Starting phenix.real_space_refine on Fri Dec 8 23:42:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/12_2023/7wlj_32585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/12_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_32585/12_2023/7wlj_32585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/12_2023/7wlj_32585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/12_2023/7wlj_32585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/12_2023/7wlj_32585.pdb" } resolution = 3.9 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= 0.009 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-1.21rc1-5172/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: 237 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: 237 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: 10.26, per 1000 atoms: 1.09 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: 4.27 Conformation dependent library (CDL) restraints added in 3.4 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: 1.03 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: 3.14 Time building geometry restraints manager: 4.58 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 - 35.67: 5893 35.67 - 71.34: 149 71.34 - 107.01: 18 107.01 - 142.68: 3 142.68 - 178.35: 3 Dihedral angle restraints: 6066 sinusoidal: 2747 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 6063 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: 1.000 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: 3.980 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 37.020 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.210 ------------------------------------------------------------------------------- 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 : 16.923 178.349 3901 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 % Allowed : 0.20 % Favored : 99.70 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 231 HIS 0.014 0.001 HIS A1440 PHE 0.029 0.002 PHE A 772 TYR 0.014 0.002 TYR A1473 ARG 0.009 0.001 ARG A1278 *********************** 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 : 0.998 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: 0.1649 time to fit residues: 63.2660 Evaluate side-chains 189 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4275 ------------------------------------------------------------------------------- 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 ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9669 Z= 0.230 Angle : 0.795 12.588 13119 Z= 0.389 Chirality : 0.045 0.243 1537 Planarity : 0.004 0.038 1580 Dihedral : 12.932 140.418 1781 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.49 % Allowed : 14.71 % Favored : 83.80 % 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: 0.04 (0.25), residues: 1130 helix: 0.93 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1382 HIS 0.013 0.002 HIS A1440 PHE 0.024 0.002 PHE A1434 TYR 0.029 0.002 TYR A1473 ARG 0.006 0.001 ARG A1278 *********************** 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 224 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.112 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 outliers start: 15 outliers final: 8 residues processed: 218 average time/residue: 0.1686 time to fit residues: 55.4817 Evaluate side-chains 191 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0954 time to fit residues: 2.8797 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9669 Z= 0.199 Angle : 0.777 15.502 13119 Z= 0.376 Chirality : 0.045 0.245 1537 Planarity : 0.004 0.036 1580 Dihedral : 12.054 135.437 1781 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.99 % Allowed : 16.60 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.25), residues: 1130 helix: 0.86 (0.19), residues: 775 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1382 HIS 0.006 0.001 HIS A1358 PHE 0.024 0.002 PHE A1246 TYR 0.020 0.001 TYR A1473 ARG 0.005 0.001 ARG A1355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.211 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 outliers start: 20 outliers final: 5 residues processed: 224 average time/residue: 0.1745 time to fit residues: 58.5377 Evaluate side-chains 194 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1086 time to fit residues: 2.4473 ------------------------------------------------------------------------------- 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: 0.4980 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2714 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= 0.193 Angle : 0.772 15.341 13119 Z= 0.374 Chirality : 0.045 0.245 1537 Planarity : 0.004 0.038 1580 Dihedral : 11.382 145.991 1781 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.49 % Allowed : 18.39 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1130 helix: 0.90 (0.19), residues: 775 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.005 0.001 HIS A1358 PHE 0.024 0.002 PHE A1631 TYR 0.016 0.001 TYR A 345 ARG 0.003 0.000 ARG A1191 *********************** 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 223 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 0.988 Fit side-chains 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 outliers start: 15 outliers final: 8 residues processed: 213 average time/residue: 0.1674 time to fit residues: 53.5677 Evaluate side-chains 199 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1075 time to fit residues: 2.9455 ------------------------------------------------------------------------------- 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: 0.6980 chunk 1 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1723 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9669 Z= 0.201 Angle : 0.767 13.098 13119 Z= 0.374 Chirality : 0.045 0.251 1537 Planarity : 0.004 0.040 1580 Dihedral : 10.994 152.929 1781 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.29 % Allowed : 20.48 % Favored : 78.23 % 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: -0.05 (0.25), residues: 1130 helix: 0.87 (0.19), residues: 777 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.006 0.001 HIS A1403 PHE 0.031 0.002 PHE A 694 TYR 0.018 0.001 TYR A1473 ARG 0.004 0.000 ARG A1191 *********************** 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 217 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 1.159 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 TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 209 average time/residue: 0.1973 time to fit residues: 61.6726 Evaluate side-chains 192 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0973 time to fit residues: 2.4882 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9669 Z= 0.247 Angle : 0.794 16.058 13119 Z= 0.385 Chirality : 0.045 0.241 1537 Planarity : 0.004 0.039 1580 Dihedral : 10.830 157.184 1781 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.39 % Allowed : 21.27 % Favored : 77.34 % 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: 0.00 (0.25), residues: 1130 helix: 0.91 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -2.04 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.007 0.001 HIS A1358 PHE 0.025 0.002 PHE A1246 TYR 0.017 0.001 TYR A 345 ARG 0.004 0.000 ARG A1191 *********************** 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 215 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.154 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: 14 outliers final: 9 residues processed: 209 average time/residue: 0.1789 time to fit residues: 56.8108 Evaluate side-chains 198 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1160 time to fit residues: 3.3198 ------------------------------------------------------------------------------- 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: 0.0040 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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: 0.7977 moved from start: 0.3391 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= 0.194 Angle : 0.789 16.642 13119 Z= 0.380 Chirality : 0.044 0.240 1537 Planarity : 0.004 0.039 1580 Dihedral : 10.363 159.852 1781 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.30 % Allowed : 22.37 % Favored : 77.34 % 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: 0.88 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.005 0.001 HIS A1358 PHE 0.028 0.001 PHE A1246 TYR 0.017 0.001 TYR A1473 ARG 0.011 0.000 ARG A 191 *********************** 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 202 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 199 time to evaluate : 1.094 Fit side-chains revert: symmetry clash 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: 3 outliers final: 2 residues processed: 200 average time/residue: 0.1783 time to fit residues: 52.9536 Evaluate side-chains 183 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1062 time to fit residues: 1.7237 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9669 Z= 0.215 Angle : 0.816 14.007 13119 Z= 0.390 Chirality : 0.044 0.241 1537 Planarity : 0.004 0.040 1580 Dihedral : 10.040 162.366 1781 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.60 % Allowed : 22.66 % Favored : 76.74 % 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: 0.02 (0.25), residues: 1130 helix: 0.86 (0.19), residues: 783 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.005 0.001 HIS A1358 PHE 0.029 0.002 PHE A1246 TYR 0.019 0.001 TYR A 364 ARG 0.007 0.000 ARG A 191 *********************** 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 203 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 1.150 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: 6 outliers final: 4 residues processed: 199 average time/residue: 0.1850 time to fit residues: 54.7598 Evaluate side-chains 190 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1312 time to fit residues: 2.7738 ------------------------------------------------------------------------------- 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: 0.9990 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9669 Z= 0.199 Angle : 0.801 16.877 13119 Z= 0.390 Chirality : 0.044 0.244 1537 Planarity : 0.004 0.040 1580 Dihedral : 9.740 166.250 1781 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.20 % Allowed : 23.46 % Favored : 76.34 % 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: 0.00 (0.25), residues: 1130 helix: 0.89 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -2.03 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.004 0.001 HIS A1358 PHE 0.038 0.002 PHE A1181 TYR 0.017 0.001 TYR A1470 ARG 0.006 0.000 ARG A 191 *********************** 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 193 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.093 Fit side-chains revert: symmetry clash 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 revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 192 average time/residue: 0.1868 time to fit residues: 52.9972 Evaluate side-chains 182 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1288 time to fit residues: 1.8950 ------------------------------------------------------------------------------- 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: 0.0010 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 0.0070 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 ASN ** 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: 0.7972 moved from start: 0.3876 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= 0.208 Angle : 0.821 13.373 13119 Z= 0.397 Chirality : 0.044 0.260 1537 Planarity : 0.004 0.041 1580 Dihedral : 9.664 173.110 1781 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.40 % Allowed : 23.86 % Favored : 75.75 % 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: -0.04 (0.25), residues: 1130 helix: 0.84 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.004 0.001 HIS A1358 PHE 0.033 0.002 PHE A1246 TYR 0.018 0.001 TYR A1470 ARG 0.007 0.001 ARG A1278 ********************** 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 193 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.100 Fit side-chains revert: symmetry clash 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: 4 outliers final: 2 residues processed: 190 average time/residue: 0.1803 time to fit residues: 51.3366 Evaluate side-chains 187 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0994 time to fit residues: 1.7620 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.123295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087910 restraints weight = 33228.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091281 restraints weight = 14356.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093391 restraints weight = 9077.415| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9669 Z= 0.208 Angle : 0.853 14.706 13119 Z= 0.412 Chirality : 0.045 0.254 1537 Planarity : 0.004 0.043 1580 Dihedral : 9.560 173.513 1781 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.50 % Allowed : 24.65 % Favored : 74.85 % 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: -0.09 (0.25), residues: 1130 helix: 0.79 (0.19), residues: 783 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.004 0.001 HIS A1358 PHE 0.033 0.002 PHE A1246 TYR 0.018 0.001 TYR A1470 ARG 0.008 0.000 ARG A1278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2133.59 seconds wall clock time: 39 minutes 31.63 seconds (2371.63 seconds total)