalent geometry : angle 0.40917 (10907) hydrogen bonds : bond 0.03673 ( 734) hydrogen bonds : angle 5.18722 ( 2154) *********************** 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 : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0336 time to fit residues: 3.5338 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 143 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.039965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029920 restraints weight = 116632.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.030003 restraints weight = 107321.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.030003 restraints weight = 97066.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.030029 restraints weight = 90214.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030064 restraints weight = 88452.829| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7833 Z= 0.168 Angle : 0.413 5.195 10907 Z= 0.270 Chirality : 0.039 0.158 1504 Planarity : 0.002 0.018 1577 Dihedral : 4.292 30.754 1577 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.23), residues: 1570 helix: 2.15 (0.17), residues: 966 sheet: -1.68 (0.62), residues: 71 loop : -1.90 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7833) covalent geometry : angle 0.41275 (10907) hydrogen bonds : bond 0.03547 ( 734) hydrogen bonds : angle 5.10319 ( 2154) *********************** 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 : 0.289 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0342 time to fit residues: 3.5852 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 : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.3102 r_free = 0.3102 target = 0.039908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.029649 restraints weight = 115239.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.029898 restraints weight = 100510.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.030032 restraints weight = 90311.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030218 restraints weight = 83859.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.030293 restraints weight = 78685.758| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7833 Z= 0.156 Angle : 0.401 5.669 10907 Z= 0.261 Chirality : 0.039 0.178 1504 Planarity : 0.002 0.017 1577 Dihedral : 4.241 30.993 1577 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.23), residues: 1570 helix: 2.30 (0.17), residues: 969 sheet: -1.46 (0.63), residues: 70 loop : -1.90 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 7833) covalent geometry : angle 0.40086 (10907) hydrogen bonds : bond 0.03400 ( 734) hydrogen bonds : angle 4.92007 ( 2154) *********************** 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 : 0.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0353 time to fit residues: 3.7071 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 157 optimal weight: 0.0170 chunk 39 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.0030 chunk 151 optimal weight: 8.9990 overall best weight: 0.5428 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.040786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.030175 restraints weight = 113371.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.030438 restraints weight = 97377.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.030657 restraints weight = 86880.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.030825 restraints weight = 79687.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.030915 restraints weight = 74333.768| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.007 7833 Z= 0.072 Angle : 0.340 4.349 10907 Z= 0.215 Chirality : 0.038 0.150 1504 Planarity : 0.002 0.018 1577 Dihedral : 3.702 25.236 1577 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.23), residues: 1570 helix: 2.97 (0.17), residues: 958 sheet: -1.06 (0.65), residues: 70 loop : -1.63 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00096 ( 7833) covalent geometry : angle 0.33966 (10907) hydrogen bonds : bond 0.02657 ( 734) hydrogen bonds : angle 4.29656 ( 2154) *********************** 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 : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0327 time to fit residues: 3.4573 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 118 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 overall best weight: 2.3922 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.040137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.029614 restraints weight = 115560.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.029876 restraints weight = 100410.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030047 restraints weight = 89409.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.030220 restraints weight = 82479.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.030309 restraints weight = 77068.153| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3513 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= 0.115 Angle : 0.356 5.049 10907 Z= 0.229 Chirality : 0.038 0.154 1504 Planarity : 0.002 0.017 1577 Dihedral : 3.732 25.644 1577 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.23), residues: 1570 helix: 3.02 (0.17), residues: 968 sheet: -0.95 (0.65), residues: 70 loop : -1.66 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00153 ( 7833) covalent geometry : angle 0.35640 (10907) hydrogen bonds : bond 0.02837 ( 734) hydrogen bonds : angle 4.36038 ( 2154) *********************** 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 : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0340 time to fit residues: 3.5408 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 119 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.039310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.029118 restraints weight = 117288.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029390 restraints weight = 101093.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.029593 restraints weight = 90010.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.029717 restraints weight = 82458.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029815 restraints weight = 77741.834| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4080 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= 0.185 Angle : 0.428 4.943 10907 Z= 0.283 Chirality : 0.039 0.147 1504 Planarity : 0.002 0.016 1577 Dihedral : 4.403 31.208 1577 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.23), residues: 1570 helix: 2.38 (0.17), residues: 967 sheet: -1.35 (0.62), residues: 71 loop : -1.82 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7833) covalent geometry : angle 0.42834 (10907) hydrogen bonds : bond 0.03590 ( 734) hydrogen bonds : angle 4.96002 ( 2154) *********************** 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 : 0.374 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0351 time to fit residues: 3.7270 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 : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 35 optimal weight: 10.0000 chunk 147 optimal weight: 50.0000 chunk 82 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.038490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.029100 restraints weight = 117443.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.028947 restraints weight = 107077.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.028961 restraints weight = 98218.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.028997 restraints weight = 95724.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.029025 restraints weight = 93637.722| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7833 Z= 0.256 Angle : 0.494 5.416 10907 Z= 0.333 Chirality : 0.040 0.150 1504 Planarity : 0.003 0.013 1577 Dihedral : 4.937 27.162 1577 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1570 helix: 1.33 (0.17), residues: 957 sheet: -1.99 (0.59), residues: 71 loop : -2.00 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7833) covalent geometry : angle 0.49425 (10907) hydrogen bonds : bond 0.04269 ( 734) hydrogen bonds : angle 5.48646 ( 2154) *********************** 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 : 0.296 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0357 time to fit residues: 3.7478 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.039653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.029335 restraints weight = 114371.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.029597 restraints weight = 97391.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.029841 restraints weight = 86878.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.029983 restraints weight = 78991.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.030030 restraints weight = 73895.933| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4946 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= 0.086 Angle : 0.349 5.039 10907 Z= 0.223 Chirality : 0.038 0.149 1504 Planarity : 0.002 0.013 1577 Dihedral : 4.088 26.074 1577 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.88 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.23), residues: 1570 helix: 2.59 (0.17), residues: 959 sheet: -1.80 (0.59), residues: 70 loop : -1.82 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00113 ( 7833) covalent geometry : angle 0.34853 (10907) hydrogen bonds : bond 0.02928 ( 734) hydrogen bonds : angle 4.56033 ( 2154) ********************** 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 : 0.298 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0322 time to fit residues: 3.3905 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 157 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 2.0062 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.039533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029321 restraints weight = 115474.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.029586 restraints weight = 99507.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029685 restraints weight = 88996.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029685 restraints weight = 82518.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029685 restraints weight = 82518.204| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 7833 Z= 0.109 Angle : 0.352 4.570 10907 Z= 0.227 Chirality : 0.038 0.146 1504 Planarity : 0.002 0.013 1577 Dihedral : 3.856 26.525 1577 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.23), residues: 1570 helix: 2.87 (0.17), residues: 967 sheet: -1.62 (0.60), residues: 71 loop : -1.73 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 7 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 13 Details of bonding type rmsd covalent geometry : bond 0.00146 ( 7833) covalent geometry : angle 0.35164 (10907) hydrogen bonds : bond 0.02833 ( 734) hydrogen bonds : angle 4.38681 ( 2154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.79 seconds wall clock time: 28 minutes 37.37 seconds (1717.37 seconds total)