Starting phenix.real_space_refine on Fri Mar 15 21:10:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kld_0707/03_2024/6kld_0707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kld_0707/03_2024/6kld_0707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kld_0707/03_2024/6kld_0707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kld_0707/03_2024/6kld_0707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kld_0707/03_2024/6kld_0707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kld_0707/03_2024/6kld_0707.pdb" } resolution = 3.58 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= 0.011 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 1 6.06 5 S 86 5.16 5 C 8159 2.51 5 N 2148 2.21 5 O 2399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A TYR 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1454": "OE1" <-> "OE2" Residue "A ASP 1488": "OD1" <-> "OD2" Residue "A ASP 1504": "OD1" <-> "OD2" Residue "A PHE 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1557": "OD1" <-> "OD2" Residue "A PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1692": "OE1" <-> "OE2" Residue "A PHE 1715": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12794 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1619, 12794 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'peptide': 1617, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 48, 'TRANS': 1568, None: 2} Not linked: pdbres="GLN A1815 " pdbres=" MN A2301 " Not linked: pdbres=" MN A2301 " pdbres=" ZN A2302 " Chain breaks: 16 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 129 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 284 40.315 69.743 28.123 1.00 52.57 S ATOM 2195 SG CYS A 287 43.390 69.962 25.837 1.00 53.80 S ATOM 3474 SG CYS A 470 39.712 71.589 24.834 1.00 87.91 S Time building chain proxies: 6.53, per 1000 atoms: 0.51 Number of scatterers: 12794 At special positions: 0 Unit cell: (114.24, 114.24, 119.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Mn 1 24.99 S 86 16.00 O 2399 8.00 N 2148 7.00 C 8159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " Number of angles added : 3 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 10 sheets defined 54.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.768A pdb=" N GLU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.547A pdb=" N GLY A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 57 removed outlier: 4.515A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 removed outlier: 3.638A pdb=" N ILE A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 133 removed outlier: 3.510A pdb=" N LYS A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.965A pdb=" N ARG A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.742A pdb=" N LEU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.961A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.545A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.693A pdb=" N LEU A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.584A pdb=" N ASN A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 417 " --> pdb=" O TRP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.979A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.541A pdb=" N MET A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 501 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 579 through 583 removed outlier: 4.440A pdb=" N PHE A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 605 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.639A pdb=" N GLN A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.556A pdb=" N LEU A 655 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 679 removed outlier: 4.266A pdb=" N VAL A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.535A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 864 through 874 removed outlier: 3.618A pdb=" N LEU A 868 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 869 " --> pdb=" O THR A 865 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 898 through 921 removed outlier: 3.652A pdb=" N ASP A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 967 removed outlier: 3.626A pdb=" N VAL A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 3.728A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 removed outlier: 3.527A pdb=" N LYS A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1249 Processing helix chain 'A' and resid 1264 through 1273 Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 3.835A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.668A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1450 Processing helix chain 'A' and resid 1472 through 1485 Processing helix chain 'A' and resid 1488 through 1507 Processing helix chain 'A' and resid 1513 through 1520 removed outlier: 3.778A pdb=" N ASN A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.913A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1625 Processing helix chain 'A' and resid 1639 through 1645 removed outlier: 3.733A pdb=" N VAL A1643 " --> pdb=" O TYR A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1669 removed outlier: 3.659A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.638A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1699 removed outlier: 3.861A pdb=" N SER A1699 " --> pdb=" O TRP A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 3.775A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1783 removed outlier: 3.535A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1787 through 1793 removed outlier: 3.677A pdb=" N HIS A1791 " --> pdb=" O GLY A1787 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A1793 " --> pdb=" O ILE A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1809 removed outlier: 3.549A pdb=" N ALA A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1805 through 1809' Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.506A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 6.167A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.744A pdb=" N GLU A1237 " --> pdb=" O PHE A1117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1119 through 1122 Processing sheet with id=AA7, first strand: chain 'A' and resid 1379 through 1380 Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA9, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AB1, first strand: chain 'A' and resid 1716 through 1719 612 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4135 1.34 - 1.46: 2880 1.46 - 1.58: 5874 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 13013 Sorted by residual: bond pdb=" CG GLU A 220 " pdb=" CD GLU A 220 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" CB ASP A1488 " pdb=" CG ASP A1488 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" CA SER A 950 " pdb=" C SER A 950 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.10e-02 2.27e+03 8.79e-01 bond pdb=" CA ASP A1488 " pdb=" CB ASP A1488 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.36e-01 bond pdb=" N ASP A1488 " pdb=" CA ASP A1488 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.66e-01 ... (remaining 13008 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.95: 161 104.95 - 112.21: 6615 112.21 - 119.47: 4356 119.47 - 126.73: 6295 126.73 - 133.99: 127 Bond angle restraints: 17554 Sorted by residual: angle pdb=" C ASN A 219 " pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta sigma weight residual 122.38 114.97 7.41 1.81e+00 3.05e-01 1.68e+01 angle pdb=" C ASP A 248 " pdb=" N GLU A 249 " pdb=" CA GLU A 249 " ideal model delta sigma weight residual 122.08 116.53 5.55 1.53e+00 4.27e-01 1.32e+01 angle pdb=" N GLU A 220 " pdb=" CA GLU A 220 " pdb=" CB GLU A 220 " ideal model delta sigma weight residual 110.44 115.30 -4.86 1.53e+00 4.27e-01 1.01e+01 angle pdb=" N ILE A1435 " pdb=" CA ILE A1435 " pdb=" C ILE A1435 " ideal model delta sigma weight residual 111.81 109.12 2.69 8.60e-01 1.35e+00 9.80e+00 angle pdb=" N GLU A 249 " pdb=" CA GLU A 249 " pdb=" C GLU A 249 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.59e+00 ... (remaining 17549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.25: 7171 18.25 - 36.51: 619 36.51 - 54.76: 105 54.76 - 73.01: 12 73.01 - 91.27: 14 Dihedral angle restraints: 7921 sinusoidal: 3195 harmonic: 4726 Sorted by residual: dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 60 " pdb=" CB CYS A 60 " ideal model delta sinusoidal sigma weight residual 93.00 4.33 88.67 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CA ASP A1467 " pdb=" C ASP A1467 " pdb=" N TRP A1468 " pdb=" CA TRP A1468 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASP A 826 " pdb=" C ASP A 826 " pdb=" N GLU A 827 " pdb=" CA GLU A 827 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 7918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1454 0.041 - 0.082: 454 0.082 - 0.123: 100 0.123 - 0.163: 17 0.163 - 0.204: 2 Chirality restraints: 2027 Sorted by residual: chirality pdb=" CB VAL A1465 " pdb=" CA VAL A1465 " pdb=" CG1 VAL A1465 " pdb=" CG2 VAL A1465 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU A 618 " pdb=" CB LEU A 618 " pdb=" CD1 LEU A 618 " pdb=" CD2 LEU A 618 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA ASP A1488 " pdb=" N ASP A1488 " pdb=" C ASP A1488 " pdb=" CB ASP A1488 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2024 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1753 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A1754 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1754 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1754 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 36 " 0.029 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 37 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1488 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ASP A1488 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP A1488 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A1489 " 0.008 2.00e-02 2.50e+03 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1115 2.74 - 3.28: 13252 3.28 - 3.82: 19806 3.82 - 4.36: 22620 4.36 - 4.90: 39718 Nonbonded interactions: 96511 Sorted by model distance: nonbonded pdb=" OD1 ASP A1188 " pdb="MN MN A2301 " model vdw 2.199 2.320 nonbonded pdb=" ND2 ASN A 788 " pdb=" OE1 GLU A1209 " model vdw 2.217 2.520 nonbonded pdb=" OE2 GLU A 102 " pdb=" NZ LYS A 122 " model vdw 2.219 2.520 nonbonded pdb=" NH1 ARG A 553 " pdb=" OH TYR A 555 " model vdw 2.223 2.520 nonbonded pdb=" O LYS A 757 " pdb=" OG SER A 761 " model vdw 2.249 2.440 ... (remaining 96506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 2.380 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 36.790 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.003 0.031 13013 Z= 0.217 Angle : 0.635 10.003 17554 Z= 0.323 Chirality : 0.041 0.204 2027 Planarity : 0.004 0.044 2219 Dihedral : 14.001 91.266 4835 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1583 helix: 1.10 (0.19), residues: 821 sheet: -0.84 (0.51), residues: 95 loop : -2.65 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1717 HIS 0.004 0.001 HIS A 472 PHE 0.013 0.001 PHE A 286 TYR 0.023 0.001 TYR A 701 ARG 0.006 0.000 ARG A1473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.422 Fit side-chains REVERT: A 146 ASN cc_start: 0.8554 (p0) cc_final: 0.8195 (p0) REVERT: A 189 HIS cc_start: 0.8212 (t-90) cc_final: 0.7974 (t70) REVERT: A 300 PHE cc_start: 0.8810 (m-10) cc_final: 0.8580 (m-10) REVERT: A 478 MET cc_start: 0.8340 (mtm) cc_final: 0.8126 (mtm) REVERT: A 639 LEU cc_start: 0.9120 (tp) cc_final: 0.8780 (tp) REVERT: A 658 GLU cc_start: 0.7516 (pp20) cc_final: 0.7310 (pp20) REVERT: A 860 LEU cc_start: 0.7457 (pt) cc_final: 0.7200 (pp) REVERT: A 892 LEU cc_start: 0.8019 (mm) cc_final: 0.7566 (mm) REVERT: A 958 ILE cc_start: 0.8084 (mt) cc_final: 0.7836 (mt) REVERT: A 999 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6855 (pm20) REVERT: A 1097 TYR cc_start: 0.7591 (t80) cc_final: 0.7331 (t80) REVERT: A 1352 LEU cc_start: 0.9309 (tp) cc_final: 0.9091 (tp) REVERT: A 1655 CYS cc_start: 0.8117 (m) cc_final: 0.7665 (t) REVERT: A 1695 GLU cc_start: 0.7313 (pp20) cc_final: 0.7044 (pp20) REVERT: A 1733 MET cc_start: 0.3958 (tpt) cc_final: 0.3738 (tpt) REVERT: A 1780 ASP cc_start: 0.7815 (t70) cc_final: 0.7507 (t70) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2373 time to fit residues: 92.1455 Evaluate side-chains 207 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 76 optimal weight: 0.0050 chunk 93 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 ASN A1514 ASN A1791 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13013 Z= 0.194 Angle : 0.589 9.320 17554 Z= 0.295 Chirality : 0.040 0.156 2027 Planarity : 0.003 0.040 2219 Dihedral : 4.188 21.718 1715 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 1.38 % Allowed : 9.37 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.21), residues: 1583 helix: 1.26 (0.19), residues: 831 sheet: -0.78 (0.52), residues: 95 loop : -2.60 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1717 HIS 0.008 0.001 HIS A 472 PHE 0.021 0.001 PHE A1621 TYR 0.013 0.001 TYR A1097 ARG 0.003 0.000 ARG A1769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8460 (p0) cc_final: 0.8007 (p0) REVERT: A 189 HIS cc_start: 0.8186 (t-90) cc_final: 0.7940 (t70) REVERT: A 639 LEU cc_start: 0.9120 (tp) cc_final: 0.8765 (tp) REVERT: A 640 MET cc_start: 0.8748 (mmm) cc_final: 0.8514 (mmm) REVERT: A 658 GLU cc_start: 0.7467 (pp20) cc_final: 0.7258 (pp20) REVERT: A 860 LEU cc_start: 0.7426 (pt) cc_final: 0.7204 (pp) REVERT: A 888 GLU cc_start: 0.7591 (pm20) cc_final: 0.7152 (pm20) REVERT: A 892 LEU cc_start: 0.8083 (mm) cc_final: 0.7441 (mm) REVERT: A 958 ILE cc_start: 0.8080 (mt) cc_final: 0.7811 (mt) REVERT: A 999 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7036 (pm20) REVERT: A 1352 LEU cc_start: 0.9193 (tp) cc_final: 0.8982 (tp) REVERT: A 1393 THR cc_start: 0.8974 (p) cc_final: 0.8747 (p) REVERT: A 1533 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6400 (t80) REVERT: A 1540 GLU cc_start: 0.6728 (mp0) cc_final: 0.6414 (mp0) REVERT: A 1655 CYS cc_start: 0.8128 (m) cc_final: 0.7772 (t) REVERT: A 1717 TRP cc_start: 0.8110 (p-90) cc_final: 0.7752 (p-90) REVERT: A 1771 LYS cc_start: 0.6223 (tptt) cc_final: 0.5949 (tptt) REVERT: A 1780 ASP cc_start: 0.7956 (t70) cc_final: 0.7647 (t70) outliers start: 20 outliers final: 13 residues processed: 251 average time/residue: 0.2217 time to fit residues: 83.4613 Evaluate side-chains 219 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1533 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 40 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A 901 GLN A1034 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13013 Z= 0.210 Angle : 0.578 9.544 17554 Z= 0.291 Chirality : 0.040 0.151 2027 Planarity : 0.003 0.037 2219 Dihedral : 4.144 22.451 1715 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.72 % Favored : 91.22 % Rotamer: Outliers : 2.48 % Allowed : 13.51 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.21), residues: 1583 helix: 1.36 (0.19), residues: 830 sheet: -0.85 (0.51), residues: 95 loop : -2.62 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1549 HIS 0.007 0.001 HIS A 472 PHE 0.020 0.001 PHE A1025 TYR 0.018 0.001 TYR A1097 ARG 0.003 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8456 (p0) cc_final: 0.7949 (p0) REVERT: A 189 HIS cc_start: 0.8191 (t-90) cc_final: 0.7902 (t70) REVERT: A 639 LEU cc_start: 0.9147 (tp) cc_final: 0.8825 (tp) REVERT: A 640 MET cc_start: 0.8718 (mmm) cc_final: 0.8481 (mmm) REVERT: A 888 GLU cc_start: 0.7725 (pm20) cc_final: 0.7258 (pm20) REVERT: A 892 LEU cc_start: 0.8048 (mm) cc_final: 0.7304 (mm) REVERT: A 999 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7084 (pm20) REVERT: A 1097 TYR cc_start: 0.7488 (t80) cc_final: 0.7215 (t80) REVERT: A 1352 LEU cc_start: 0.9189 (tp) cc_final: 0.8971 (tp) REVERT: A 1393 THR cc_start: 0.9040 (p) cc_final: 0.8829 (p) REVERT: A 1540 GLU cc_start: 0.7016 (mp0) cc_final: 0.6579 (mp0) REVERT: A 1655 CYS cc_start: 0.8135 (m) cc_final: 0.7702 (t) REVERT: A 1780 ASP cc_start: 0.8072 (t70) cc_final: 0.7759 (t70) outliers start: 36 outliers final: 25 residues processed: 245 average time/residue: 0.2188 time to fit residues: 80.8207 Evaluate side-chains 230 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1356 CYS Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1533 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13013 Z= 0.198 Angle : 0.572 9.748 17554 Z= 0.286 Chirality : 0.039 0.156 2027 Planarity : 0.003 0.033 2219 Dihedral : 4.112 21.908 1715 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 2.83 % Allowed : 15.44 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.22), residues: 1583 helix: 1.45 (0.19), residues: 830 sheet: -0.93 (0.51), residues: 97 loop : -2.64 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1717 HIS 0.007 0.001 HIS A 472 PHE 0.022 0.001 PHE A1621 TYR 0.016 0.001 TYR A1097 ARG 0.008 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8498 (p0) cc_final: 0.8102 (p0) REVERT: A 189 HIS cc_start: 0.8154 (t-90) cc_final: 0.7878 (t70) REVERT: A 639 LEU cc_start: 0.9150 (tp) cc_final: 0.8836 (tp) REVERT: A 640 MET cc_start: 0.8637 (mmm) cc_final: 0.8341 (mmm) REVERT: A 827 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: A 867 TYR cc_start: 0.8717 (t80) cc_final: 0.8416 (t80) REVERT: A 888 GLU cc_start: 0.7815 (pm20) cc_final: 0.7374 (pm20) REVERT: A 892 LEU cc_start: 0.8094 (mm) cc_final: 0.7357 (mm) REVERT: A 999 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6935 (pm20) REVERT: A 1018 SER cc_start: 0.8964 (p) cc_final: 0.8764 (p) REVERT: A 1097 TYR cc_start: 0.7375 (t80) cc_final: 0.6957 (t80) REVERT: A 1352 LEU cc_start: 0.9143 (tp) cc_final: 0.8922 (tp) REVERT: A 1393 THR cc_start: 0.8985 (p) cc_final: 0.8755 (p) REVERT: A 1466 LYS cc_start: 0.7917 (tmtt) cc_final: 0.7539 (tmtt) REVERT: A 1540 GLU cc_start: 0.7120 (mp0) cc_final: 0.6770 (mp0) REVERT: A 1655 CYS cc_start: 0.8183 (m) cc_final: 0.7717 (t) outliers start: 41 outliers final: 31 residues processed: 255 average time/residue: 0.2155 time to fit residues: 83.9243 Evaluate side-chains 237 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 800 ASN Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1356 CYS Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1793 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 0.0040 chunk 132 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 139 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13013 Z= 0.147 Angle : 0.544 10.191 17554 Z= 0.273 Chirality : 0.038 0.155 2027 Planarity : 0.003 0.036 2219 Dihedral : 3.957 20.094 1715 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 2.55 % Allowed : 17.64 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.22), residues: 1583 helix: 1.59 (0.19), residues: 834 sheet: -0.57 (0.54), residues: 87 loop : -2.55 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1717 HIS 0.005 0.001 HIS A 472 PHE 0.020 0.001 PHE A 91 TYR 0.013 0.001 TYR A1097 ARG 0.004 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 CYS cc_start: 0.5540 (OUTLIER) cc_final: 0.5177 (p) REVERT: A 146 ASN cc_start: 0.8512 (p0) cc_final: 0.8216 (p0) REVERT: A 189 HIS cc_start: 0.8094 (t70) cc_final: 0.7886 (t70) REVERT: A 376 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7580 (mmm-85) REVERT: A 639 LEU cc_start: 0.9066 (tp) cc_final: 0.8763 (tp) REVERT: A 867 TYR cc_start: 0.8714 (t80) cc_final: 0.8461 (t80) REVERT: A 888 GLU cc_start: 0.7808 (pm20) cc_final: 0.7362 (pm20) REVERT: A 892 LEU cc_start: 0.8078 (mm) cc_final: 0.7307 (mm) REVERT: A 999 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6995 (pm20) REVERT: A 1352 LEU cc_start: 0.9111 (tp) cc_final: 0.8886 (tp) REVERT: A 1393 THR cc_start: 0.8798 (p) cc_final: 0.8598 (p) REVERT: A 1466 LYS cc_start: 0.7843 (tmtt) cc_final: 0.7454 (tmtt) REVERT: A 1717 TRP cc_start: 0.7953 (p-90) cc_final: 0.7702 (p-90) outliers start: 37 outliers final: 28 residues processed: 249 average time/residue: 0.2068 time to fit residues: 78.5272 Evaluate side-chains 233 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 800 ASN Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1793 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 38 optimal weight: 0.0040 chunk 155 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13013 Z= 0.244 Angle : 0.602 10.972 17554 Z= 0.302 Chirality : 0.040 0.164 2027 Planarity : 0.003 0.033 2219 Dihedral : 4.082 22.067 1715 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.41 % Favored : 90.52 % Rotamer: Outliers : 3.03 % Allowed : 19.09 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.22), residues: 1583 helix: 1.57 (0.19), residues: 832 sheet: -0.87 (0.51), residues: 97 loop : -2.60 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.006 0.001 HIS A 472 PHE 0.019 0.001 PHE A 91 TYR 0.018 0.001 TYR A 782 ARG 0.004 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 210 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 60 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5577 (p) REVERT: A 146 ASN cc_start: 0.8497 (p0) cc_final: 0.8160 (p0) REVERT: A 189 HIS cc_start: 0.8201 (t70) cc_final: 0.7879 (t70) REVERT: A 376 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7754 (mmm-85) REVERT: A 485 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7803 (mmm160) REVERT: A 867 TYR cc_start: 0.8817 (t80) cc_final: 0.8549 (t80) REVERT: A 888 GLU cc_start: 0.7858 (pm20) cc_final: 0.7422 (pm20) REVERT: A 892 LEU cc_start: 0.8174 (mm) cc_final: 0.7426 (mm) REVERT: A 999 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6943 (pm20) REVERT: A 1196 MET cc_start: 0.7769 (mtt) cc_final: 0.7263 (mtt) REVERT: A 1352 LEU cc_start: 0.9171 (tp) cc_final: 0.8924 (tp) REVERT: A 1393 THR cc_start: 0.8964 (p) cc_final: 0.8747 (p) REVERT: A 1417 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 1466 LYS cc_start: 0.7850 (tmtt) cc_final: 0.7397 (tmtt) REVERT: A 1771 LYS cc_start: 0.6275 (tptt) cc_final: 0.6013 (tptt) REVERT: A 1813 ILE cc_start: 0.8245 (mp) cc_final: 0.8019 (tt) outliers start: 44 outliers final: 35 residues processed: 241 average time/residue: 0.2103 time to fit residues: 77.1282 Evaluate side-chains 237 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1793 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 113 optimal weight: 0.0010 chunk 131 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13013 Z= 0.189 Angle : 0.585 12.093 17554 Z= 0.292 Chirality : 0.039 0.152 2027 Planarity : 0.003 0.032 2219 Dihedral : 4.058 20.685 1715 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.72 % Favored : 91.22 % Rotamer: Outliers : 3.38 % Allowed : 19.64 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1583 helix: 1.60 (0.19), residues: 832 sheet: -0.78 (0.52), residues: 97 loop : -2.60 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1717 HIS 0.005 0.001 HIS A 472 PHE 0.020 0.001 PHE A 91 TYR 0.023 0.001 TYR A 782 ARG 0.003 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 213 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 60 CYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5535 (p) REVERT: A 146 ASN cc_start: 0.8520 (p0) cc_final: 0.8159 (p0) REVERT: A 189 HIS cc_start: 0.8169 (t70) cc_final: 0.7878 (t70) REVERT: A 485 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7748 (mmm160) REVERT: A 639 LEU cc_start: 0.8990 (tp) cc_final: 0.8578 (tp) REVERT: A 640 MET cc_start: 0.8549 (mmm) cc_final: 0.8290 (mmm) REVERT: A 867 TYR cc_start: 0.8822 (t80) cc_final: 0.8535 (t80) REVERT: A 888 GLU cc_start: 0.7843 (pm20) cc_final: 0.7413 (pm20) REVERT: A 892 LEU cc_start: 0.8119 (mm) cc_final: 0.7360 (mm) REVERT: A 999 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6950 (pm20) REVERT: A 1352 LEU cc_start: 0.9142 (tp) cc_final: 0.8902 (tp) REVERT: A 1393 THR cc_start: 0.8875 (p) cc_final: 0.8651 (p) REVERT: A 1466 LYS cc_start: 0.7858 (tmtt) cc_final: 0.7423 (tmtt) REVERT: A 1813 ILE cc_start: 0.8218 (mp) cc_final: 0.8008 (tt) outliers start: 49 outliers final: 39 residues processed: 244 average time/residue: 0.2166 time to fit residues: 80.6373 Evaluate side-chains 246 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1356 CYS Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1793 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.0670 chunk 14 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13013 Z= 0.198 Angle : 0.599 12.392 17554 Z= 0.298 Chirality : 0.040 0.175 2027 Planarity : 0.003 0.033 2219 Dihedral : 4.072 21.578 1715 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.16 % Favored : 90.78 % Rotamer: Outliers : 3.38 % Allowed : 19.99 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.22), residues: 1583 helix: 1.55 (0.19), residues: 842 sheet: -0.68 (0.53), residues: 95 loop : -2.53 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1549 HIS 0.005 0.001 HIS A 472 PHE 0.026 0.001 PHE A1025 TYR 0.016 0.001 TYR A 782 ARG 0.003 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 207 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 60 CYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5564 (p) REVERT: A 146 ASN cc_start: 0.8529 (p0) cc_final: 0.8149 (p0) REVERT: A 189 HIS cc_start: 0.8228 (t70) cc_final: 0.7922 (t70) REVERT: A 485 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7790 (mmm160) REVERT: A 639 LEU cc_start: 0.9070 (tp) cc_final: 0.8624 (tp) REVERT: A 640 MET cc_start: 0.8564 (mmm) cc_final: 0.8317 (mmm) REVERT: A 867 TYR cc_start: 0.8817 (t80) cc_final: 0.8564 (t80) REVERT: A 888 GLU cc_start: 0.7840 (pm20) cc_final: 0.7417 (pm20) REVERT: A 892 LEU cc_start: 0.8154 (mm) cc_final: 0.7393 (mm) REVERT: A 999 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6950 (pm20) REVERT: A 1196 MET cc_start: 0.8006 (mtt) cc_final: 0.7575 (mtt) REVERT: A 1352 LEU cc_start: 0.9156 (tp) cc_final: 0.8913 (tp) REVERT: A 1393 THR cc_start: 0.8866 (p) cc_final: 0.8638 (p) REVERT: A 1466 LYS cc_start: 0.7862 (tmtt) cc_final: 0.7416 (tmtt) REVERT: A 1813 ILE cc_start: 0.8224 (mp) cc_final: 0.8021 (tt) outliers start: 49 outliers final: 43 residues processed: 237 average time/residue: 0.2101 time to fit residues: 76.4262 Evaluate side-chains 248 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1356 CYS Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1793 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13013 Z= 0.159 Angle : 0.585 12.609 17554 Z= 0.290 Chirality : 0.039 0.170 2027 Planarity : 0.003 0.033 2219 Dihedral : 4.003 20.226 1715 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.84 % Favored : 91.09 % Rotamer: Outliers : 2.76 % Allowed : 20.54 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.22), residues: 1583 helix: 1.64 (0.19), residues: 839 sheet: -0.66 (0.53), residues: 95 loop : -2.50 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1549 HIS 0.004 0.001 HIS A 472 PHE 0.022 0.001 PHE A 91 TYR 0.013 0.001 TYR A 782 ARG 0.003 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 60 CYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5482 (p) REVERT: A 146 ASN cc_start: 0.8532 (p0) cc_final: 0.8150 (p0) REVERT: A 485 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7706 (mmm160) REVERT: A 639 LEU cc_start: 0.8977 (tp) cc_final: 0.8557 (tp) REVERT: A 640 MET cc_start: 0.8569 (mmm) cc_final: 0.8315 (mmm) REVERT: A 867 TYR cc_start: 0.8794 (t80) cc_final: 0.8493 (t80) REVERT: A 888 GLU cc_start: 0.7817 (pm20) cc_final: 0.7400 (pm20) REVERT: A 892 LEU cc_start: 0.8167 (mm) cc_final: 0.7394 (mm) REVERT: A 999 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6947 (pm20) REVERT: A 1196 MET cc_start: 0.7991 (mtt) cc_final: 0.7542 (mtt) REVERT: A 1352 LEU cc_start: 0.9123 (tp) cc_final: 0.8887 (tp) REVERT: A 1466 LYS cc_start: 0.7856 (tmtt) cc_final: 0.7427 (tmtt) REVERT: A 1771 LYS cc_start: 0.5915 (tptt) cc_final: 0.5693 (tptt) REVERT: A 1813 ILE cc_start: 0.8220 (mp) cc_final: 0.8007 (tt) outliers start: 40 outliers final: 34 residues processed: 238 average time/residue: 0.2143 time to fit residues: 77.9574 Evaluate side-chains 243 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 800 ASN Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1793 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 39 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13013 Z= 0.166 Angle : 0.599 12.486 17554 Z= 0.296 Chirality : 0.039 0.170 2027 Planarity : 0.003 0.036 2219 Dihedral : 3.989 19.942 1715 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.91 % Favored : 91.03 % Rotamer: Outliers : 2.62 % Allowed : 21.50 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.22), residues: 1583 helix: 1.71 (0.19), residues: 833 sheet: -0.72 (0.52), residues: 95 loop : -2.42 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1549 HIS 0.005 0.001 HIS A 189 PHE 0.022 0.001 PHE A 91 TYR 0.014 0.001 TYR A1097 ARG 0.003 0.000 ARG A 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 1.959 Fit side-chains revert: symmetry clash REVERT: A 60 CYS cc_start: 0.5804 (OUTLIER) cc_final: 0.5446 (p) REVERT: A 146 ASN cc_start: 0.8534 (p0) cc_final: 0.8147 (p0) REVERT: A 639 LEU cc_start: 0.8979 (tp) cc_final: 0.8542 (tp) REVERT: A 640 MET cc_start: 0.8557 (mmm) cc_final: 0.8298 (mmm) REVERT: A 701 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.9052 (m-80) REVERT: A 867 TYR cc_start: 0.8803 (t80) cc_final: 0.8506 (t80) REVERT: A 888 GLU cc_start: 0.7820 (pm20) cc_final: 0.6822 (tt0) REVERT: A 892 LEU cc_start: 0.8187 (mm) cc_final: 0.7391 (mm) REVERT: A 989 LYS cc_start: 0.8462 (tptp) cc_final: 0.8237 (tptt) REVERT: A 999 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6963 (pm20) REVERT: A 1196 MET cc_start: 0.7986 (mtt) cc_final: 0.7534 (mtt) REVERT: A 1352 LEU cc_start: 0.9129 (tp) cc_final: 0.8892 (tp) REVERT: A 1466 LYS cc_start: 0.7868 (tmtt) cc_final: 0.7434 (tmtt) REVERT: A 1765 MET cc_start: 0.2013 (mtm) cc_final: 0.0731 (tpp) REVERT: A 1771 LYS cc_start: 0.5891 (tptt) cc_final: 0.5643 (tptt) REVERT: A 1813 ILE cc_start: 0.8219 (mp) cc_final: 0.8007 (tt) outliers start: 38 outliers final: 34 residues processed: 237 average time/residue: 0.2286 time to fit residues: 82.6221 Evaluate side-chains 246 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 800 ASN Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1160 CYS Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1533 TYR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1793 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 35 optimal weight: 0.0980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113466 restraints weight = 18507.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116134 restraints weight = 11737.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117017 restraints weight = 8924.459| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13013 Z= 0.173 Angle : 0.607 12.394 17554 Z= 0.298 Chirality : 0.039 0.171 2027 Planarity : 0.003 0.036 2219 Dihedral : 4.015 19.718 1715 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 2.69 % Allowed : 21.85 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.22), residues: 1583 helix: 1.73 (0.19), residues: 831 sheet: -0.72 (0.52), residues: 95 loop : -2.44 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1549 HIS 0.006 0.001 HIS A 189 PHE 0.022 0.001 PHE A 91 TYR 0.013 0.001 TYR A 558 ARG 0.004 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2477.47 seconds wall clock time: 45 minutes 44.28 seconds (2744.28 seconds total)