Starting phenix.real_space_refine on Thu Mar 14 18:20:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/03_2024/7wlj_32585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/03_2024/7wlj_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_32585/03_2024/7wlj_32585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/03_2024/7wlj_32585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/03_2024/7wlj_32585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlj_32585/03_2024/7wlj_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-dev-5265/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: 9.63, 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: 3.77 Conformation dependent library (CDL) restraints added in 3.3 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: 0.93 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: 2.97 Time building geometry restraints manager: 4.11 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: 0.700 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: 3.940 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 35.240 Find NCS groups from input model: 0.250 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- 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 : 1.011 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 REVERT: A 208 MET cc_start: 0.7518 (mtm) cc_final: 0.6461 (mtm) REVERT: A 373 TYR cc_start: 0.8538 (m-80) cc_final: 0.8123 (m-10) REVERT: A 387 PHE cc_start: 0.8873 (t80) cc_final: 0.8655 (t80) REVERT: A 400 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8465 (mm-40) REVERT: A 694 PHE cc_start: 0.8407 (m-80) cc_final: 0.7991 (m-10) REVERT: A 767 MET cc_start: 0.7189 (mtt) cc_final: 0.6484 (mmt) REVERT: A 839 SER cc_start: 0.9509 (p) cc_final: 0.9303 (p) REVERT: A 1181 PHE cc_start: 0.8662 (t80) cc_final: 0.8422 (t80) REVERT: A 1244 ASP cc_start: 0.9079 (m-30) cc_final: 0.8856 (m-30) REVERT: A 1386 MET cc_start: 0.8989 (ttp) cc_final: 0.8569 (ttp) REVERT: A 1501 VAL cc_start: 0.9655 (t) cc_final: 0.9396 (t) REVERT: A 1504 MET cc_start: 0.8741 (mpp) cc_final: 0.8251 (mpp) REVERT: A 1522 CYS cc_start: 0.9503 (m) cc_final: 0.9214 (p) REVERT: A 1662 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7964 (mm-30) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.1646 time to fit residues: 62.7717 Evaluate side-chains 190 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9669 Z= 0.246 Angle : 0.800 12.449 13119 Z= 0.392 Chirality : 0.045 0.235 1537 Planarity : 0.004 0.037 1580 Dihedral : 13.177 141.570 1781 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.59 % Allowed : 13.62 % Favored : 84.79 % 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: 773 sheet: None (None), residues: 0 loop : -2.02 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1382 HIS 0.014 0.002 HIS A1440 PHE 0.025 0.002 PHE A1546 TYR 0.029 0.002 TYR A1473 ARG 0.006 0.001 ARG A1355 *********************** 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 225 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 209 time to evaluate : 0.904 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 REVERT: A 167 LEU cc_start: 0.9183 (tp) cc_final: 0.8970 (tt) REVERT: A 208 MET cc_start: 0.7736 (mtm) cc_final: 0.6927 (mtm) REVERT: A 373 TYR cc_start: 0.8512 (m-80) cc_final: 0.8220 (m-10) REVERT: A 387 PHE cc_start: 0.8906 (t80) cc_final: 0.8649 (t80) REVERT: A 400 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8392 (mm110) REVERT: A 694 PHE cc_start: 0.8296 (m-80) cc_final: 0.8001 (m-80) REVERT: A 717 TRP cc_start: 0.8802 (m100) cc_final: 0.8546 (t60) REVERT: A 759 MET cc_start: 0.8729 (ppp) cc_final: 0.8374 (tmm) REVERT: A 767 MET cc_start: 0.7228 (mtt) cc_final: 0.6559 (mmt) REVERT: A 778 ILE cc_start: 0.9369 (mm) cc_final: 0.8991 (tt) REVERT: A 1181 PHE cc_start: 0.8674 (t80) cc_final: 0.8308 (t80) REVERT: A 1184 CYS cc_start: 0.9341 (m) cc_final: 0.9140 (m) REVERT: A 1364 ASP cc_start: 0.8293 (m-30) cc_final: 0.8061 (t0) REVERT: A 1488 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: A 1501 VAL cc_start: 0.9673 (t) cc_final: 0.9287 (t) REVERT: A 1504 MET cc_start: 0.8671 (mpp) cc_final: 0.8366 (mpp) REVERT: A 1519 LEU cc_start: 0.9578 (mp) cc_final: 0.8945 (pp) REVERT: A 1522 CYS cc_start: 0.9465 (m) cc_final: 0.9142 (p) REVERT: A 1662 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 1704 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7830 (t80) outliers start: 16 outliers final: 9 residues processed: 218 average time/residue: 0.1649 time to fit residues: 53.8497 Evaluate side-chains 195 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 1203 PHE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2172 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= 0.188 Angle : 0.748 14.401 13119 Z= 0.368 Chirality : 0.044 0.246 1537 Planarity : 0.004 0.039 1580 Dihedral : 12.110 132.988 1781 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.09 % Allowed : 16.10 % Favored : 81.81 % 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: 0.96 (0.19), residues: 769 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.005 0.001 HIS A1358 PHE 0.027 0.002 PHE A 683 TYR 0.020 0.001 TYR A1473 ARG 0.012 0.001 ARG A 407 *********************** 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 231 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 1.246 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 revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8667 (t80) REVERT: A 167 LEU cc_start: 0.9152 (tp) cc_final: 0.8922 (tt) REVERT: A 208 MET cc_start: 0.7766 (mtm) cc_final: 0.6938 (mtm) REVERT: A 387 PHE cc_start: 0.8850 (t80) cc_final: 0.8583 (t80) REVERT: A 400 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8197 (mm110) REVERT: A 687 MET cc_start: 0.8961 (mtm) cc_final: 0.8744 (mpp) REVERT: A 694 PHE cc_start: 0.8334 (m-80) cc_final: 0.8093 (m-80) REVERT: A 717 TRP cc_start: 0.8794 (m100) cc_final: 0.8520 (t60) REVERT: A 759 MET cc_start: 0.8618 (ppp) cc_final: 0.8291 (tmm) REVERT: A 767 MET cc_start: 0.7145 (mtt) cc_final: 0.6513 (mmt) REVERT: A 778 ILE cc_start: 0.9327 (mm) cc_final: 0.9070 (tt) REVERT: A 1364 ASP cc_start: 0.8263 (m-30) cc_final: 0.8025 (t0) REVERT: A 1488 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: A 1501 VAL cc_start: 0.9669 (t) cc_final: 0.9265 (t) REVERT: A 1504 MET cc_start: 0.8639 (mpp) cc_final: 0.8291 (mpp) REVERT: A 1519 LEU cc_start: 0.9605 (mp) cc_final: 0.9002 (pp) REVERT: A 1522 CYS cc_start: 0.9459 (m) cc_final: 0.9125 (p) REVERT: A 1598 LEU cc_start: 0.9579 (mp) cc_final: 0.8905 (mm) REVERT: A 1704 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7783 (t80) outliers start: 21 outliers final: 6 residues processed: 220 average time/residue: 0.1793 time to fit residues: 57.7982 Evaluate side-chains 203 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1353 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2495 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 : 0.741 15.354 13119 Z= 0.363 Chirality : 0.044 0.244 1537 Planarity : 0.004 0.037 1580 Dihedral : 11.496 145.774 1781 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.99 % Allowed : 18.09 % Favored : 79.92 % 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: 0.97 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.006 0.001 HIS A1358 PHE 0.023 0.001 PHE A1246 TYR 0.013 0.001 TYR A 345 ARG 0.008 0.001 ARG A 407 *********************** 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 224 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 1.169 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8648 (t80) REVERT: A 167 LEU cc_start: 0.9132 (tp) cc_final: 0.8900 (tt) REVERT: A 363 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: A 367 MET cc_start: 0.8540 (mtm) cc_final: 0.8278 (mtp) REVERT: A 387 PHE cc_start: 0.8857 (t80) cc_final: 0.8515 (t80) REVERT: A 694 PHE cc_start: 0.8261 (m-80) cc_final: 0.8000 (m-80) REVERT: A 717 TRP cc_start: 0.8797 (m100) cc_final: 0.8518 (t60) REVERT: A 759 MET cc_start: 0.8541 (ppp) cc_final: 0.8135 (tmm) REVERT: A 767 MET cc_start: 0.7127 (mtt) cc_final: 0.6533 (mmt) REVERT: A 778 ILE cc_start: 0.9380 (mm) cc_final: 0.8981 (tt) REVERT: A 1364 ASP cc_start: 0.8246 (m-30) cc_final: 0.7992 (t0) REVERT: A 1425 MET cc_start: 0.8836 (mtm) cc_final: 0.8581 (mtm) REVERT: A 1488 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: A 1519 LEU cc_start: 0.9619 (mp) cc_final: 0.9016 (pp) REVERT: A 1522 CYS cc_start: 0.9440 (m) cc_final: 0.9174 (p) REVERT: A 1568 LEU cc_start: 0.9451 (mt) cc_final: 0.9248 (mt) REVERT: A 1601 MET cc_start: 0.8190 (pmm) cc_final: 0.7975 (tpt) REVERT: A 1609 LEU cc_start: 0.9148 (mm) cc_final: 0.8396 (pp) REVERT: A 1662 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7585 (mm-30) REVERT: A 1704 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7759 (t80) outliers start: 20 outliers final: 12 residues processed: 216 average time/residue: 0.1681 time to fit residues: 54.3339 Evaluate side-chains 205 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.3980 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9669 Z= 0.260 Angle : 0.759 15.564 13119 Z= 0.370 Chirality : 0.045 0.241 1537 Planarity : 0.004 0.040 1580 Dihedral : 11.183 155.895 1781 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.39 % Allowed : 18.99 % Favored : 78.63 % 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: 0.89 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.007 0.001 HIS A1358 PHE 0.025 0.002 PHE A1246 TYR 0.017 0.001 TYR A1473 ARG 0.006 0.000 ARG A 407 *********************** 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 227 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 0.980 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 revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8720 (t80) REVERT: A 167 LEU cc_start: 0.9159 (tp) cc_final: 0.8938 (tt) REVERT: A 363 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.7837 (tmm) REVERT: A 387 PHE cc_start: 0.8902 (t80) cc_final: 0.8631 (t80) REVERT: A 687 MET cc_start: 0.8929 (mtm) cc_final: 0.8695 (mpp) REVERT: A 694 PHE cc_start: 0.8257 (m-80) cc_final: 0.7993 (m-80) REVERT: A 717 TRP cc_start: 0.8836 (m100) cc_final: 0.8536 (t60) REVERT: A 759 MET cc_start: 0.8592 (ppp) cc_final: 0.8197 (tmm) REVERT: A 767 MET cc_start: 0.7186 (mtt) cc_final: 0.6583 (mmt) REVERT: A 778 ILE cc_start: 0.9376 (mm) cc_final: 0.9012 (tt) REVERT: A 822 ASP cc_start: 0.8507 (t0) cc_final: 0.8138 (t70) REVERT: A 1364 ASP cc_start: 0.8214 (m-30) cc_final: 0.7929 (t0) REVERT: A 1407 MET cc_start: 0.8891 (mmp) cc_final: 0.8574 (mmt) REVERT: A 1425 MET cc_start: 0.8884 (mtm) cc_final: 0.8573 (mtm) REVERT: A 1488 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: A 1519 LEU cc_start: 0.9621 (mp) cc_final: 0.9056 (mm) REVERT: A 1522 CYS cc_start: 0.9404 (m) cc_final: 0.9141 (p) REVERT: A 1609 LEU cc_start: 0.9140 (mm) cc_final: 0.8388 (pp) REVERT: A 1662 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 1704 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7744 (t80) outliers start: 24 outliers final: 16 residues processed: 214 average time/residue: 0.1621 time to fit residues: 52.6157 Evaluate side-chains 214 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** 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: 0.8024 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9669 Z= 0.216 Angle : 0.769 16.438 13119 Z= 0.369 Chirality : 0.045 0.276 1537 Planarity : 0.004 0.038 1580 Dihedral : 10.844 160.172 1781 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.58 % Allowed : 20.38 % Favored : 77.04 % 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: 779 sheet: None (None), residues: 0 loop : -2.10 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.006 0.001 HIS A1358 PHE 0.030 0.002 PHE A 218 TYR 0.012 0.001 TYR A1633 ARG 0.007 0.000 ARG A 191 *********************** 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 227 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 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 revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9539 (mt) cc_final: 0.9275 (tp) REVERT: A 125 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8761 (t80) REVERT: A 167 LEU cc_start: 0.9118 (tp) cc_final: 0.8889 (tt) REVERT: A 363 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8001 (tmm) REVERT: A 387 PHE cc_start: 0.8860 (t80) cc_final: 0.8572 (t80) REVERT: A 687 MET cc_start: 0.8929 (mtm) cc_final: 0.8710 (mpp) REVERT: A 694 PHE cc_start: 0.8318 (m-80) cc_final: 0.8043 (m-80) REVERT: A 717 TRP cc_start: 0.8824 (m100) cc_final: 0.8529 (t60) REVERT: A 759 MET cc_start: 0.8545 (ppp) cc_final: 0.8149 (tmm) REVERT: A 767 MET cc_start: 0.7135 (mtt) cc_final: 0.6544 (mmt) REVERT: A 778 ILE cc_start: 0.9348 (mm) cc_final: 0.9027 (tt) REVERT: A 822 ASP cc_start: 0.8451 (t0) cc_final: 0.8062 (t70) REVERT: A 1364 ASP cc_start: 0.8245 (m-30) cc_final: 0.7967 (t0) REVERT: A 1407 MET cc_start: 0.8854 (mmp) cc_final: 0.8556 (mmt) REVERT: A 1425 MET cc_start: 0.8872 (mtm) cc_final: 0.8581 (mtm) REVERT: A 1488 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: A 1519 LEU cc_start: 0.9615 (mp) cc_final: 0.9033 (mm) REVERT: A 1522 CYS cc_start: 0.9396 (m) cc_final: 0.9126 (p) REVERT: A 1609 LEU cc_start: 0.9090 (mm) cc_final: 0.8308 (pp) REVERT: A 1662 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 1704 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7722 (t80) outliers start: 26 outliers final: 14 residues processed: 213 average time/residue: 0.1682 time to fit residues: 53.9919 Evaluate side-chains 213 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 93 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 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 400 GLN ** 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: 0.8000 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 : 0.003 0.082 9669 Z= 0.202 Angle : 0.792 16.961 13119 Z= 0.376 Chirality : 0.044 0.241 1537 Planarity : 0.004 0.040 1580 Dihedral : 10.404 165.285 1781 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.99 % Allowed : 20.58 % Favored : 77.44 % 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 (0.26), residues: 1130 helix: 0.95 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.005 0.001 HIS A1358 PHE 0.035 0.002 PHE A 218 TYR 0.019 0.001 TYR A1473 ARG 0.004 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 1.067 Fit side-chains 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 revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9523 (mt) cc_final: 0.9263 (tp) REVERT: A 125 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8703 (t80) REVERT: A 134 MET cc_start: 0.8936 (mpp) cc_final: 0.7620 (mpp) REVERT: A 167 LEU cc_start: 0.9097 (tp) cc_final: 0.8867 (tt) REVERT: A 363 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7931 (tmm) REVERT: A 387 PHE cc_start: 0.8816 (t80) cc_final: 0.8478 (t80) REVERT: A 694 PHE cc_start: 0.8296 (m-80) cc_final: 0.8042 (m-80) REVERT: A 717 TRP cc_start: 0.8798 (m100) cc_final: 0.8518 (t60) REVERT: A 759 MET cc_start: 0.8510 (ppp) cc_final: 0.8117 (tmm) REVERT: A 767 MET cc_start: 0.7118 (mtt) cc_final: 0.6525 (mmt) REVERT: A 778 ILE cc_start: 0.9333 (mm) cc_final: 0.9073 (tt) REVERT: A 822 ASP cc_start: 0.8423 (t0) cc_final: 0.8019 (t70) REVERT: A 855 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8029 (t0) REVERT: A 1364 ASP cc_start: 0.8233 (m-30) cc_final: 0.7945 (t0) REVERT: A 1407 MET cc_start: 0.8839 (mmp) cc_final: 0.8547 (mmt) REVERT: A 1425 MET cc_start: 0.8847 (mtm) cc_final: 0.8619 (mtm) REVERT: A 1488 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: A 1497 ILE cc_start: 0.9589 (mm) cc_final: 0.9250 (tt) REVERT: A 1519 LEU cc_start: 0.9608 (mp) cc_final: 0.8984 (mm) REVERT: A 1522 CYS cc_start: 0.9386 (m) cc_final: 0.9156 (p) REVERT: A 1533 GLU cc_start: 0.8913 (pp20) cc_final: 0.8659 (pp20) REVERT: A 1601 MET cc_start: 0.8193 (pmm) cc_final: 0.7741 (tpt) REVERT: A 1662 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 1704 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7675 (t80) outliers start: 20 outliers final: 13 residues processed: 218 average time/residue: 0.1697 time to fit residues: 55.4581 Evaluate side-chains 212 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1546 PHE Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE 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: 4.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9669 Z= 0.238 Angle : 0.798 16.509 13119 Z= 0.382 Chirality : 0.044 0.241 1537 Planarity : 0.004 0.039 1580 Dihedral : 10.131 174.531 1781 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.09 % Allowed : 22.17 % 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: 0.08 (0.25), residues: 1130 helix: 0.94 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -1.98 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.006 0.001 HIS A1358 PHE 0.035 0.002 PHE A 218 TYR 0.010 0.001 TYR A1633 ARG 0.004 0.000 ARG A 407 *********************** 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 219 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.037 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 revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9540 (mt) cc_final: 0.9279 (tp) REVERT: A 125 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8688 (t80) REVERT: A 167 LEU cc_start: 0.9120 (tp) cc_final: 0.8896 (tt) REVERT: A 363 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7970 (tmm) REVERT: A 387 PHE cc_start: 0.8832 (t80) cc_final: 0.8585 (t80) REVERT: A 694 PHE cc_start: 0.8314 (m-80) cc_final: 0.8045 (m-80) REVERT: A 717 TRP cc_start: 0.8814 (m100) cc_final: 0.8520 (t60) REVERT: A 759 MET cc_start: 0.8502 (ppp) cc_final: 0.8091 (tmm) REVERT: A 767 MET cc_start: 0.7138 (mtt) cc_final: 0.6537 (mmt) REVERT: A 778 ILE cc_start: 0.9251 (mm) cc_final: 0.8975 (tt) REVERT: A 822 ASP cc_start: 0.8469 (t0) cc_final: 0.8068 (t70) REVERT: A 855 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8111 (t0) REVERT: A 1185 ILE cc_start: 0.9412 (mt) cc_final: 0.9122 (mt) REVERT: A 1364 ASP cc_start: 0.8247 (m-30) cc_final: 0.7972 (t0) REVERT: A 1407 MET cc_start: 0.8862 (mmp) cc_final: 0.8588 (mmt) REVERT: A 1425 MET cc_start: 0.8856 (mtm) cc_final: 0.8620 (mtm) REVERT: A 1488 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: A 1497 ILE cc_start: 0.9573 (mm) cc_final: 0.9197 (tt) REVERT: A 1519 LEU cc_start: 0.9619 (mp) cc_final: 0.9010 (mm) REVERT: A 1601 MET cc_start: 0.8242 (pmm) cc_final: 0.7837 (tpt) REVERT: A 1662 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 1704 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7688 (t80) outliers start: 21 outliers final: 13 residues processed: 208 average time/residue: 0.1767 time to fit residues: 55.7233 Evaluate side-chains 213 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1546 PHE Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE 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: 0.6980 chunk 62 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9669 Z= 0.198 Angle : 0.801 16.137 13119 Z= 0.384 Chirality : 0.045 0.241 1537 Planarity : 0.004 0.040 1580 Dihedral : 9.572 164.657 1781 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.89 % Allowed : 22.76 % Favored : 75.35 % 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 (0.26), residues: 1130 helix: 0.96 (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 0.009 0.001 TRP A1382 HIS 0.005 0.001 HIS A1358 PHE 0.032 0.002 PHE A1246 TYR 0.017 0.001 TYR A1473 ARG 0.007 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 220 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 1.142 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9529 (mt) cc_final: 0.9267 (tp) REVERT: A 125 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8697 (t80) REVERT: A 167 LEU cc_start: 0.9086 (tp) cc_final: 0.8796 (tt) REVERT: A 363 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: A 387 PHE cc_start: 0.8791 (t80) cc_final: 0.8413 (t80) REVERT: A 694 PHE cc_start: 0.8303 (m-80) cc_final: 0.8046 (m-80) REVERT: A 717 TRP cc_start: 0.8819 (m100) cc_final: 0.8525 (t60) REVERT: A 759 MET cc_start: 0.8499 (ppp) cc_final: 0.8078 (tmm) REVERT: A 767 MET cc_start: 0.7083 (mtt) cc_final: 0.6523 (mmt) REVERT: A 778 ILE cc_start: 0.9337 (mm) cc_final: 0.9070 (tt) REVERT: A 822 ASP cc_start: 0.8411 (t0) cc_final: 0.7986 (t70) REVERT: A 855 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8101 (t0) REVERT: A 1185 ILE cc_start: 0.9400 (mt) cc_final: 0.9175 (mt) REVERT: A 1364 ASP cc_start: 0.8235 (m-30) cc_final: 0.7953 (t0) REVERT: A 1407 MET cc_start: 0.8832 (mmp) cc_final: 0.8554 (mmt) REVERT: A 1434 PHE cc_start: 0.9225 (t80) cc_final: 0.8994 (t80) REVERT: A 1488 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: A 1533 GLU cc_start: 0.8920 (pp20) cc_final: 0.8679 (pp20) REVERT: A 1601 MET cc_start: 0.8229 (pmm) cc_final: 0.7673 (tpt) REVERT: A 1662 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 1704 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7685 (t80) outliers start: 19 outliers final: 12 residues processed: 209 average time/residue: 0.1606 time to fit residues: 50.7096 Evaluate side-chains 211 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9669 Z= 0.308 Angle : 0.848 15.352 13119 Z= 0.407 Chirality : 0.046 0.241 1537 Planarity : 0.004 0.040 1580 Dihedral : 9.598 152.564 1781 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.99 % Allowed : 23.26 % Favored : 74.75 % 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: -0.07 (0.25), residues: 1130 helix: 0.81 (0.19), residues: 793 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.008 0.001 HIS A1358 PHE 0.033 0.002 PHE A1246 TYR 0.010 0.001 TYR A1633 ARG 0.006 0.000 ARG A 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.053 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 revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9556 (mt) cc_final: 0.9296 (tp) REVERT: A 363 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8024 (tmm) REVERT: A 387 PHE cc_start: 0.8899 (t80) cc_final: 0.8432 (t80) REVERT: A 694 PHE cc_start: 0.8370 (m-80) cc_final: 0.8068 (m-80) REVERT: A 717 TRP cc_start: 0.8840 (m100) cc_final: 0.8537 (t60) REVERT: A 759 MET cc_start: 0.8513 (ppp) cc_final: 0.8076 (tmm) REVERT: A 767 MET cc_start: 0.7173 (mtt) cc_final: 0.6582 (mmt) REVERT: A 822 ASP cc_start: 0.8530 (t0) cc_final: 0.7964 (t70) REVERT: A 855 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8336 (m-40) REVERT: A 1185 ILE cc_start: 0.9426 (mt) cc_final: 0.9134 (mt) REVERT: A 1364 ASP cc_start: 0.8253 (m-30) cc_final: 0.7960 (t0) REVERT: A 1386 MET cc_start: 0.9190 (ttp) cc_final: 0.8938 (ttp) REVERT: A 1407 MET cc_start: 0.8902 (mmp) cc_final: 0.8604 (mmt) REVERT: A 1488 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: A 1601 MET cc_start: 0.8251 (pmm) cc_final: 0.7896 (tpt) REVERT: A 1704 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7717 (t80) outliers start: 20 outliers final: 13 residues processed: 205 average time/residue: 0.1591 time to fit residues: 49.0498 Evaluate side-chains 206 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1470 TYR Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.118582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082803 restraints weight = 33179.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.085992 restraints weight = 14263.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087984 restraints weight = 9060.601| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9669 Z= 0.286 Angle : 0.853 15.446 13119 Z= 0.418 Chirality : 0.047 0.250 1537 Planarity : 0.004 0.043 1580 Dihedral : 9.533 149.265 1781 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.79 % Allowed : 24.06 % Favored : 74.16 % 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: 0.81 (0.19), residues: 793 sheet: None (None), residues: 0 loop : -2.10 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.007 0.001 HIS A1358 PHE 0.039 0.002 PHE A 218 TYR 0.011 0.001 TYR A1633 ARG 0.006 0.000 ARG A 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.38 seconds wall clock time: 37 minutes 34.32 seconds (2254.32 seconds total)