Starting phenix.real_space_refine on Wed Feb 14 14:51:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wll_32587/02_2024/7wll_32587.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wll_32587/02_2024/7wll_32587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wll_32587/02_2024/7wll_32587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wll_32587/02_2024/7wll_32587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wll_32587/02_2024/7wll_32587.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wll_32587/02_2024/7wll_32587.pdb" } resolution = 3.6 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= -0.004 sd= 0.106 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 78 5.16 5 C 6358 2.51 5 N 1504 2.21 5 O 1595 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1466": "NH1" <-> "NH2" Residue "A PHE 1546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1653": "OE1" <-> "OE2" Residue "A GLU 1662": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9540 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1156, 9529 Unusual residues: {' CA': 2, '1II': 1, '3PE': 9, 'NAG': 2, 'Y01': 7} Classifications: {'peptide': 1135, 'undetermined': 21} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 21} Not linked: pdbres="LYS A1738 " pdbres="1II A2301 " Not linked: pdbres="1II A2301 " pdbres="3PE A2302 " Not linked: pdbres="3PE A2302 " pdbres="3PE A2303 " Not linked: pdbres="3PE A2303 " pdbres="3PE A2304 " Not linked: pdbres="3PE A2304 " pdbres="3PE A2305 " ... (remaining 16 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'3PE:plan-1': 8, '3PE:plan-2': 8, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Conformer: "B" Number of residues, atoms: 1156, 9529 Unusual residues: {' CA': 2, '1II': 1, '3PE': 9, 'NAG': 2, 'Y01': 7} Classifications: {'peptide': 1135, 'undetermined': 21} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 21} Not linked: pdbres="LYS A1738 " pdbres="1II A2301 " Not linked: pdbres="1II A2301 " pdbres="3PE A2302 " Not linked: pdbres="3PE A2302 " pdbres="3PE A2303 " Not linked: pdbres="3PE A2303 " pdbres="3PE A2304 " Not linked: pdbres="3PE A2304 " pdbres="3PE A2305 " ... (remaining 16 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'3PE:plan-1': 8, '3PE:plan-2': 8, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 bond proxies already assigned to first conformer: 9732 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 854 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 854 " occ=0.50 Time building chain proxies: 10.18, per 1000 atoms: 1.07 Number of scatterers: 9540 At special positions: 0 Unit cell: (111.28, 122.72, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 78 16.00 P 1 15.00 F 2 9.00 O 1595 8.00 N 1504 7.00 C 6358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1349 " distance=2.03 Simple disulfide: pdb=" SG CYS A1646 " - pdb=" SG CYS A1652 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1698 " 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=1, symmetry=0 Links applied NAG-ASN " NAG A2313 " - " ASN A1345 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 3.3 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 1 sheets defined 74.8% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 removed outlier: 4.243A pdb=" N CYS A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N MET A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.566A pdb=" N GLU A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 138 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 177 through 191 Proline residue: A 185 - end of helix removed outlier: 3.578A pdb=" N ASN A 190 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 209 through 231 removed outlier: 4.304A pdb=" N PHE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 343 through 355 Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.021A pdb=" N ILE A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.680A pdb=" N MET A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.912A pdb=" N ILE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 3.530A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 695 removed outlier: 3.933A pdb=" N ASN A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 4.337A pdb=" N ASN A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 721 removed outlier: 3.783A pdb=" N ILE A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.931A pdb=" N LEU A 735 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 742 " --> pdb=" O LEU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 784 removed outlier: 3.674A pdb=" N ARG A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 806 through 819 Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.827A pdb=" N VAL A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 838 through 851 removed outlier: 3.914A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 865 Processing helix chain 'A' and resid 1171 through 1188 removed outlier: 3.701A pdb=" N VAL A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1227 Processing helix chain 'A' and resid 1238 through 1260 Processing helix chain 'A' and resid 1267 through 1279 Processing helix chain 'A' and resid 1289 through 1304 removed outlier: 3.595A pdb=" N LYS A1304 " --> pdb=" O ILE A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1328 Processing helix chain 'A' and resid 1345 through 1353 Processing helix chain 'A' and resid 1366 through 1378 Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.627A pdb=" N ILE A1385 " --> pdb=" O GLY A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1406 No H-bonds generated for 'chain 'A' and resid 1404 through 1406' Processing helix chain 'A' and resid 1407 through 1462 removed outlier: 4.051A pdb=" N LEU A1415 " --> pdb=" O PHE A1411 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A1442 " --> pdb=" O ARG A1438 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA A1443 " --> pdb=" O GLN A1439 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A1444 " --> pdb=" O HIS A1440 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A1447 " --> pdb=" O ALA A1443 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1505 removed outlier: 3.540A pdb=" N ASP A1490 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A1492 " --> pdb=" O TYR A1488 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A1493 " --> pdb=" O LEU A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1541 Processing helix chain 'A' and resid 1542 through 1547 removed outlier: 3.630A pdb=" N PHE A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1542 through 1547' Processing helix chain 'A' and resid 1551 through 1575 removed outlier: 3.589A pdb=" N ASP A1555 " --> pdb=" O TRP A1551 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A1571 " --> pdb=" O THR A1567 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A1572 " --> pdb=" O LEU A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1591 removed outlier: 3.892A pdb=" N ILE A1584 " --> pdb=" O ASN A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1601 removed outlier: 3.806A pdb=" N LYS A1597 " --> pdb=" O ARG A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1614 Processing helix chain 'A' and resid 1615 through 1642 Processing helix chain 'A' and resid 1664 through 1676 removed outlier: 3.601A pdb=" N THR A1670 " --> pdb=" O MET A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1688 Processing helix chain 'A' and resid 1701 through 1738 Proline residue: A1707 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 1333 through 1334 608 hydrogen bonds defined for protein. 1734 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: 2.66 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1427 1.29 - 1.42: 2525 1.42 - 1.55: 5558 1.55 - 1.68: 121 1.68 - 1.82: 127 Bond restraints: 9758 Sorted by residual: bond pdb=" C12 1II A2301 " pdb=" N04 1II A2301 " ideal model delta sigma weight residual 1.449 1.204 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C16 1II A2301 " pdb=" O03 1II A2301 " ideal model delta sigma weight residual 1.219 1.396 -0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" C21 3PE A2302 " pdb=" O21 3PE A2302 " ideal model delta sigma weight residual 1.316 1.469 -0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C31 3PE A2302 " pdb=" O31 3PE A2302 " ideal model delta sigma weight residual 1.331 1.471 -0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C PRO A 333 " pdb=" O PRO A 333 " ideal model delta sigma weight residual 1.233 1.160 0.073 1.18e-02 7.18e+03 3.88e+01 ... (remaining 9753 not shown) Histogram of bond angle deviations from ideal: 81.25 - 91.81: 3 91.81 - 102.38: 70 102.38 - 112.94: 5562 112.94 - 123.50: 7330 123.50 - 134.07: 257 Bond angle restraints: 13222 Sorted by residual: angle pdb=" N THR A1186 " pdb=" CA THR A1186 " pdb=" C THR A1186 " ideal model delta sigma weight residual 113.50 97.99 15.51 1.23e+00 6.61e-01 1.59e+02 angle pdb=" CAE Y01 A2312 " pdb=" CBI Y01 A2312 " pdb=" CAU Y01 A2312 " ideal model delta sigma weight residual 111.22 81.82 29.40 3.00e+00 1.11e-01 9.60e+01 angle pdb=" CAE Y01 A2312 " pdb=" CBI Y01 A2312 " pdb=" CBE Y01 A2312 " ideal model delta sigma weight residual 110.21 81.25 28.96 3.00e+00 1.11e-01 9.32e+01 angle pdb=" CA PHE A1426 " pdb=" CB PHE A1426 " pdb=" CG PHE A1426 " ideal model delta sigma weight residual 113.80 123.17 -9.37 1.00e+00 1.00e+00 8.77e+01 angle pdb=" CAE Y01 A2312 " pdb=" CBI Y01 A2312 " pdb=" CBG Y01 A2312 " ideal model delta sigma weight residual 112.07 88.02 24.05 3.00e+00 1.11e-01 6.43e+01 ... (remaining 13217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 5972 35.62 - 71.24: 188 71.24 - 106.87: 9 106.87 - 142.49: 1 142.49 - 178.11: 5 Dihedral angle restraints: 6175 sinusoidal: 2856 harmonic: 3319 Sorted by residual: dihedral pdb=" CB CYS A1646 " pdb=" SG CYS A1646 " pdb=" SG CYS A1652 " pdb=" CB CYS A1652 " ideal model delta sinusoidal sigma weight residual 93.00 168.65 -75.65 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " pdb=" SG CYS A 280 " pdb=" CB CYS A 280 " ideal model delta sinusoidal sigma weight residual 93.00 156.60 -63.60 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS A1691 " pdb=" SG CYS A1691 " pdb=" SG CYS A1698 " pdb=" CB CYS A1698 " ideal model delta sinusoidal sigma weight residual -86.00 -38.88 -47.12 1 1.00e+01 1.00e-02 3.07e+01 ... (remaining 6172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.377: 1535 0.377 - 0.753: 7 0.753 - 1.130: 0 1.130 - 1.506: 0 1.506 - 1.883: 1 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CBI Y01 A2312 " pdb=" CAU Y01 A2312 " pdb=" CBE Y01 A2312 " pdb=" CBG Y01 A2312 " both_signs ideal model delta sigma weight residual False 2.94 1.05 1.88 2.00e-01 2.50e+01 8.86e+01 chirality pdb=" CBG Y01 A2314 " pdb=" CAQ Y01 A2314 " pdb=" CBD Y01 A2314 " pdb=" CBI Y01 A2314 " both_signs ideal model delta sigma weight residual False -2.33 -2.88 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CBG Y01 A2315 " pdb=" CAQ Y01 A2315 " pdb=" CBD Y01 A2315 " pdb=" CBI Y01 A2315 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 1540 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1426 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C PHE A1426 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE A1426 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL A1427 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1185 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C ILE A1185 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A1185 " -0.018 2.00e-02 2.50e+03 pdb=" N THR A1186 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 331 " 0.013 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C ALA A 331 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA A 331 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 332 " 0.016 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 95 2.60 - 3.18: 9029 3.18 - 3.75: 14414 3.75 - 4.33: 19773 4.33 - 4.90: 31754 Nonbonded interactions: 75065 Sorted by model distance: nonbonded pdb=" OD1 ASN A 850 " pdb=" O03 1II A2301 " model vdw 2.026 3.040 nonbonded pdb=" OE2 GLU A1445 " pdb=" OD1 ASP A1734 " model vdw 2.085 3.040 nonbonded pdb=" OH TYR A1524 " pdb=" OE1 GLU A1569 " model vdw 2.140 2.440 nonbonded pdb=" OD1 ASN A1345 " pdb=" OG SER A1347 " model vdw 2.165 2.440 nonbonded pdb=" OG SER A1238 " pdb=" OD1 ASN A1241 " model vdw 2.170 2.440 ... (remaining 75060 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=0.50 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: 1.250 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: 4.150 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.250 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.012 0.245 9758 Z= 0.793 Angle : 1.188 29.399 13222 Z= 0.600 Chirality : 0.084 1.883 1543 Planarity : 0.005 0.057 1582 Dihedral : 16.938 178.108 4010 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 0.50 % Allowed : 0.40 % Favored : 99.11 % Cbeta Deviations : 0.19 % 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: -0.42 (0.25), residues: 1130 helix: 0.49 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -1.93 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 231 HIS 0.010 0.002 HIS A1169 PHE 0.035 0.002 PHE A1181 TYR 0.015 0.002 TYR A 165 ARG 0.008 0.001 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 235 time to evaluate : 1.166 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9301 (mt) cc_final: 0.8854 (mt) REVERT: A 156 PHE cc_start: 0.9226 (t80) cc_final: 0.8984 (t80) REVERT: A 177 ILE cc_start: 0.9273 (tt) cc_final: 0.8992 (tt) REVERT: A 708 ASP cc_start: 0.8876 (m-30) cc_final: 0.8637 (m-30) REVERT: A 866 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6086 (mt0) REVERT: A 1259 LEU cc_start: 0.8962 (mm) cc_final: 0.8726 (mm) REVERT: A 1438 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8407 (tmm-80) REVERT: A 1592 ILE cc_start: 0.9073 (tp) cc_final: 0.8872 (tp) REVERT: A 1601 MET cc_start: 0.8670 (mpp) cc_final: 0.7958 (mpp) REVERT: A 1639 GLU cc_start: 0.8429 (tp30) cc_final: 0.8188 (tp30) outliers start: 5 outliers final: 0 residues processed: 240 average time/residue: 0.1817 time to fit residues: 63.5133 Evaluate side-chains 192 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 1438 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN A1183 ASN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9758 Z= 0.190 Angle : 0.793 30.270 13222 Z= 0.363 Chirality : 0.063 1.827 1543 Planarity : 0.004 0.049 1582 Dihedral : 13.970 172.273 1897 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.79 % Allowed : 11.53 % Favored : 86.68 % 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: 0.25 (0.25), residues: 1130 helix: 1.05 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.90 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1680 HIS 0.006 0.001 HIS A1169 PHE 0.038 0.002 PHE A1181 TYR 0.017 0.001 TYR A 364 ARG 0.006 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 389 MET cc_start: 0.8243 (tpp) cc_final: 0.7595 (ttt) REVERT: A 708 ASP cc_start: 0.8848 (m-30) cc_final: 0.8637 (m-30) REVERT: A 835 SER cc_start: 0.8670 (p) cc_final: 0.8417 (p) REVERT: A 1246 PHE cc_start: 0.8997 (t80) cc_final: 0.8766 (t80) REVERT: A 1436 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8507 (mtpp) REVERT: A 1592 ILE cc_start: 0.9001 (tp) cc_final: 0.8773 (tp) REVERT: A 1601 MET cc_start: 0.8618 (mpp) cc_final: 0.7804 (mpp) REVERT: A 1610 ASP cc_start: 0.8887 (t70) cc_final: 0.8633 (t70) REVERT: A 1704 PHE cc_start: 0.8023 (t80) cc_final: 0.7626 (t80) outliers start: 18 outliers final: 10 residues processed: 222 average time/residue: 0.1742 time to fit residues: 58.3108 Evaluate side-chains 208 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.3980 chunk 32 optimal weight: 0.0370 chunk 86 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9758 Z= 0.173 Angle : 0.761 30.269 13222 Z= 0.344 Chirality : 0.062 1.830 1543 Planarity : 0.004 0.040 1582 Dihedral : 13.152 173.042 1890 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.79 % Allowed : 13.52 % Favored : 84.69 % 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: 0.67 (0.26), residues: 1130 helix: 1.38 (0.19), residues: 769 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.022 0.001 PHE A1246 TYR 0.018 0.001 TYR A 364 ARG 0.005 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 148 ASP cc_start: 0.8594 (t0) cc_final: 0.8341 (t70) REVERT: A 157 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9135 (mp) REVERT: A 389 MET cc_start: 0.8193 (tpp) cc_final: 0.7513 (ttt) REVERT: A 708 ASP cc_start: 0.8732 (m-30) cc_final: 0.8475 (m-30) REVERT: A 835 SER cc_start: 0.8636 (p) cc_final: 0.8325 (p) REVERT: A 1246 PHE cc_start: 0.9071 (t80) cc_final: 0.8824 (t80) REVERT: A 1438 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8397 (tmm-80) REVERT: A 1592 ILE cc_start: 0.8956 (tp) cc_final: 0.8738 (tp) REVERT: A 1601 MET cc_start: 0.8627 (mpp) cc_final: 0.7784 (mpp) REVERT: A 1631 PHE cc_start: 0.8423 (t80) cc_final: 0.7985 (t80) REVERT: A 1704 PHE cc_start: 0.7956 (t80) cc_final: 0.7630 (t80) outliers start: 18 outliers final: 10 residues processed: 228 average time/residue: 0.1777 time to fit residues: 60.0095 Evaluate side-chains 207 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1611 THR Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1440 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9758 Z= 0.199 Angle : 0.774 30.185 13222 Z= 0.351 Chirality : 0.062 1.819 1543 Planarity : 0.004 0.037 1582 Dihedral : 12.857 173.879 1890 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.29 % Allowed : 15.11 % Favored : 82.60 % 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: 0.66 (0.25), residues: 1130 helix: 1.37 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -1.69 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.027 0.001 PHE A1181 TYR 0.020 0.001 TYR A 364 ARG 0.004 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 157 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9145 (mp) REVERT: A 389 MET cc_start: 0.8088 (tpp) cc_final: 0.7491 (ttt) REVERT: A 694 PHE cc_start: 0.6667 (t80) cc_final: 0.6302 (t80) REVERT: A 835 SER cc_start: 0.8660 (p) cc_final: 0.8435 (p) REVERT: A 1174 TYR cc_start: 0.8373 (m-80) cc_final: 0.7831 (m-80) REVERT: A 1246 PHE cc_start: 0.9123 (t80) cc_final: 0.8900 (t80) REVERT: A 1438 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8408 (tmm-80) REVERT: A 1483 MET cc_start: 0.4705 (ppp) cc_final: 0.4028 (tmm) REVERT: A 1524 TYR cc_start: 0.7428 (m-10) cc_final: 0.7091 (t80) REVERT: A 1592 ILE cc_start: 0.8971 (tp) cc_final: 0.8762 (tp) REVERT: A 1601 MET cc_start: 0.8689 (mpp) cc_final: 0.7917 (mpp) REVERT: A 1631 PHE cc_start: 0.8463 (t80) cc_final: 0.8059 (t80) REVERT: A 1704 PHE cc_start: 0.8048 (t80) cc_final: 0.7767 (t80) outliers start: 23 outliers final: 16 residues processed: 215 average time/residue: 0.1792 time to fit residues: 57.7505 Evaluate side-chains 216 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1611 THR Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9758 Z= 0.154 Angle : 0.748 30.345 13222 Z= 0.336 Chirality : 0.061 1.802 1543 Planarity : 0.003 0.039 1582 Dihedral : 12.500 175.184 1890 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.99 % Allowed : 16.90 % Favored : 81.11 % 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: 0.88 (0.26), residues: 1130 helix: 1.56 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1382 HIS 0.003 0.001 HIS A1169 PHE 0.019 0.001 PHE A1246 TYR 0.011 0.001 TYR A 364 ARG 0.004 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 157 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9157 (mp) REVERT: A 389 MET cc_start: 0.8116 (tpp) cc_final: 0.7539 (ttt) REVERT: A 1174 TYR cc_start: 0.8443 (m-80) cc_final: 0.7899 (m-80) REVERT: A 1246 PHE cc_start: 0.9156 (t80) cc_final: 0.8809 (t80) REVERT: A 1438 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8330 (tmm-80) REVERT: A 1524 TYR cc_start: 0.7468 (m-10) cc_final: 0.7111 (t80) REVERT: A 1592 ILE cc_start: 0.8968 (tp) cc_final: 0.8718 (tp) REVERT: A 1601 MET cc_start: 0.8631 (mpp) cc_final: 0.7803 (mpp) REVERT: A 1704 PHE cc_start: 0.7967 (t80) cc_final: 0.7485 (t80) outliers start: 20 outliers final: 14 residues processed: 226 average time/residue: 0.1715 time to fit residues: 58.6790 Evaluate side-chains 213 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1611 THR Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.0010 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9758 Z= 0.191 Angle : 0.766 30.237 13222 Z= 0.343 Chirality : 0.062 1.806 1543 Planarity : 0.003 0.040 1582 Dihedral : 12.488 174.896 1890 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.29 % Allowed : 17.20 % Favored : 80.52 % 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: 0.97 (0.26), residues: 1130 helix: 1.63 (0.19), residues: 761 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 PHE 0.016 0.001 PHE A1246 TYR 0.019 0.001 TYR A 364 ARG 0.004 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 157 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9143 (mp) REVERT: A 389 MET cc_start: 0.8174 (tpp) cc_final: 0.7704 (ttt) REVERT: A 694 PHE cc_start: 0.6379 (t80) cc_final: 0.5946 (t80) REVERT: A 761 ASN cc_start: 0.8471 (t160) cc_final: 0.8259 (t0) REVERT: A 1246 PHE cc_start: 0.9208 (t80) cc_final: 0.8841 (t80) REVERT: A 1438 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8334 (tmm-80) REVERT: A 1483 MET cc_start: 0.4468 (ppp) cc_final: 0.3926 (tmm) REVERT: A 1524 TYR cc_start: 0.7519 (m-10) cc_final: 0.7073 (t80) REVERT: A 1592 ILE cc_start: 0.8998 (tp) cc_final: 0.8772 (tp) REVERT: A 1601 MET cc_start: 0.8651 (mpp) cc_final: 0.7880 (mpp) REVERT: A 1631 PHE cc_start: 0.8367 (t80) cc_final: 0.8021 (t80) REVERT: A 1704 PHE cc_start: 0.8037 (t80) cc_final: 0.7581 (t80) outliers start: 23 outliers final: 18 residues processed: 217 average time/residue: 0.1932 time to fit residues: 64.6544 Evaluate side-chains 215 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1610 ASP Chi-restraints excluded: chain A residue 1611 THR Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.0570 chunk 44 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9758 Z= 0.171 Angle : 0.760 30.315 13222 Z= 0.340 Chirality : 0.062 1.798 1543 Planarity : 0.003 0.040 1582 Dihedral : 12.364 175.527 1890 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.29 % Allowed : 17.59 % Favored : 80.12 % 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: 0.92 (0.26), residues: 1130 helix: 1.60 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 PHE 0.015 0.001 PHE A 642 TYR 0.018 0.001 TYR A 364 ARG 0.003 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 157 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9134 (mp) REVERT: A 389 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7700 (ttm) REVERT: A 694 PHE cc_start: 0.6210 (t80) cc_final: 0.5729 (t80) REVERT: A 1174 TYR cc_start: 0.8399 (m-80) cc_final: 0.7964 (m-80) REVERT: A 1246 PHE cc_start: 0.9236 (t80) cc_final: 0.9032 (t80) REVERT: A 1438 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8335 (tmm-80) REVERT: A 1483 MET cc_start: 0.4480 (ppp) cc_final: 0.3780 (tmm) REVERT: A 1524 TYR cc_start: 0.7613 (m-10) cc_final: 0.7040 (t80) REVERT: A 1586 ILE cc_start: 0.6145 (tp) cc_final: 0.5778 (tp) REVERT: A 1592 ILE cc_start: 0.8995 (tp) cc_final: 0.8728 (tp) REVERT: A 1601 MET cc_start: 0.8659 (mpp) cc_final: 0.7987 (mpp) REVERT: A 1704 PHE cc_start: 0.8025 (t80) cc_final: 0.7597 (t80) outliers start: 23 outliers final: 15 residues processed: 215 average time/residue: 0.1797 time to fit residues: 58.3200 Evaluate side-chains 214 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1611 THR Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 0.0010 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9758 Z= 0.161 Angle : 0.792 30.364 13222 Z= 0.352 Chirality : 0.062 1.797 1543 Planarity : 0.004 0.089 1582 Dihedral : 12.381 175.716 1890 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.29 % Allowed : 18.29 % Favored : 79.42 % 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: 0.96 (0.26), residues: 1130 helix: 1.63 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1382 HIS 0.004 0.001 HIS A 370 PHE 0.015 0.001 PHE A1246 TYR 0.017 0.001 TYR A 364 ARG 0.012 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 111 ARG cc_start: 0.5380 (mmt180) cc_final: 0.5109 (ttm-80) REVERT: A 157 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9135 (mp) REVERT: A 694 PHE cc_start: 0.6144 (t80) cc_final: 0.5718 (t80) REVERT: A 1174 TYR cc_start: 0.8433 (m-80) cc_final: 0.7927 (m-80) REVERT: A 1438 ARG cc_start: 0.8629 (ttp80) cc_final: 0.8356 (tmm-80) REVERT: A 1483 MET cc_start: 0.3985 (ppp) cc_final: 0.3754 (tmm) REVERT: A 1524 TYR cc_start: 0.7570 (m-10) cc_final: 0.6974 (t80) REVERT: A 1592 ILE cc_start: 0.8984 (tp) cc_final: 0.8726 (tp) REVERT: A 1601 MET cc_start: 0.8628 (mpp) cc_final: 0.7967 (mpp) REVERT: A 1704 PHE cc_start: 0.8082 (t80) cc_final: 0.7677 (t80) REVERT: A 1731 LYS cc_start: 0.8687 (tptt) cc_final: 0.7890 (ttmm) outliers start: 23 outliers final: 16 residues processed: 214 average time/residue: 0.1665 time to fit residues: 53.9192 Evaluate side-chains 219 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1611 THR Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9758 Z= 0.181 Angle : 0.792 30.288 13222 Z= 0.355 Chirality : 0.062 1.798 1543 Planarity : 0.004 0.083 1582 Dihedral : 12.257 175.554 1890 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.79 % Allowed : 19.18 % Favored : 79.03 % 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: 0.91 (0.26), residues: 1130 helix: 1.59 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 PHE 0.020 0.001 PHE A1246 TYR 0.018 0.001 TYR A 364 ARG 0.015 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 157 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9136 (mp) REVERT: A 389 MET cc_start: 0.7678 (ttm) cc_final: 0.7205 (ttt) REVERT: A 1174 TYR cc_start: 0.8429 (m-80) cc_final: 0.7999 (m-80) REVERT: A 1483 MET cc_start: 0.4085 (ppp) cc_final: 0.3842 (tmm) REVERT: A 1524 TYR cc_start: 0.7586 (m-10) cc_final: 0.6976 (t80) REVERT: A 1592 ILE cc_start: 0.8964 (tp) cc_final: 0.8695 (tp) REVERT: A 1601 MET cc_start: 0.8609 (mpp) cc_final: 0.7997 (mpp) REVERT: A 1704 PHE cc_start: 0.8101 (t80) cc_final: 0.7691 (t80) REVERT: A 1731 LYS cc_start: 0.8693 (tptt) cc_final: 0.7872 (ttmm) outliers start: 18 outliers final: 17 residues processed: 218 average time/residue: 0.1633 time to fit residues: 53.8845 Evaluate side-chains 222 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1611 THR Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 97 optimal weight: 5.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9758 Z= 0.175 Angle : 0.794 30.327 13222 Z= 0.355 Chirality : 0.062 1.795 1543 Planarity : 0.004 0.072 1582 Dihedral : 12.213 175.770 1890 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.59 % Allowed : 19.28 % Favored : 79.13 % 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: 0.93 (0.26), residues: 1130 helix: 1.61 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1382 HIS 0.003 0.001 HIS A1169 PHE 0.020 0.001 PHE A1492 TYR 0.018 0.001 TYR A 364 ARG 0.014 0.000 ARG A1585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 157 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9133 (mp) REVERT: A 694 PHE cc_start: 0.6109 (t80) cc_final: 0.5719 (t80) REVERT: A 1174 TYR cc_start: 0.8448 (m-80) cc_final: 0.8012 (m-80) REVERT: A 1246 PHE cc_start: 0.9116 (t80) cc_final: 0.8898 (t80) REVERT: A 1524 TYR cc_start: 0.7561 (m-10) cc_final: 0.6927 (t80) REVERT: A 1592 ILE cc_start: 0.8949 (tp) cc_final: 0.8680 (tp) REVERT: A 1601 MET cc_start: 0.8587 (mpp) cc_final: 0.7984 (mpp) REVERT: A 1704 PHE cc_start: 0.8087 (t80) cc_final: 0.7697 (t80) REVERT: A 1731 LYS cc_start: 0.8649 (tptt) cc_final: 0.7909 (ttmm) outliers start: 16 outliers final: 14 residues processed: 215 average time/residue: 0.1729 time to fit residues: 56.1548 Evaluate side-chains 219 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.148225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102373 restraints weight = 25859.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106038 restraints weight = 11393.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106977 restraints weight = 6814.823| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9758 Z= 0.273 Angle : 0.832 30.515 13222 Z= 0.382 Chirality : 0.064 1.806 1543 Planarity : 0.004 0.084 1582 Dihedral : 12.498 174.572 1890 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.59 % Allowed : 19.58 % Favored : 78.83 % 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: 0.84 (0.25), residues: 1130 helix: 1.50 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.022 0.002 PHE A1434 TYR 0.023 0.001 TYR A 364 ARG 0.015 0.000 ARG A1585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.41 seconds wall clock time: 41 minutes 22.22 seconds (2482.22 seconds total)