Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 09:38:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/04_2023/7wlj_32585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/04_2023/7wlj_32585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/04_2023/7wlj_32585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/04_2023/7wlj_32585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/04_2023/7wlj_32585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/04_2023/7wlj_32585.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.009 sd= 0.094 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 1 9.91 5 P 1 5.49 5 S 78 5.16 5 C 6272 2.51 5 N 1504 2.21 5 O 1593 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A GLU 1432": "OE1" <-> "OE2" Residue "A ARG 1466": "NH1" <-> "NH2" Residue "A GLU 1569": "OE1" <-> "OE2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A GLU 1653": "OE1" <-> "OE2" Residue "A GLU 1662": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9450 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1150, 9439 Unusual residues: {' CA': 1, '3PE': 5, 'MWV': 1, 'NAG': 2, 'Y01': 6} Classifications: {'peptide': 1135, 'undetermined': 15} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 15} Not linked: pdbres="LYS A1738 " pdbres="MWV A2301 " Not linked: pdbres="MWV 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 10 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'3PE:plan-1': 4, '3PE:plan-2': 4, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Conformer: "B" Number of residues, atoms: 1150, 9439 Unusual residues: {' CA': 1, '3PE': 5, 'MWV': 1, 'NAG': 2, 'Y01': 6} Classifications: {'peptide': 1135, 'undetermined': 15} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103, None: 15} Not linked: pdbres="LYS A1738 " pdbres="MWV A2301 " Not linked: pdbres="MWV 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 10 not shown) Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'3PE:plan-1': 4, '3PE:plan-2': 4, 'TRP:plan': 1, 'Y01:plan-2': 1, 'Y01:plan-1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 bond proxies already assigned to first conformer: 9643 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: 9.61, per 1000 atoms: 1.02 Number of scatterers: 9450 At special positions: 0 Unit cell: (113.36, 123.76, 108.16, 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 1 19.99 S 78 16.00 P 1 15.00 F 1 9.00 O 1593 8.00 N 1504 7.00 C 6272 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=0, symmetry=0 Links applied NAG-ASN " NAG A2310 " - " ASN A1345 " " NAG A2312 " - " ASN A1342 " Time building additional restraints: 3.96 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: 59 helices and 2 sheets defined 77.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 4.226A pdb=" N CYS A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N MET A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 76 " --> pdb=" O CYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.853A pdb=" N GLU A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 136 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 180 through 191 Proline residue: A 185 - end of helix removed outlier: 3.963A pdb=" N ILE A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.812A pdb=" N PHE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.547A pdb=" N ARG A 236 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.706A pdb=" N ASP A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.561A 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 342 through 355 removed outlier: 3.747A pdb=" N ALA A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 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 Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.808A pdb=" N LYS A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 3.960A pdb=" N GLU A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 695 removed outlier: 3.586A pdb=" N ASN A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 4.247A pdb=" N ASN A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 721 removed outlier: 3.935A pdb=" N ILE A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.790A pdb=" N VAL A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.865A pdb=" N LEU A 735 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 736 " --> pdb=" O PHE A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 785 removed outlier: 3.825A pdb=" N ARG A 749 " --> pdb=" O MET A 745 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 4.085A 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: 4.318A 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: 3.898A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 866 removed outlier: 3.504A pdb=" N VAL A 858 " --> pdb=" O BPHE A 854 " (cutoff:3.500A) 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: 3.740A 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 1284 through 1289 Processing helix chain 'A' and resid 1289 through 1304 removed outlier: 3.850A 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 1365 through 1377 Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.606A pdb=" N ILE A1385 " --> pdb=" O GLY A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1444 removed outlier: 4.012A pdb=" N TYR A1410 " --> pdb=" O TRP A1406 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A1415 " --> pdb=" O PHE A1411 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS A1440 " --> pdb=" O LYS A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1460 removed outlier: 3.621A pdb=" N ARG A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A1450 " --> pdb=" O ALA A1446 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1463 No H-bonds generated for 'chain 'A' and resid 1461 through 1463' Processing helix chain 'A' and resid 1468 through 1473 removed outlier: 4.210A pdb=" N THR A1472 " --> pdb=" O PRO A1468 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A1473 " --> pdb=" O TYR A1469 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1468 through 1473' Processing helix chain 'A' and resid 1482 through 1485 Processing helix chain 'A' and resid 1486 through 1505 removed outlier: 3.704A pdb=" N ASP A1490 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 4.170A 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: 3.936A pdb=" N PHE A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1574 removed outlier: 3.597A pdb=" N LEU A1568 " --> pdb=" O MET A1564 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A1569 " --> pdb=" O GLY A1565 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1571 " --> pdb=" O THR A1567 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1572 " --> pdb=" O LEU A1568 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1591 Processing helix chain 'A' and resid 1592 through 1596 Processing helix chain 'A' and resid 1597 through 1602 removed outlier: 4.001A pdb=" N MET A1601 " --> 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 1675 removed outlier: 3.668A pdb=" N ALA A1667 " --> pdb=" O ASN A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1688 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 4.063A pdb=" N LEU A1699 " --> pdb=" O GLU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1738 removed outlier: 3.619A pdb=" N VAL A1705 " --> pdb=" O SER A1701 " (cutoff:3.500A) Proline residue: A1707 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.526A pdb=" N ARG A 238 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.538A 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 1335 596 hydrogen bonds defined for protein. 1725 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: 3.32 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1432 1.32 - 1.44: 2587 1.44 - 1.57: 5459 1.57 - 1.69: 64 1.69 - 1.82: 127 Bond restraints: 9669 Sorted by residual: bond pdb=" C21 3PE A2302 " pdb=" O21 3PE A2302 " ideal model delta sigma weight residual 1.316 1.465 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C31 3PE A2302 " pdb=" O31 3PE A2302 " ideal model delta sigma weight residual 1.331 1.469 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C04 MWV A2301 " pdb=" O06 MWV A2301 " ideal model delta sigma weight residual 1.322 1.432 -0.110 2.00e-02 2.50e+03 3.05e+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 A2306 " pdb=" C32 3PE A2306 " ideal model delta sigma weight residual 1.504 1.604 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 9664 not shown) Histogram of bond angle deviations from ideal: 95.77 - 103.46: 120 103.46 - 111.14: 3930 111.14 - 118.83: 3913 118.83 - 126.52: 5042 126.52 - 134.20: 114 Bond angle restraints: 13119 Sorted by residual: 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 2.30e+01 angle pdb=" N ILE A 177 " pdb=" CA ILE A 177 " pdb=" C ILE A 177 " ideal model delta sigma weight residual 113.39 106.40 6.99 1.47e+00 4.63e-01 2.26e+01 angle pdb=" C ARG A1341 " pdb=" N ASN A1342 " pdb=" CA ASN A1342 " ideal model delta sigma weight residual 122.61 129.43 -6.82 1.56e+00 4.11e-01 1.91e+01 angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 114.39 108.37 6.02 1.45e+00 4.76e-01 1.73e+01 angle pdb=" CB MET A 687 " pdb=" CG MET A 687 " pdb=" SD MET A 687 " ideal model delta sigma weight residual 112.70 124.37 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 13114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 5274 24.22 - 48.45: 328 48.45 - 72.67: 35 72.67 - 96.89: 5 96.89 - 121.12: 2 Dihedral angle restraints: 5644 sinusoidal: 2325 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 93.00 166.57 -73.57 1 1.00e+01 1.00e-02 6.88e+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 93.00 146.34 -53.34 1 1.00e+01 1.00e-02 3.87e+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 -40.00 -46.00 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 5641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.953: 1536 0.953 - 1.906: 0 1.906 - 2.859: 0 2.859 - 3.812: 0 3.812 - 4.766: 1 Chirality restraints: 1537 Sorted by residual: chirality pdb=" C33 MWV A2301 " pdb=" C07 MWV A2301 " pdb=" C27 MWV A2301 " pdb=" C34 MWV A2301 " both_signs ideal model delta sigma weight residual False 2.33 -2.44 4.77 2.00e-01 2.50e+01 5.68e+02 chirality pdb=" CBG Y01 A2311 " pdb=" CAQ Y01 A2311 " pdb=" CBD Y01 A2311 " pdb=" CBI Y01 A2311 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" CBG Y01 A2313 " pdb=" CAQ Y01 A2313 " pdb=" CBD Y01 A2313 " pdb=" CBI Y01 A2313 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.26e+00 ... (remaining 1534 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 702 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 703 " 0.086 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 delta sigma weight rms_deltas residual plane pdb=" C VAL A 192 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 193 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1191 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A1192 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1192 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1192 " -0.026 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 57 2.51 - 3.11: 7724 3.11 - 3.70: 14803 3.70 - 4.30: 20488 4.30 - 4.90: 32605 Nonbonded interactions: 75677 Sorted by model distance: nonbonded pdb=" CD ARG A1191 " pdb=" CA ASN A1663 " model vdw 1.912 3.870 nonbonded pdb=" CG ARG A1191 " pdb=" O GLU A1662 " model vdw 2.067 3.440 nonbonded pdb=" CD1 LEU A 861 " pdb=" CD2 LEU A1423 " model vdw 2.092 3.880 nonbonded pdb=" O TYR A1633 " pdb=" OH TYR A1709 " model vdw 2.130 2.440 nonbonded pdb=" OD1 ASP A1380 " pdb=" ND2 ASN A1681 " model vdw 2.185 2.520 ... (remaining 75672 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: 1.410 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: 4.410 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 33.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.009 0.149 9669 Z= 0.569 Angle : 1.012 14.374 13119 Z= 0.496 Chirality : 0.138 4.766 1537 Planarity : 0.004 0.050 1580 Dihedral : 14.589 121.117 3479 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: 0.03 (0.26), residues: 1130 helix: 0.85 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.61 (0.34), residues: 384 *********************** 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 256 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.1738 time to fit residues: 66.7272 Evaluate side-chains 189 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4864 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A 653 ASN A 820 GLN A 855 ASN ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1510 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9669 Z= 0.233 Angle : 0.788 12.552 13119 Z= 0.390 Chirality : 0.045 0.247 1537 Planarity : 0.004 0.038 1580 Dihedral : 10.292 114.610 1359 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % 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: -0.01 (0.25), residues: 1130 helix: 0.89 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 356 *********************** 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 221 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 1.176 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 revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 216 average time/residue: 0.1759 time to fit residues: 57.2180 Evaluate side-chains 189 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0996 time to fit residues: 3.0706 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1362 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1552 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9669 Z= 0.201 Angle : 0.784 14.977 13119 Z= 0.380 Chirality : 0.045 0.253 1537 Planarity : 0.004 0.039 1580 Dihedral : 9.847 111.530 1359 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 1.99 % 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: -0.03 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 362 *********************** 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 234 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.064 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. 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 revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 223 average time/residue: 0.1811 time to fit residues: 60.5121 Evaluate side-chains 194 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1090 time to fit residues: 2.3171 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1362 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9669 Z= 0.206 Angle : 0.769 15.633 13119 Z= 0.373 Chirality : 0.044 0.251 1537 Planarity : 0.004 0.038 1580 Dihedral : 9.583 111.307 1359 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: -0.01 (0.25), residues: 1130 helix: 0.90 (0.19), residues: 775 sheet: None (None), residues: 0 loop : -2.05 (0.32), residues: 355 *********************** 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 219 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 210 average time/residue: 0.1780 time to fit residues: 56.5217 Evaluate side-chains 199 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1034 time to fit residues: 2.8480 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 ASN ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 ASN A1723 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 9669 Z= 0.327 Angle : 0.811 14.747 13119 Z= 0.397 Chirality : 0.046 0.248 1537 Planarity : 0.004 0.039 1580 Dihedral : 9.587 109.654 1359 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 1.59 % 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: -0.20 (0.25), residues: 1130 helix: 0.75 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 352 *********************** 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 218 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 1.180 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 0.1713 time to fit residues: 54.9189 Evaluate side-chains 198 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1020 time to fit residues: 3.3428 ------------------------------------------------------------------------------- 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: 9.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 9669 Z= 0.204 Angle : 0.794 16.504 13119 Z= 0.382 Chirality : 0.044 0.248 1537 Planarity : 0.004 0.038 1580 Dihedral : 9.375 109.822 1359 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % 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: -0.10 (0.25), residues: 1130 helix: 0.84 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 354 *********************** 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 220 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 214 average time/residue: 0.1776 time to fit residues: 57.6936 Evaluate side-chains 199 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1121 time to fit residues: 2.7284 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 9669 Z= 0.216 Angle : 0.804 16.904 13119 Z= 0.384 Chirality : 0.045 0.249 1537 Planarity : 0.004 0.040 1580 Dihedral : 9.202 109.365 1359 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: -0.06 (0.25), residues: 1130 helix: 0.85 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 348 *********************** 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 210 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 1.130 Fit side-chains TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 205 average time/residue: 0.1779 time to fit residues: 55.3325 Evaluate side-chains 197 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1184 time to fit residues: 2.9303 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 9669 Z= 0.275 Angle : 0.857 16.998 13119 Z= 0.413 Chirality : 0.047 0.261 1537 Planarity : 0.004 0.040 1580 Dihedral : 9.197 108.973 1359 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 0.50 % 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: -0.11 (0.25), residues: 1130 helix: 0.77 (0.19), residues: 781 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 349 *********************** 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 200 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 1.260 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 198 average time/residue: 0.1774 time to fit residues: 53.1611 Evaluate side-chains 190 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1014 time to fit residues: 2.1072 ------------------------------------------------------------------------------- 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: 3.9990 chunk 106 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.0970 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 9669 Z= 0.203 Angle : 0.828 13.950 13119 Z= 0.400 Chirality : 0.045 0.248 1537 Planarity : 0.004 0.041 1580 Dihedral : 8.911 108.594 1359 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1130 helix: 0.83 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -2.08 (0.32), residues: 348 *********************** 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 201 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 1.091 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 198 average time/residue: 0.1897 time to fit residues: 57.1536 Evaluate side-chains 195 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1079 time to fit residues: 2.1732 ------------------------------------------------------------------------------- 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: 0.3980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 114 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9669 Z= 0.199 Angle : 0.846 12.720 13119 Z= 0.409 Chirality : 0.045 0.268 1537 Planarity : 0.004 0.040 1580 Dihedral : 8.845 108.499 1359 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % 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: -0.08 (0.26), residues: 1130 helix: 0.82 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -2.05 (0.32), residues: 348 ********************** 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 195 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 1.152 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 193 average time/residue: 0.1915 time to fit residues: 55.0070 Evaluate side-chains 188 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1123 time to fit residues: 1.8313 ------------------------------------------------------------------------------- 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: 0.7980 chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** 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 = 0.3840 r_free = 0.3840 target = 0.121556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086062 restraints weight = 33279.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.089349 restraints weight = 14418.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091421 restraints weight = 9147.208| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9669 Z= 0.210 Angle : 0.840 12.006 13119 Z= 0.409 Chirality : 0.045 0.276 1537 Planarity : 0.004 0.043 1580 Dihedral : 8.828 108.344 1359 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 0.30 % 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: -0.06 (0.26), residues: 1130 helix: 0.82 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -2.05 (0.32), residues: 343 =============================================================================== Job complete usr+sys time: 2065.24 seconds wall clock time: 38 minutes 15.11 seconds (2295.11 seconds total)