Starting phenix.real_space_refine on Thu Jul 2 21:22:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wll_32587/07_2026/7wll_32587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wll_32587/07_2026/7wll_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_32587/07_2026/7wll_32587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wll_32587/07_2026/7wll_32587.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wll_32587/07_2026/7wll_32587.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wll_32587/07_2026/7wll_32587.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wll_32587/07_2026/7wll_32587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wll_32587/07_2026/7wll_32587.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'TRP:plan': 1, 'ARG:plan': 3} 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: {'TRP:plan': 1, 'ARG:plan': 3} 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: 246 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'3PE:plan-1': 8, '3PE:plan-2': 8, 'Y01:plan-1': 3, 'Y01:plan-2': 1} 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: 3.92, per 1000 atoms: 0.41 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: 0.97 Conformation dependent library (CDL) restraints added in 779.5 milliseconds 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: 0.17 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: 1.14 Time building geometry restraints manager: 1.24 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 - 24.06: 5293 24.06 - 48.13: 371 48.13 - 72.19: 40 72.19 - 96.25: 5 96.25 - 120.31: 1 Dihedral angle restraints: 5710 sinusoidal: 2391 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 5707 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 9765 Z= 0.615 Angle : 1.189 29.399 13235 Z= 0.600 Chirality : 0.084 1.883 1543 Planarity : 0.005 0.057 1582 Dihedral : 15.087 120.313 3545 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A1585 TYR 0.015 0.002 TYR A 165 PHE 0.035 0.002 PHE A1181 TRP 0.028 0.002 TRP A 231 HIS 0.010 0.002 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.01218 / 0.61 ( 9758) covalent geometry : angle 1.18847 / 0.60 (13222) SS BOND : bond 0.00198 / 0.11 ( 5) SS BOND : angle 1.04773 / 0.60 ( 10) hydrogen bonds : bond 0.14829 / 9.85 ( 608) hydrogen bonds : angle 6.00006 / 4.30 ( 1734) Misc. bond : bond 0.00232 / 0.12 ( 1) link_NAG-ASN : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : angle 2.12582 / 1.05 ( 3) *********************** 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 : 0.221 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: 0.0639 time to fit residues: 23.1726 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 : 0.211 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN A1183 ASN A1424 ASN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.144911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099883 restraints weight = 25482.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103612 restraints weight = 10335.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105949 restraints weight = 6508.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106975 restraints weight = 5208.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107723 restraints weight = 4736.139| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9765 Z= 0.141 Angle : 0.800 30.029 13235 Z= 0.371 Chirality : 0.065 1.945 1543 Planarity : 0.004 0.053 1582 Dihedral : 9.677 111.738 1432 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.99 % Allowed : 11.13 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.25), residues: 1130 helix: 1.00 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 410 TYR 0.016 0.001 TYR A 364 PHE 0.038 0.002 PHE A1181 TRP 0.014 0.001 TRP A1680 HIS 0.006 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9758) covalent geometry : angle 0.79996 / 0.37 (13222) SS BOND : bond 0.00118 / 0.07 ( 5) SS BOND : angle 0.81992 / 0.45 ( 10) hydrogen bonds : bond 0.04371 / 2.78 ( 608) hydrogen bonds : angle 4.74721 / 3.41 ( 1734) Misc. bond : bond 0.00060 / 0.03 ( 1) link_NAG-ASN : bond 0.00104 / 0.05 ( 1) link_NAG-ASN : angle 1.01716 / 0.53 ( 3) *********************** 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 238 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.304 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 148 ASP cc_start: 0.8665 (t0) cc_final: 0.8453 (t70) REVERT: A 389 MET cc_start: 0.8196 (tpp) cc_final: 0.7586 (ttt) REVERT: A 708 ASP cc_start: 0.8876 (m-30) cc_final: 0.8660 (m-30) REVERT: A 835 SER cc_start: 0.8691 (p) cc_final: 0.8426 (p) REVERT: A 1246 PHE cc_start: 0.9023 (t80) cc_final: 0.8793 (t80) REVERT: A 1436 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8633 (mtpp) REVERT: A 1592 ILE cc_start: 0.8944 (tp) cc_final: 0.8728 (tp) REVERT: A 1601 MET cc_start: 0.8704 (mpp) cc_final: 0.7792 (mpp) REVERT: A 1704 PHE cc_start: 0.8063 (t80) cc_final: 0.7628 (t80) outliers start: 20 outliers final: 9 residues processed: 227 average time/residue: 0.0623 time to fit residues: 21.7374 Evaluate side-chains 212 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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: 113 random chunks: chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099835 restraints weight = 30409.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103818 restraints weight = 11803.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105583 restraints weight = 6572.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105411 restraints weight = 5673.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105856 restraints weight = 5676.142| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9765 Z= 0.143 Angle : 0.780 29.863 13235 Z= 0.359 Chirality : 0.065 1.951 1543 Planarity : 0.004 0.053 1582 Dihedral : 9.254 113.265 1425 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.09 % Allowed : 13.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1130 helix: 1.30 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 410 TYR 0.018 0.001 TYR A 364 PHE 0.021 0.002 PHE A1246 TRP 0.023 0.001 TRP A1382 HIS 0.006 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9758) covalent geometry : angle 0.78045 / 0.36 (13222) SS BOND : bond 0.00080 / 0.04 ( 5) SS BOND : angle 0.67191 / 0.36 ( 10) hydrogen bonds : bond 0.04065 / 2.58 ( 608) hydrogen bonds : angle 4.63605 / 3.32 ( 1734) Misc. bond : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.08217 / 0.55 ( 3) *********************** 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 227 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.364 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: 0.8642 (t0) cc_final: 0.8318 (t70) REVERT: A 157 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9092 (mp) REVERT: A 365 TYR cc_start: 0.8406 (m-10) cc_final: 0.7968 (m-10) REVERT: A 389 MET cc_start: 0.8106 (tpp) cc_final: 0.7496 (ttt) REVERT: A 708 ASP cc_start: 0.8907 (m-30) cc_final: 0.8667 (m-30) REVERT: A 835 SER cc_start: 0.8683 (p) cc_final: 0.8414 (p) REVERT: A 1246 PHE cc_start: 0.9149 (t80) cc_final: 0.8874 (t80) REVERT: A 1436 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8529 (mtpp) REVERT: A 1438 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8353 (tmm-80) REVERT: A 1601 MET cc_start: 0.8711 (mpp) cc_final: 0.7813 (mpp) REVERT: A 1631 PHE cc_start: 0.8483 (t80) cc_final: 0.8096 (t80) REVERT: A 1704 PHE cc_start: 0.8104 (t80) cc_final: 0.7699 (t80) outliers start: 21 outliers final: 10 residues processed: 213 average time/residue: 0.0667 time to fit residues: 21.7321 Evaluate side-chains 205 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 105 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 70 optimal weight: 0.3980 chunk 88 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3846 r_free = 0.3846 target = 0.141741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095539 restraints weight = 35535.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099538 restraints weight = 12471.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102055 restraints weight = 7246.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.103535 restraints weight = 5551.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104255 restraints weight = 4873.136| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9765 Z= 0.158 Angle : 0.783 29.692 13235 Z= 0.360 Chirality : 0.065 1.945 1543 Planarity : 0.004 0.052 1582 Dihedral : 9.179 112.396 1425 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.09 % Allowed : 14.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.25), residues: 1130 helix: 1.37 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.015 0.001 TYR A 364 PHE 0.020 0.001 PHE A1246 TRP 0.023 0.001 TRP A1382 HIS 0.006 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9758) covalent geometry : angle 0.78285 / 0.36 (13222) SS BOND : bond 0.00120 / 0.06 ( 5) SS BOND : angle 0.67226 / 0.37 ( 10) hydrogen bonds : bond 0.04044 / 2.56 ( 608) hydrogen bonds : angle 4.62171 / 3.31 ( 1734) Misc. bond : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : bond 0.00022 / 0.01 ( 1) link_NAG-ASN : angle 1.16658 / 0.59 ( 3) *********************** 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 225 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.281 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: 0.8611 (t0) cc_final: 0.8304 (t70) REVERT: A 157 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9132 (mp) REVERT: A 364 TYR cc_start: 0.8418 (m-10) cc_final: 0.8152 (m-10) REVERT: A 365 TYR cc_start: 0.8465 (m-10) cc_final: 0.8040 (m-10) REVERT: A 389 MET cc_start: 0.8180 (tpp) cc_final: 0.7648 (ttt) REVERT: A 708 ASP cc_start: 0.8715 (m-30) cc_final: 0.8512 (m-30) REVERT: A 1246 PHE cc_start: 0.9155 (t80) cc_final: 0.8914 (t80) REVERT: A 1438 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8343 (tmm-80) REVERT: A 1483 MET cc_start: 0.4994 (ppp) cc_final: 0.4102 (tmm) REVERT: A 1564 MET cc_start: 0.9204 (mtm) cc_final: 0.8767 (mtm) REVERT: A 1601 MET cc_start: 0.8762 (mpp) cc_final: 0.7846 (mpp) REVERT: A 1631 PHE cc_start: 0.8525 (t80) cc_final: 0.8151 (t80) REVERT: A 1655 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8075 (ptm) REVERT: A 1704 PHE cc_start: 0.8126 (t80) cc_final: 0.7773 (t80) outliers start: 21 outliers final: 14 residues processed: 214 average time/residue: 0.0703 time to fit residues: 23.2599 Evaluate side-chains 206 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 388 PHE 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 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 1610 ASP 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 89 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096387 restraints weight = 32468.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100796 restraints weight = 12510.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100650 restraints weight = 6714.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102468 restraints weight = 7247.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101917 restraints weight = 6490.122| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9765 Z= 0.288 Angle : 0.866 29.269 13235 Z= 0.405 Chirality : 0.068 1.960 1543 Planarity : 0.004 0.051 1582 Dihedral : 9.778 106.804 1425 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.19 % Allowed : 16.40 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1130 helix: 1.11 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1585 TYR 0.017 0.002 TYR A 256 PHE 0.022 0.002 PHE A 772 TRP 0.024 0.002 TRP A1382 HIS 0.009 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.29 ( 9758) covalent geometry : angle 0.86586 / 0.40 (13222) SS BOND : bond 0.00276 / 0.15 ( 5) SS BOND : angle 0.91777 / 0.53 ( 10) hydrogen bonds : bond 0.04668 / 2.95 ( 608) hydrogen bonds : angle 4.85527 / 3.50 ( 1734) Misc. bond : bond 0.00208 / 0.11 ( 1) link_NAG-ASN : bond 0.00242 / 0.13 ( 1) link_NAG-ASN : angle 1.98261 / 0.99 ( 3) *********************** 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 216 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.354 Fit side-chains TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 115 LEU cc_start: 0.9350 (mm) cc_final: 0.9122 (mm) REVERT: A 157 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9109 (mp) REVERT: A 164 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8075 (tp30) REVERT: A 364 TYR cc_start: 0.8439 (m-10) cc_final: 0.8233 (m-10) REVERT: A 365 TYR cc_start: 0.8649 (m-10) cc_final: 0.8331 (m-10) REVERT: A 389 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7851 (ttt) REVERT: A 403 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7783 (pp20) REVERT: A 1246 PHE cc_start: 0.9305 (t80) cc_final: 0.9040 (t80) REVERT: A 1271 LEU cc_start: 0.9305 (mt) cc_final: 0.9104 (mm) REVERT: A 1564 MET cc_start: 0.9285 (mtm) cc_final: 0.8831 (mtm) REVERT: A 1601 MET cc_start: 0.8754 (mpp) cc_final: 0.7971 (mpp) REVERT: A 1704 PHE cc_start: 0.8312 (t80) cc_final: 0.7971 (t80) outliers start: 22 outliers final: 14 residues processed: 204 average time/residue: 0.0666 time to fit residues: 21.1913 Evaluate side-chains 210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 388 PHE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 403 GLU 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 1277 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 25 optimal weight: 0.5980 chunk 86 optimal weight: 0.0670 chunk 82 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3921 r_free = 0.3921 target = 0.146888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101161 restraints weight = 31756.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105216 restraints weight = 11573.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107813 restraints weight = 6931.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108959 restraints weight = 5406.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109865 restraints weight = 4881.939| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9765 Z= 0.124 Angle : 0.777 29.888 13235 Z= 0.351 Chirality : 0.064 1.915 1543 Planarity : 0.004 0.053 1582 Dihedral : 9.206 113.368 1425 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.69 % Allowed : 17.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1130 helix: 1.44 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.014 0.001 TYR A 699 PHE 0.021 0.001 PHE A1181 TRP 0.028 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9758) covalent geometry : angle 0.77698 / 0.35 (13222) SS BOND : bond 0.00118 / 0.06 ( 5) SS BOND : angle 0.63063 / 0.34 ( 10) hydrogen bonds : bond 0.03800 / 2.43 ( 608) hydrogen bonds : angle 4.58842 / 3.27 ( 1734) Misc. bond : bond 0.00065 / 0.03 ( 1) link_NAG-ASN : bond 0.00235 / 0.12 ( 1) link_NAG-ASN : angle 0.76450 / 0.38 ( 3) *********************** 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 223 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 115 LEU cc_start: 0.9352 (mm) cc_final: 0.9118 (mm) REVERT: A 148 ASP cc_start: 0.8605 (t0) cc_final: 0.8215 (t70) REVERT: A 157 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9141 (mp) REVERT: A 389 MET cc_start: 0.8160 (tpp) cc_final: 0.7646 (ttt) REVERT: A 835 SER cc_start: 0.8587 (p) cc_final: 0.8307 (p) REVERT: A 1246 PHE cc_start: 0.9189 (t80) cc_final: 0.8766 (t80) REVERT: A 1271 LEU cc_start: 0.9206 (mt) cc_final: 0.8952 (mm) REVERT: A 1438 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8361 (tmm-80) REVERT: A 1483 MET cc_start: 0.4621 (ppp) cc_final: 0.4302 (tmm) REVERT: A 1601 MET cc_start: 0.8620 (mpp) cc_final: 0.7872 (mpp) outliers start: 17 outliers final: 11 residues processed: 216 average time/residue: 0.0592 time to fit residues: 19.6736 Evaluate side-chains 208 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1409 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 81 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102468 restraints weight = 30262.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106515 restraints weight = 11430.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109053 restraints weight = 6975.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110468 restraints weight = 5492.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110953 restraints weight = 4902.019| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9765 Z= 0.126 Angle : 0.767 29.820 13235 Z= 0.348 Chirality : 0.064 1.932 1543 Planarity : 0.004 0.053 1582 Dihedral : 8.911 112.713 1425 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.19 % Allowed : 17.79 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1130 helix: 1.49 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.020 0.001 TYR A 364 PHE 0.021 0.001 PHE A1181 TRP 0.024 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9758) covalent geometry : angle 0.76665 / 0.35 (13222) SS BOND : bond 0.00080 / 0.04 ( 5) SS BOND : angle 0.53125 / 0.29 ( 10) hydrogen bonds : bond 0.03678 / 2.34 ( 608) hydrogen bonds : angle 4.49569 / 3.20 ( 1734) Misc. bond : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : bond 0.00101 / 0.05 ( 1) link_NAG-ASN : angle 0.94647 / 0.48 ( 3) *********************** 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 228 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.325 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 115 LEU cc_start: 0.9376 (mm) cc_final: 0.9090 (mm) REVERT: A 148 ASP cc_start: 0.8636 (t0) cc_final: 0.8223 (t70) REVERT: A 157 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9125 (mp) REVERT: A 389 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7648 (ttt) REVERT: A 835 SER cc_start: 0.8607 (p) cc_final: 0.8371 (p) REVERT: A 1246 PHE cc_start: 0.9263 (t80) cc_final: 0.8829 (t80) REVERT: A 1438 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8278 (tmm-80) REVERT: A 1483 MET cc_start: 0.4601 (ppp) cc_final: 0.3967 (tmm) REVERT: A 1601 MET cc_start: 0.8612 (mpp) cc_final: 0.7797 (mpp) REVERT: A 1687 THR cc_start: 0.9399 (t) cc_final: 0.9148 (t) outliers start: 22 outliers final: 15 residues processed: 215 average time/residue: 0.0675 time to fit residues: 22.2300 Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 389 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1279 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN A1365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101153 restraints weight = 32321.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105235 restraints weight = 12026.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107846 restraints weight = 7249.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109299 restraints weight = 5662.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109756 restraints weight = 5025.413| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9765 Z= 0.138 Angle : 0.788 29.670 13235 Z= 0.359 Chirality : 0.064 1.930 1543 Planarity : 0.004 0.051 1582 Dihedral : 8.866 112.644 1425 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.19 % Allowed : 17.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1130 helix: 1.52 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.020 0.001 TYR A 364 PHE 0.020 0.001 PHE A1181 TRP 0.026 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9758) covalent geometry : angle 0.78828 / 0.36 (13222) SS BOND : bond 0.00087 / 0.04 ( 5) SS BOND : angle 0.58594 / 0.32 ( 10) hydrogen bonds : bond 0.03695 / 2.35 ( 608) hydrogen bonds : angle 4.47931 / 3.20 ( 1734) Misc. bond : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : angle 0.95927 / 0.49 ( 3) *********************** 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 224 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.248 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 115 LEU cc_start: 0.9398 (mm) cc_final: 0.9116 (mm) REVERT: A 157 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9126 (mp) REVERT: A 389 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7679 (ttt) REVERT: A 694 PHE cc_start: 0.6675 (t80) cc_final: 0.6284 (t80) REVERT: A 835 SER cc_start: 0.8649 (p) cc_final: 0.8416 (p) REVERT: A 1246 PHE cc_start: 0.9255 (t80) cc_final: 0.8864 (t80) REVERT: A 1288 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8507 (mmt-90) REVERT: A 1483 MET cc_start: 0.4481 (ppp) cc_final: 0.4019 (tmm) REVERT: A 1601 MET cc_start: 0.8642 (mpp) cc_final: 0.7880 (mpp) REVERT: A 1704 PHE cc_start: 0.8076 (t80) cc_final: 0.7515 (t80) REVERT: A 1731 LYS cc_start: 0.8432 (tptt) cc_final: 0.7794 (mtpp) outliers start: 22 outliers final: 16 residues processed: 212 average time/residue: 0.0682 time to fit residues: 22.0080 Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 359 TRP 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 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1279 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.0010 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103146 restraints weight = 34145.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107342 restraints weight = 12298.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109997 restraints weight = 7294.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111431 restraints weight = 5636.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111934 restraints weight = 4996.587| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9765 Z= 0.131 Angle : 0.813 29.756 13235 Z= 0.369 Chirality : 0.064 1.927 1543 Planarity : 0.005 0.108 1582 Dihedral : 8.834 112.937 1425 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.59 % Allowed : 18.69 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1130 helix: 1.56 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.50 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1585 TYR 0.019 0.001 TYR A 364 PHE 0.020 0.001 PHE A1546 TRP 0.032 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9758) covalent geometry : angle 0.81337 / 0.37 (13222) SS BOND : bond 0.00076 / 0.04 ( 5) SS BOND : angle 0.55763 / 0.30 ( 10) hydrogen bonds : bond 0.03643 / 2.33 ( 608) hydrogen bonds : angle 4.43273 / 3.18 ( 1734) Misc. bond : bond 0.00404 / 0.21 ( 1) link_NAG-ASN : bond 0.00152 / 0.08 ( 1) link_NAG-ASN : angle 0.84634 / 0.43 ( 3) *********************** 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 225 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.346 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 115 LEU cc_start: 0.9388 (mm) cc_final: 0.9109 (mm) REVERT: A 157 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9111 (mp) REVERT: A 389 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7715 (ttt) REVERT: A 694 PHE cc_start: 0.6580 (t80) cc_final: 0.6113 (t80) REVERT: A 835 SER cc_start: 0.8627 (p) cc_final: 0.8407 (p) REVERT: A 1174 TYR cc_start: 0.8394 (m-10) cc_final: 0.8003 (m-80) REVERT: A 1235 TYR cc_start: 0.8430 (t80) cc_final: 0.8211 (t80) REVERT: A 1246 PHE cc_start: 0.9257 (t80) cc_final: 0.9054 (t80) REVERT: A 1288 ARG cc_start: 0.8925 (mtt90) cc_final: 0.8624 (mmt-90) REVERT: A 1483 MET cc_start: 0.4545 (ppp) cc_final: 0.3933 (tmm) REVERT: A 1601 MET cc_start: 0.8660 (mpp) cc_final: 0.7895 (mpp) REVERT: A 1687 THR cc_start: 0.9404 (t) cc_final: 0.9159 (t) REVERT: A 1704 PHE cc_start: 0.8051 (t80) cc_final: 0.7495 (t80) REVERT: A 1731 LYS cc_start: 0.8375 (tptt) cc_final: 0.7756 (mtpp) outliers start: 16 outliers final: 13 residues processed: 216 average time/residue: 0.0681 time to fit residues: 22.5016 Evaluate side-chains 219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1279 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.146599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100148 restraints weight = 37903.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104979 restraints weight = 12962.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107189 restraints weight = 6687.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107054 restraints weight = 6327.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107163 restraints weight = 5870.124| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9765 Z= 0.155 Angle : 0.823 29.529 13235 Z= 0.375 Chirality : 0.065 1.934 1543 Planarity : 0.005 0.107 1582 Dihedral : 8.850 112.166 1425 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.79 % Allowed : 18.89 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1130 helix: 1.54 (0.19), residues: 761 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1585 TYR 0.021 0.001 TYR A 364 PHE 0.027 0.002 PHE A1546 TRP 0.044 0.002 TRP A1382 HIS 0.005 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 9758) covalent geometry : angle 0.82333 / 0.38 (13222) SS BOND : bond 0.00102 / 0.05 ( 5) SS BOND : angle 0.62630 / 0.35 ( 10) hydrogen bonds : bond 0.03792 / 2.42 ( 608) hydrogen bonds : angle 4.47215 / 3.22 ( 1734) Misc. bond : bond 0.00419 / 0.22 ( 1) link_NAG-ASN : bond 0.00062 / 0.03 ( 1) link_NAG-ASN : angle 1.04163 / 0.53 ( 3) ********************** 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 to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.367 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 115 LEU cc_start: 0.9354 (mm) cc_final: 0.9103 (mm) REVERT: A 157 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9094 (mp) REVERT: A 389 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7778 (ttt) REVERT: A 694 PHE cc_start: 0.6430 (t80) cc_final: 0.5999 (t80) REVERT: A 835 SER cc_start: 0.8671 (p) cc_final: 0.8449 (p) REVERT: A 1174 TYR cc_start: 0.8460 (m-10) cc_final: 0.8117 (m-80) REVERT: A 1235 TYR cc_start: 0.8458 (t80) cc_final: 0.8224 (t80) REVERT: A 1246 PHE cc_start: 0.9328 (t80) cc_final: 0.9119 (t80) REVERT: A 1288 ARG cc_start: 0.8975 (mtt90) cc_final: 0.8704 (mmt-90) REVERT: A 1601 MET cc_start: 0.8681 (mpp) cc_final: 0.8021 (mpp) REVERT: A 1704 PHE cc_start: 0.8192 (t80) cc_final: 0.7636 (t80) REVERT: A 1731 LYS cc_start: 0.8377 (tptt) cc_final: 0.7636 (ttmm) outliers start: 18 outliers final: 13 residues processed: 211 average time/residue: 0.0726 time to fit residues: 23.5105 Evaluate side-chains 217 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 755 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1279 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.0370 chunk 6 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 0.6670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101499 restraints weight = 37825.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107080 restraints weight = 12853.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107401 restraints weight = 6361.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107475 restraints weight = 6419.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107858 restraints weight = 6154.592| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9765 Z= 0.130 Angle : 0.814 29.704 13235 Z= 0.370 Chirality : 0.064 1.928 1543 Planarity : 0.004 0.088 1582 Dihedral : 8.785 113.054 1425 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.59 % Allowed : 19.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1130 helix: 1.56 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1585 TYR 0.018 0.001 TYR A 364 PHE 0.027 0.001 PHE A1546 TRP 0.037 0.001 TRP A1382 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9758) covalent geometry : angle 0.81387 / 0.37 (13222) SS BOND : bond 0.00078 / 0.04 ( 5) SS BOND : angle 0.57078 / 0.31 ( 10) hydrogen bonds : bond 0.03671 / 2.35 ( 608) hydrogen bonds : angle 4.42020 / 3.18 ( 1734) Misc. bond : bond 0.00327 / 0.17 ( 1) link_NAG-ASN : bond 0.00176 / 0.09 ( 1) link_NAG-ASN : angle 0.83077 / 0.42 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.93 seconds wall clock time: 31 minutes 38.33 seconds (1898.33 seconds total)