Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 09:05:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlk_32586/08_2023/7wlk_32586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlk_32586/08_2023/7wlk_32586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlk_32586/08_2023/7wlk_32586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlk_32586/08_2023/7wlk_32586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlk_32586/08_2023/7wlk_32586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlk_32586/08_2023/7wlk_32586.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 78 5.16 5 C 6283 2.51 5 N 1503 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 800": "OD1" <-> "OD2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1396": "OD1" <-> "OD2" Residue "A ARG 1466": "NH1" <-> "NH2" Residue "A TYR 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1516": "OE1" <-> "OE2" Residue "A TYR 1524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1555": "OD1" <-> "OD2" Residue "A PHE 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1713": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 9461 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1152, 9450 Unusual residues: {' CA': 2, '3PE': 6, '7TB': 1, 'NAG': 2, 'Y01': 6} Classifications: {'peptide': 1135, 'undetermined': 17} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 17} Not linked: pdbres="LYS A1738 " pdbres="7TB A2301 " Not linked: pdbres="7TB A2301 " pdbres="3PE A2302 " Not linked: pdbres="3PE A2302 " pdbres="3PE A2303 " Not linked: pdbres="3PE A2303 " pdbres=" CA A2304 " Not linked: pdbres=" CA A2304 " pdbres="3PE A2305 " ... (remaining 12 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'3PE:plan-1': 5, '3PE:plan-2': 5, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Conformer: "B" Number of residues, atoms: 1152, 9450 Unusual residues: {' CA': 2, '3PE': 6, '7TB': 1, 'NAG': 2, 'Y01': 6} Classifications: {'peptide': 1135, 'undetermined': 17} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 17} Not linked: pdbres="LYS A1738 " pdbres="7TB A2301 " Not linked: pdbres="7TB A2301 " pdbres="3PE A2302 " Not linked: pdbres="3PE A2302 " pdbres="3PE A2303 " Not linked: pdbres="3PE A2303 " pdbres=" CA A2304 " Not linked: pdbres=" CA A2304 " pdbres="3PE A2305 " ... (remaining 12 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'3PE:plan-1': 5, '3PE:plan-2': 5, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 bond proxies already assigned to first conformer: 9650 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: 9.74, per 1000 atoms: 1.03 Number of scatterers: 9461 At special positions: 0 Unit cell: (112.32, 124.8, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 78 16.00 P 1 15.00 O 1594 8.00 N 1503 7.00 C 6283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1349 " distance=2.03 Simple disulfide: pdb=" SG CYS A1646 " - pdb=" SG CYS A1652 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1698 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A2311 " - " ASN A1345 " " NAG A2313 " - " ASN A1342 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 2.5 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 2 sheets defined 76.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.879A pdb=" N CYS A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N MET A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.691A 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 190 Proline residue: A 185 - end of helix removed outlier: 3.563A pdb=" N ILE A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 209 through 232 removed outlier: 3.600A pdb=" N PHE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.522A pdb=" N ASN A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.555A pdb=" N ARG A 321 " --> pdb=" O ASN A 318 " (cutoff:3.500A) 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: 3.590A pdb=" N ILE A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.832A pdb=" N MET A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.924A pdb=" N LYS A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 4.232A pdb=" N GLU A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.512A pdb=" N LEU A 691 " --> pdb=" O MET A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 4.431A pdb=" N ASN A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 721 removed outlier: 3.723A 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: 3.641A pdb=" N LEU A 735 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 785 removed outlier: 3.531A pdb=" N ARG A 749 " --> pdb=" O MET A 745 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 763 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N THR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.842A 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: 3.678A 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: 4.032A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 866 Processing helix chain 'A' and resid 1171 through 1188 Processing helix chain 'A' and resid 1198 through 1227 Processing helix chain 'A' and resid 1234 through 1237 removed outlier: 3.733A pdb=" N ARG A1237 " --> pdb=" O ALA A1234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1234 through 1237' Processing helix chain 'A' and resid 1238 through 1260 Processing helix chain 'A' and resid 1267 through 1281 Processing helix chain 'A' and resid 1289 through 1304 removed outlier: 3.684A 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: 3.619A 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: 3.718A pdb=" N LEU A1415 " --> pdb=" O PHE A1411 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A1440 " --> pdb=" O LYS A1436 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA A1443 " --> pdb=" O GLN A1439 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A1444 " --> pdb=" O HIS A1440 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1505 removed outlier: 4.109A pdb=" N ASP A1490 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1491 " --> pdb=" O HIS A1487 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A1492 " --> pdb=" O TYR A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1541 Processing helix chain 'A' and resid 1542 through 1549 removed outlier: 3.951A pdb=" N PHE A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1575 removed outlier: 3.700A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1591 removed outlier: 3.966A pdb=" N ILE A1584 " --> pdb=" O ASN A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1600 removed outlier: 3.648A pdb=" N LYS A1597 " --> pdb=" O ARG A1594 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1600 " --> pdb=" O LYS A1597 " (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 1663 through 1676 removed outlier: 3.963A 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 1696 through 1700 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 238 through 239 removed outlier: 3.705A pdb=" N ARG A 238 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 327 " --> pdb=" O ARG A 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1333 through 1334 612 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1432 1.31 - 1.43: 2565 1.43 - 1.56: 5473 1.56 - 1.69: 79 1.69 - 1.81: 127 Bond restraints: 9676 Sorted by residual: bond pdb=" C21 3PE A2302 " pdb=" O21 3PE A2302 " ideal model delta sigma weight residual 1.316 1.461 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C31 3PE A2302 " pdb=" O31 3PE A2302 " ideal model delta sigma weight residual 1.331 1.467 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C32 7TB A2301 " pdb=" N07 7TB A2301 " ideal model delta sigma weight residual 1.366 1.494 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 3PE A2302 " pdb=" C22 3PE A2302 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C31 3PE A2305 " pdb=" C32 3PE A2305 " ideal model delta sigma weight residual 1.504 1.603 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 9671 not shown) Histogram of bond angle deviations from ideal: 96.24 - 103.83: 128 103.83 - 111.43: 4424 111.43 - 119.02: 3502 119.02 - 126.62: 4951 126.62 - 134.21: 114 Bond angle restraints: 13119 Sorted by residual: angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 114.39 106.32 8.07 1.45e+00 4.76e-01 3.10e+01 angle pdb=" N ILE A 177 " pdb=" CA ILE A 177 " pdb=" C ILE A 177 " ideal model delta sigma weight residual 113.39 106.33 7.06 1.47e+00 4.63e-01 2.31e+01 angle pdb=" O12 3PE A2302 " pdb=" P 3PE A2302 " pdb=" O14 3PE A2302 " ideal model delta sigma weight residual 123.79 109.42 14.37 3.00e+00 1.11e-01 2.29e+01 angle pdb=" N ILE A1412 " pdb=" CA ILE A1412 " pdb=" C ILE A1412 " ideal model delta sigma weight residual 111.81 108.64 3.17 8.60e-01 1.35e+00 1.35e+01 angle pdb=" C TYR A1354 " pdb=" N ARG A1355 " pdb=" CA ARG A1355 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 ... (remaining 13114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.02: 5292 24.02 - 48.04: 331 48.04 - 72.06: 42 72.06 - 96.09: 5 96.09 - 120.11: 1 Dihedral angle restraints: 5671 sinusoidal: 2352 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 93.00 175.52 -82.52 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CA ASN A 332 " pdb=" C ASN A 332 " pdb=" N PRO A 333 " pdb=" CA PRO A 333 " ideal model delta harmonic sigma weight residual -180.00 -151.17 -28.83 0 5.00e+00 4.00e-02 3.32e+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 -41.98 -44.02 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 5668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1452 0.106 - 0.212: 63 0.212 - 0.318: 11 0.318 - 0.424: 3 0.424 - 0.531: 6 Chirality restraints: 1535 Sorted by residual: chirality pdb=" CBG Y01 A2312 " pdb=" CAQ Y01 A2312 " pdb=" CBD Y01 A2312 " pdb=" CBI Y01 A2312 " both_signs ideal model delta sigma weight residual False -2.33 -2.86 0.53 2.00e-01 2.50e+01 7.04e+00 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 -2.84 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CBG Y01 A2309 " pdb=" CAQ Y01 A2309 " pdb=" CBD Y01 A2309 " pdb=" CBI Y01 A2309 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 1532 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1626 " -0.026 2.00e-02 2.50e+03 2.02e-02 7.13e+00 pdb=" CG PHE A1626 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A1626 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1626 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1626 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1626 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A1626 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1616 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A1617 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A1617 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1617 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 702 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 703 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 703 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 703 " 0.028 5.00e-02 4.00e+02 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 39 2.46 - 3.07: 6950 3.07 - 3.68: 14079 3.68 - 4.29: 20647 4.29 - 4.90: 33706 Nonbonded interactions: 75421 Sorted by model distance: nonbonded pdb=" CD1 LEU A 861 " pdb=" CD2 LEU A1423 " model vdw 1.853 3.880 nonbonded pdb=" OG SER A1238 " pdb=" OD1 ASN A1241 " model vdw 2.170 2.440 nonbonded pdb=" O HIS A1481 " pdb=" OG1 THR A1485 " model vdw 2.182 2.440 nonbonded pdb=" N GLN A1164 " pdb=" O VAL A1224 " model vdw 2.215 2.520 nonbonded pdb=" OE2 GLU A 660 " pdb=" NE2 GLN A1326 " model vdw 2.221 2.520 ... (remaining 75416 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 33.790 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.010 0.145 9676 Z= 0.665 Angle : 0.989 14.370 13119 Z= 0.482 Chirality : 0.064 0.531 1535 Planarity : 0.004 0.052 1581 Dihedral : 14.693 120.107 3506 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1130 helix: 0.91 (0.18), residues: 761 sheet: None (None), residues: 0 loop : -1.31 (0.35), residues: 369 *********************** 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 205 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.014 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1659 time to fit residues: 51.0672 Evaluate side-chains 153 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.0020 chunk 48 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1481 HIS ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9676 Z= 0.180 Angle : 0.637 9.739 13119 Z= 0.324 Chirality : 0.041 0.261 1535 Planarity : 0.004 0.042 1581 Dihedral : 8.872 112.179 1386 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1130 helix: 1.31 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.29 (0.35), residues: 350 *********************** 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 201 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 1.115 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 190 average time/residue: 0.1908 time to fit residues: 53.1929 Evaluate side-chains 162 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0940 time to fit residues: 2.4433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9676 Z= 0.273 Angle : 0.657 9.793 13119 Z= 0.331 Chirality : 0.042 0.261 1535 Planarity : 0.004 0.038 1581 Dihedral : 8.642 111.611 1386 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1130 helix: 1.34 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 351 *********************** 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 173 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.026 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 167 average time/residue: 0.1855 time to fit residues: 45.9805 Evaluate side-chains 158 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0934 time to fit residues: 3.1822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1481 HIS ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9676 Z= 0.187 Angle : 0.618 14.787 13119 Z= 0.305 Chirality : 0.040 0.252 1535 Planarity : 0.004 0.035 1581 Dihedral : 8.266 112.705 1386 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1130 helix: 1.53 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -1.27 (0.35), residues: 354 *********************** 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 182 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 0.979 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 176 average time/residue: 0.1795 time to fit residues: 47.2550 Evaluate side-chains 158 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0902 time to fit residues: 2.3340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.0270 chunk 99 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9676 Z= 0.160 Angle : 0.600 13.464 13119 Z= 0.295 Chirality : 0.039 0.249 1535 Planarity : 0.003 0.038 1581 Dihedral : 7.883 113.666 1386 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1130 helix: 1.67 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 353 *********************** 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 196 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.135 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 189 average time/residue: 0.1764 time to fit residues: 50.0320 Evaluate side-chains 168 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0897 time to fit residues: 2.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN A1500 ASN A1552 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9676 Z= 0.179 Angle : 0.630 17.073 13119 Z= 0.305 Chirality : 0.040 0.249 1535 Planarity : 0.004 0.039 1581 Dihedral : 7.940 113.443 1386 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1130 helix: 1.69 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.15 (0.35), residues: 353 *********************** 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 179 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.039 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 171 average time/residue: 0.1708 time to fit residues: 43.9149 Evaluate side-chains 168 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0886 time to fit residues: 2.5643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9676 Z= 0.219 Angle : 0.657 17.184 13119 Z= 0.317 Chirality : 0.041 0.285 1535 Planarity : 0.004 0.040 1581 Dihedral : 8.012 113.084 1386 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1130 helix: 1.63 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.12 (0.36), residues: 350 *********************** 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 178 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.113 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 175 average time/residue: 0.1812 time to fit residues: 48.0180 Evaluate side-chains 165 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0984 time to fit residues: 2.3864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 761 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9676 Z= 0.199 Angle : 0.659 17.270 13119 Z= 0.316 Chirality : 0.042 0.314 1535 Planarity : 0.004 0.040 1581 Dihedral : 7.969 113.007 1386 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1130 helix: 1.66 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -1.12 (0.35), residues: 354 *********************** 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 176 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.068 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 173 average time/residue: 0.1749 time to fit residues: 45.7502 Evaluate side-chains 163 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1387 time to fit residues: 1.7713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9676 Z= 0.199 Angle : 0.668 17.409 13119 Z= 0.323 Chirality : 0.042 0.313 1535 Planarity : 0.003 0.034 1581 Dihedral : 7.826 112.934 1386 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1130 helix: 1.66 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 353 *********************** 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 174 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.072 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 167 average time/residue: 0.1718 time to fit residues: 43.8191 Evaluate side-chains 168 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1043 time to fit residues: 2.6703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9676 Z= 0.199 Angle : 0.671 17.232 13119 Z= 0.323 Chirality : 0.042 0.330 1535 Planarity : 0.003 0.032 1581 Dihedral : 7.766 112.852 1386 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1130 helix: 1.68 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -1.04 (0.35), residues: 356 ********************** 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 163 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.121 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1749 time to fit residues: 43.0732 Evaluate side-chains 158 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121689 restraints weight = 23839.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123655 restraints weight = 11684.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123906 restraints weight = 8645.745| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9676 Z= 0.178 Angle : 0.663 17.184 13119 Z= 0.318 Chirality : 0.042 0.328 1535 Planarity : 0.003 0.032 1581 Dihedral : 7.579 112.865 1386 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1130 helix: 1.72 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -1.01 (0.35), residues: 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.19 seconds wall clock time: 36 minutes 31.02 seconds (2191.02 seconds total)