Starting phenix.real_space_refine on Sun Dec 29 10:47:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wll_32587/12_2024/7wll_32587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wll_32587/12_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/cci-nas-00/data/ceres_data/7wll_32587/12_2024/7wll_32587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wll_32587/12_2024/7wll_32587.map" model { file = "/net/cci-nas-00/data/ceres_data/7wll_32587/12_2024/7wll_32587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wll_32587/12_2024/7wll_32587.cif" } 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. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9540 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9111 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1135, 9100 Classifications: {'peptide': 1135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 1135, 9100 Classifications: {'peptide': 1135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 9289 Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 429 Unusual residues: {' CA': 2, '1II': 1, '3PE': 9, 'NAG': 2, 'Y01': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'Y01:plan-2': 1, '3PE:plan-1': 8, '3PE:plan-2': 8, 'Y01:plan-1': 3} Unresolved non-hydrogen planarities: 68 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: 10.26, per 1000 atoms: 1.08 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 2.66 Conformation dependent library (CDL) restraints added in 2.2 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: 1.10 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: 2.74 Time building geometry restraints manager: 2.91 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: 0.00 - 5.88: 13175 5.88 - 11.76: 41 11.76 - 17.64: 3 17.64 - 23.52: 0 23.52 - 29.40: 3 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 3.040 nonbonded pdb=" OD1 ASN A1345 " pdb=" OG SER A1347 " model vdw 2.165 3.040 nonbonded pdb=" OG SER A1238 " pdb=" OD1 ASN A1241 " model vdw 2.170 3.040 ... (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: 1.090 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 29.960 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 5 poor density : 235 time to evaluate : 0.946 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: 0.2057 time to fit residues: 73.3708 Evaluate side-chains 192 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9758 Z= 0.188 Angle : 0.809 30.057 13222 Z= 0.373 Chirality : 0.064 1.847 1543 Planarity : 0.004 0.053 1582 Dihedral : 14.059 171.349 1897 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.79 % Allowed : 11.03 % Favored : 87.18 % 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: 0.22 (0.25), residues: 1130 helix: 1.01 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1680 HIS 0.006 0.001 HIS A1169 PHE 0.036 0.002 PHE A1181 TYR 0.017 0.001 TYR A 364 ARG 0.006 0.001 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 237 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 1.076 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: 0.8271 (tpp) cc_final: 0.7625 (ttt) REVERT: A 708 ASP cc_start: 0.8851 (m-30) cc_final: 0.8636 (m-30) REVERT: A 835 SER cc_start: 0.8670 (p) cc_final: 0.8408 (p) REVERT: A 1436 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8626 (mtpp) REVERT: A 1592 ILE cc_start: 0.8997 (tp) cc_final: 0.8771 (tp) REVERT: A 1601 MET cc_start: 0.8689 (mpp) cc_final: 0.7831 (mpp) REVERT: A 1704 PHE cc_start: 0.8011 (t80) cc_final: 0.7602 (t80) outliers start: 18 outliers final: 11 residues processed: 227 average time/residue: 0.1736 time to fit residues: 59.8133 Evaluate side-chains 211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 1435 HIS 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: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 0.0070 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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: 0.7902 moved from start: 0.2124 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= 0.180 Angle : 0.778 30.224 13222 Z= 0.356 Chirality : 0.063 1.834 1543 Planarity : 0.004 0.052 1582 Dihedral : 13.274 172.837 1890 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.29 % Allowed : 12.82 % Favored : 84.89 % 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: 0.62 (0.25), residues: 1130 helix: 1.34 (0.19), residues: 767 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.031 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 236 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.027 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: 0.8538 (t0) cc_final: 0.8227 (t70) REVERT: A 157 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9144 (mp) REVERT: A 167 LEU cc_start: 0.9439 (mm) cc_final: 0.9166 (mp) REVERT: A 389 MET cc_start: 0.8169 (tpp) cc_final: 0.7489 (ttt) REVERT: A 708 ASP cc_start: 0.8841 (m-30) cc_final: 0.8608 (m-30) REVERT: A 835 SER cc_start: 0.8643 (p) cc_final: 0.8329 (p) REVERT: A 1436 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8610 (mtpp) REVERT: A 1438 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8376 (tmm-80) REVERT: A 1564 MET cc_start: 0.9205 (mtm) cc_final: 0.8961 (mtp) REVERT: A 1592 ILE cc_start: 0.8975 (tp) cc_final: 0.8757 (tp) REVERT: A 1601 MET cc_start: 0.8674 (mpp) cc_final: 0.7819 (mpp) REVERT: A 1631 PHE cc_start: 0.8424 (t80) cc_final: 0.7955 (t80) REVERT: A 1704 PHE cc_start: 0.8018 (t80) cc_final: 0.7643 (t80) outliers start: 23 outliers final: 10 residues processed: 222 average time/residue: 0.1798 time to fit residues: 59.8529 Evaluate side-chains 210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 1409 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9758 Z= 0.204 Angle : 0.778 30.122 13222 Z= 0.357 Chirality : 0.062 1.822 1543 Planarity : 0.004 0.053 1582 Dihedral : 12.884 174.000 1890 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.79 % Allowed : 15.21 % Favored : 83.00 % 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: 0.70 (0.25), residues: 1130 helix: 1.42 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.024 0.001 PHE A1181 TYR 0.019 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 228 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.073 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: 0.8470 (t0) cc_final: 0.8155 (t70) REVERT: A 157 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9142 (mp) REVERT: A 389 MET cc_start: 0.8192 (tpp) cc_final: 0.7615 (ttt) REVERT: A 835 SER cc_start: 0.8662 (p) cc_final: 0.8451 (p) REVERT: A 1436 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8573 (mtpp) REVERT: A 1438 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8406 (tmm-80) REVERT: A 1483 MET cc_start: 0.4734 (ppp) cc_final: 0.4088 (tmm) REVERT: A 1592 ILE cc_start: 0.8979 (tp) cc_final: 0.8747 (tp) REVERT: A 1601 MET cc_start: 0.8755 (mpp) cc_final: 0.7879 (mpp) REVERT: A 1631 PHE cc_start: 0.8457 (t80) cc_final: 0.8054 (t80) REVERT: A 1655 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8046 (ptm) REVERT: A 1704 PHE cc_start: 0.8044 (t80) cc_final: 0.7715 (t80) outliers start: 18 outliers final: 13 residues processed: 220 average time/residue: 0.1766 time to fit residues: 58.2210 Evaluate side-chains 214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1655 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** A 761 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9758 Z= 0.323 Angle : 0.813 30.397 13222 Z= 0.377 Chirality : 0.064 1.828 1543 Planarity : 0.004 0.051 1582 Dihedral : 13.069 174.057 1890 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.19 % Allowed : 16.20 % Favored : 81.61 % 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: 0.59 (0.25), residues: 1130 helix: 1.31 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1382 HIS 0.007 0.001 HIS A1169 PHE 0.019 0.002 PHE A 679 TYR 0.023 0.001 TYR A 364 ARG 0.005 0.000 ARG A1288 *********************** 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 225 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.994 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: 0.8591 (t0) cc_final: 0.8347 (t70) REVERT: A 157 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9162 (mp) REVERT: A 389 MET cc_start: 0.8214 (tpp) cc_final: 0.7733 (ttt) REVERT: A 1271 LEU cc_start: 0.9223 (mt) cc_final: 0.8975 (mm) REVERT: A 1592 ILE cc_start: 0.9031 (tp) cc_final: 0.8768 (tp) REVERT: A 1601 MET cc_start: 0.8684 (mpp) cc_final: 0.7897 (mpp) REVERT: A 1633 TYR cc_start: 0.8772 (m-80) cc_final: 0.8530 (m-80) REVERT: A 1704 PHE cc_start: 0.8159 (t80) cc_final: 0.7853 (t80) outliers start: 22 outliers final: 16 residues processed: 214 average time/residue: 0.1684 time to fit residues: 54.4311 Evaluate side-chains 210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 682 MET 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 1376 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1525 MET Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9758 Z= 0.191 Angle : 0.781 30.456 13222 Z= 0.356 Chirality : 0.062 1.798 1543 Planarity : 0.004 0.052 1582 Dihedral : 12.756 175.763 1890 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.29 % Allowed : 16.60 % 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: 0.82 (0.25), residues: 1130 helix: 1.51 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.023 0.001 PHE A1181 TYR 0.018 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 221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 1.062 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 98 MET cc_start: 0.7682 (mmm) cc_final: 0.7317 (tpt) REVERT: A 148 ASP cc_start: 0.8553 (t0) cc_final: 0.8242 (t70) REVERT: A 157 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9149 (mp) REVERT: A 389 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7684 (ttt) REVERT: A 694 PHE cc_start: 0.6460 (t80) cc_final: 0.5777 (t80) REVERT: A 835 SER cc_start: 0.8635 (p) cc_final: 0.8369 (p) REVERT: A 1483 MET cc_start: 0.4453 (ppp) cc_final: 0.3960 (tmm) REVERT: A 1592 ILE cc_start: 0.9003 (tp) cc_final: 0.8759 (tp) REVERT: A 1601 MET cc_start: 0.8666 (mpp) cc_final: 0.7895 (mpp) REVERT: A 1631 PHE cc_start: 0.8412 (t80) cc_final: 0.8028 (t80) REVERT: A 1687 THR cc_start: 0.9419 (t) cc_final: 0.9177 (t) REVERT: A 1704 PHE cc_start: 0.8103 (t80) cc_final: 0.7579 (t80) outliers start: 23 outliers final: 14 residues processed: 211 average time/residue: 0.1661 time to fit residues: 53.2884 Evaluate side-chains 209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 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 760 ASP Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9758 Z= 0.215 Angle : 0.798 30.358 13222 Z= 0.365 Chirality : 0.063 1.805 1543 Planarity : 0.004 0.052 1582 Dihedral : 12.688 175.386 1890 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.99 % Allowed : 17.40 % Favored : 80.62 % 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: 0.79 (0.25), residues: 1130 helix: 1.46 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 370 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 A1181 TYR 0.021 0.001 TYR A 364 ARG 0.004 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 221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 98 MET cc_start: 0.7689 (mmm) cc_final: 0.7326 (tpt) REVERT: A 148 ASP cc_start: 0.8588 (t0) cc_final: 0.8231 (t70) REVERT: A 157 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9160 (mp) REVERT: A 389 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7711 (ttt) REVERT: A 835 SER cc_start: 0.8664 (p) cc_final: 0.8463 (p) REVERT: A 1483 MET cc_start: 0.4443 (ppp) cc_final: 0.3850 (tmm) REVERT: A 1592 ILE cc_start: 0.9024 (tp) cc_final: 0.8756 (tp) REVERT: A 1601 MET cc_start: 0.8623 (mpp) cc_final: 0.7872 (mpp) REVERT: A 1631 PHE cc_start: 0.8443 (t80) cc_final: 0.8053 (t80) REVERT: A 1704 PHE cc_start: 0.8124 (t80) cc_final: 0.7627 (t80) outliers start: 20 outliers final: 16 residues processed: 211 average time/residue: 0.1678 time to fit residues: 54.2855 Evaluate side-chains 213 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 283 ILE 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 760 ASP Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1556 LEU 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: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.0570 chunk 95 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9758 Z= 0.169 Angle : 0.785 30.376 13222 Z= 0.356 Chirality : 0.062 1.793 1543 Planarity : 0.004 0.051 1582 Dihedral : 12.466 176.210 1890 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.89 % Allowed : 17.50 % Favored : 80.62 % 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: 0.90 (0.25), residues: 1130 helix: 1.54 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 PHE 0.020 0.001 PHE A1181 TYR 0.017 0.001 TYR A 364 ARG 0.004 0.000 ARG A 410 *********************** 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 227 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 1.095 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: 0.9390 (OUTLIER) cc_final: 0.9140 (mp) REVERT: A 389 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7657 (ttt) REVERT: A 694 PHE cc_start: 0.6350 (t80) cc_final: 0.5942 (t80) REVERT: A 835 SER cc_start: 0.8586 (p) cc_final: 0.8382 (p) REVERT: A 1174 TYR cc_start: 0.8341 (m-10) cc_final: 0.7952 (m-80) REVERT: A 1483 MET cc_start: 0.4446 (ppp) cc_final: 0.3878 (tmm) REVERT: A 1507 GLU cc_start: 0.7809 (tt0) cc_final: 0.7483 (tt0) REVERT: A 1592 ILE cc_start: 0.8998 (tp) cc_final: 0.8741 (tp) REVERT: A 1601 MET cc_start: 0.8610 (mpp) cc_final: 0.7824 (mpp) REVERT: A 1631 PHE cc_start: 0.8330 (t80) cc_final: 0.7955 (t80) REVERT: A 1687 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9126 (t) REVERT: A 1704 PHE cc_start: 0.8051 (t80) cc_final: 0.7603 (t80) REVERT: A 1731 LYS cc_start: 0.8429 (tptt) cc_final: 0.7841 (mtpp) outliers start: 19 outliers final: 12 residues processed: 217 average time/residue: 0.1758 time to fit residues: 57.9735 Evaluate side-chains 216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 760 ASP Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1687 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7969 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9758 Z= 0.304 Angle : 0.855 30.536 13222 Z= 0.393 Chirality : 0.064 1.809 1543 Planarity : 0.005 0.098 1582 Dihedral : 12.831 174.830 1890 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.69 % Allowed : 17.69 % Favored : 80.62 % 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: 0.75 (0.25), residues: 1130 helix: 1.38 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -1.40 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1382 HIS 0.006 0.001 HIS A1169 PHE 0.020 0.002 PHE A1546 TYR 0.025 0.001 TYR A 364 ARG 0.022 0.001 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 211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 98 MET cc_start: 0.7723 (mmm) cc_final: 0.7347 (tpt) REVERT: A 157 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9162 (mp) REVERT: A 389 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7812 (ttt) REVERT: A 1483 MET cc_start: 0.4176 (ppp) cc_final: 0.3813 (tmm) REVERT: A 1592 ILE cc_start: 0.9024 (tp) cc_final: 0.8789 (tp) REVERT: A 1601 MET cc_start: 0.8620 (mpp) cc_final: 0.7896 (mpp) REVERT: A 1631 PHE cc_start: 0.8558 (t80) cc_final: 0.8250 (t80) REVERT: A 1687 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9211 (t) REVERT: A 1731 LYS cc_start: 0.8450 (tptt) cc_final: 0.7849 (mtpp) outliers start: 17 outliers final: 12 residues processed: 204 average time/residue: 0.1917 time to fit residues: 60.1212 Evaluate side-chains 202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 760 ASP Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1687 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3026 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= 0.202 Angle : 0.819 30.406 13222 Z= 0.373 Chirality : 0.062 1.796 1543 Planarity : 0.005 0.098 1582 Dihedral : 12.599 176.014 1890 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.79 % Allowed : 17.99 % Favored : 80.22 % 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: 1.48 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -1.46 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.027 0.001 PHE A1546 TYR 0.025 0.001 TYR A1174 ARG 0.017 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 214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 1.258 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: 0.9395 (OUTLIER) cc_final: 0.9141 (mp) REVERT: A 389 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7738 (ttt) REVERT: A 694 PHE cc_start: 0.6378 (t80) cc_final: 0.5794 (t80) REVERT: A 835 SER cc_start: 0.8623 (p) cc_final: 0.8415 (p) REVERT: A 1507 GLU cc_start: 0.7800 (tt0) cc_final: 0.7443 (tt0) REVERT: A 1592 ILE cc_start: 0.8997 (tp) cc_final: 0.8754 (tp) REVERT: A 1601 MET cc_start: 0.8628 (mpp) cc_final: 0.7913 (mpp) REVERT: A 1631 PHE cc_start: 0.8408 (t80) cc_final: 0.8038 (t80) REVERT: A 1687 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9156 (t) REVERT: A 1704 PHE cc_start: 0.8010 (t80) cc_final: 0.7517 (t80) outliers start: 18 outliers final: 13 residues processed: 206 average time/residue: 0.1778 time to fit residues: 55.6238 Evaluate side-chains 209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 760 ASP Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1435 HIS Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1687 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.146936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103073 restraints weight = 23332.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105818 restraints weight = 11333.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107234 restraints weight = 6708.632| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3115 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= 0.207 Angle : 0.823 30.381 13222 Z= 0.377 Chirality : 0.063 1.799 1543 Planarity : 0.005 0.091 1582 Dihedral : 12.580 175.687 1890 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.59 % Allowed : 18.59 % Favored : 79.82 % 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: 0.85 (0.25), residues: 1130 helix: 1.49 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1382 HIS 0.005 0.001 HIS A1169 PHE 0.028 0.002 PHE A1546 TYR 0.044 0.001 TYR A1174 ARG 0.016 0.000 ARG A1585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.29 seconds wall clock time: 40 minutes 15.04 seconds (2415.04 seconds total)