Starting phenix.real_space_refine on Sat Dec 9 21:06:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/12_2023/5zal_6905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/12_2023/5zal_6905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/12_2023/5zal_6905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/12_2023/5zal_6905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/12_2023/5zal_6905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/12_2023/5zal_6905.pdb" } resolution = 4.7 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 57 5.49 5 S 66 5.16 5 C 7640 2.51 5 N 2122 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 944": "NH1" <-> "NH2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A PHE 1610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1736": "NH1" <-> "NH2" Residue "A TYR 1834": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 12346 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1314, 10552 Classifications: {'peptide': 1314} Link IDs: {'CIS': 18, 'PCIS': 4, 'PTRANS': 64, 'TRANS': 1227} Chain breaks: 8 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 560 Classifications: {'peptide': 75} Link IDs: {'PCIS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1234 Classifications: {'RNA': 58} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 1, 'rna3p': 56} Chain breaks: 1 Time building chain proxies: 6.92, per 1000 atoms: 0.56 Number of scatterers: 12346 At special positions: 0 Unit cell: (112.34, 101.38, 160.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 57 15.00 O 2461 8.00 N 2122 7.00 C 7640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 531 " distance=2.04 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 Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2666 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 46.5% alpha, 5.7% beta 18 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 69 through 84 removed outlier: 3.757A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.563A pdb=" N VAL A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.577A pdb=" N LYS A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.755A pdb=" N LEU A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.716A pdb=" N MET A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 316 through 336 removed outlier: 4.220A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 removed outlier: 4.088A pdb=" N LEU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 453 through 461 removed outlier: 4.007A pdb=" N LEU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.605A pdb=" N ALA A 510 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 4.136A pdb=" N LEU A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 516' Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 574 through 592 removed outlier: 4.271A pdb=" N GLU A 583 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 699 through 706 Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 839 through 857 removed outlier: 4.410A pdb=" N SER A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 903 Processing helix chain 'A' and resid 967 through 975 Processing helix chain 'A' and resid 1002 through 1011 Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 3.742A pdb=" N LYS A1019 " --> pdb=" O SER A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.834A pdb=" N LEU A1027 " --> pdb=" O LYS A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1052 Processing helix chain 'A' and resid 1053 through 1072 removed outlier: 3.690A pdb=" N ILE A1057 " --> pdb=" O CYS A1053 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A1063 " --> pdb=" O TYR A1059 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1301 Processing helix chain 'A' and resid 1312 through 1334 removed outlier: 4.253A pdb=" N MET A1317 " --> pdb=" O GLU A1313 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 removed outlier: 4.176A pdb=" N TYR A1345 " --> pdb=" O GLY A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.861A pdb=" N LEU A1356 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 Processing helix chain 'A' and resid 1558 through 1573 removed outlier: 3.768A pdb=" N CYS A1569 " --> pdb=" O ALA A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1584 Processing helix chain 'A' and resid 1592 through 1597 removed outlier: 3.598A pdb=" N ARG A1596 " --> pdb=" O VAL A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1621 removed outlier: 4.348A pdb=" N SER A1620 " --> pdb=" O LEU A1617 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A1621 " --> pdb=" O SER A1618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1617 through 1621' Processing helix chain 'A' and resid 1655 through 1663 Processing helix chain 'A' and resid 1666 through 1673 Processing helix chain 'A' and resid 1679 through 1687 removed outlier: 4.165A pdb=" N LEU A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1687 " --> pdb=" O LEU A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1697 removed outlier: 3.662A pdb=" N ILE A1697 " --> pdb=" O TYR A1694 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1722 removed outlier: 4.426A pdb=" N ALA A1710 " --> pdb=" O PHE A1706 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A1713 " --> pdb=" O ASP A1709 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A1717 " --> pdb=" O ASP A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1739 Processing helix chain 'A' and resid 1741 through 1752 removed outlier: 3.605A pdb=" N SER A1747 " --> pdb=" O THR A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1776 removed outlier: 4.047A pdb=" N PHE A1766 " --> pdb=" O SER A1762 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1807 through 1823 removed outlier: 3.827A pdb=" N ILE A1811 " --> pdb=" O ALA A1807 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A1812 " --> pdb=" O MET A1808 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR A1820 " --> pdb=" O ALA A1816 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A1821 " --> pdb=" O GLY A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1848 removed outlier: 3.937A pdb=" N TYR A1835 " --> pdb=" O TRP A1831 " (cutoff:3.500A) Proline residue: A1836 - end of helix Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1852 through 1861 Processing helix chain 'A' and resid 1896 through 1911 removed outlier: 3.708A pdb=" N ALA A1903 " --> pdb=" O ILE A1899 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A1904 " --> pdb=" O ALA A1900 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 4.003A pdb=" N SER B 299 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 123 removed outlier: 3.728A pdb=" N ILE A 149 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 172 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 203 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 removed outlier: 6.214A pdb=" N ILE A 253 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 4.870A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N MET A 775 " --> pdb=" O ARG A 800 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ARG A 800 " --> pdb=" O MET A 775 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1032 through 1033 removed outlier: 6.260A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 947 " --> pdb=" O ASP A 991 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 931 " --> pdb=" O HIS A1041 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1865 through 1866 removed outlier: 3.651A pdb=" N VAL A1882 " --> pdb=" O PHE A1890 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AA7, first strand: chain 'B' and resid 313 through 317 removed outlier: 6.841A pdb=" N GLU B 316 " --> pdb=" O GLN B 324 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN B 324 " --> pdb=" O GLU B 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 398 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2887 1.33 - 1.46: 3401 1.46 - 1.58: 6220 1.58 - 1.71: 113 1.71 - 1.84: 90 Bond restraints: 12711 Sorted by residual: bond pdb=" C PRO A 961 " pdb=" N SER A 962 " ideal model delta sigma weight residual 1.331 1.253 0.078 2.83e-02 1.25e+03 7.56e+00 bond pdb=" CA PHE A 372 " pdb=" C PHE A 372 " ideal model delta sigma weight residual 1.526 1.558 -0.032 1.28e-02 6.10e+03 6.10e+00 bond pdb=" CB TYR A1692 " pdb=" CG TYR A1692 " ideal model delta sigma weight residual 1.512 1.458 0.054 2.20e-02 2.07e+03 6.07e+00 bond pdb=" CA THR A 134 " pdb=" C THR A 134 " ideal model delta sigma weight residual 1.519 1.547 -0.028 1.19e-02 7.06e+03 5.66e+00 bond pdb=" CA GLU A 128 " pdb=" C GLU A 128 " ideal model delta sigma weight residual 1.522 1.550 -0.027 1.20e-02 6.94e+03 5.10e+00 ... (remaining 12706 not shown) Histogram of bond angle deviations from ideal: 97.97 - 106.26: 691 106.26 - 114.55: 7542 114.55 - 122.83: 7795 122.83 - 131.12: 1378 131.12 - 139.40: 62 Bond angle restraints: 17468 Sorted by residual: angle pdb=" C LEU A 649 " pdb=" N ALA A 650 " pdb=" CA ALA A 650 " ideal model delta sigma weight residual 121.70 136.28 -14.58 1.80e+00 3.09e-01 6.56e+01 angle pdb=" C THR A 134 " pdb=" N LYS A 135 " pdb=" CA LYS A 135 " ideal model delta sigma weight residual 121.70 135.75 -14.05 1.80e+00 3.09e-01 6.10e+01 angle pdb=" N GLY A 93 " pdb=" CA GLY A 93 " pdb=" C GLY A 93 " ideal model delta sigma weight residual 110.21 116.65 -6.44 9.10e-01 1.21e+00 5.00e+01 angle pdb=" N PRO A1376 " pdb=" CA PRO A1376 " pdb=" C PRO A1376 " ideal model delta sigma weight residual 110.70 118.76 -8.06 1.22e+00 6.72e-01 4.36e+01 angle pdb=" C SER A 167 " pdb=" N ASP A 168 " pdb=" CA ASP A 168 " ideal model delta sigma weight residual 121.70 132.85 -11.15 1.80e+00 3.09e-01 3.84e+01 ... (remaining 17463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 7147 18.18 - 36.37: 477 36.37 - 54.55: 97 54.55 - 72.74: 48 72.74 - 90.92: 14 Dihedral angle restraints: 7783 sinusoidal: 3680 harmonic: 4103 Sorted by residual: dihedral pdb=" CA ASN A1293 " pdb=" C ASN A1293 " pdb=" N PRO A1294 " pdb=" CA PRO A1294 " ideal model delta harmonic sigma weight residual -180.00 -112.88 -67.12 0 5.00e+00 4.00e-02 1.80e+02 dihedral pdb=" CA LEU A 164 " pdb=" C LEU A 164 " pdb=" N SER A 165 " pdb=" CA SER A 165 " ideal model delta harmonic sigma weight residual 180.00 140.91 39.09 0 5.00e+00 4.00e-02 6.11e+01 dihedral pdb=" CA TYR A1752 " pdb=" C TYR A1752 " pdb=" N ASP A1753 " pdb=" CA ASP A1753 " ideal model delta harmonic sigma weight residual 180.00 141.58 38.42 0 5.00e+00 4.00e-02 5.91e+01 ... (remaining 7780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1750 0.096 - 0.192: 261 0.192 - 0.287: 24 0.287 - 0.383: 0 0.383 - 0.479: 1 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CG LEU A 81 " pdb=" CB LEU A 81 " pdb=" CD1 LEU A 81 " pdb=" CD2 LEU A 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CB VAL A1370 " pdb=" CA VAL A1370 " pdb=" CG1 VAL A1370 " pdb=" CG2 VAL A1370 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA PRO A1294 " pdb=" N PRO A1294 " pdb=" C PRO A1294 " pdb=" CB PRO A1294 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2033 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1293 " -0.060 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO A1294 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO A1294 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A1294 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1335 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A1336 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A1336 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A1336 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1376 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A1377 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " -0.041 5.00e-02 4.00e+02 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1853 2.75 - 3.29: 12927 3.29 - 3.83: 23544 3.83 - 4.36: 27802 4.36 - 4.90: 41011 Nonbonded interactions: 107137 Sorted by model distance: nonbonded pdb=" NE2 HIS A 703 " pdb=" OD2 ASP A 709 " model vdw 2.215 2.520 nonbonded pdb=" OG1 THR B 331 " pdb=" O PRO B 333 " model vdw 2.240 2.440 nonbonded pdb=" O GLY A1568 " pdb=" OG1 THR A1572 " model vdw 2.240 2.440 nonbonded pdb=" O VAL A 75 " pdb=" OG1 THR A 78 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR A 47 " pdb=" OG1 THR A 238 " model vdw 2.248 2.440 ... (remaining 107132 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=1.00 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: 0.370 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: 1.940 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.600 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 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 : 0.008 0.103 12711 Z= 0.536 Angle : 1.440 16.091 17468 Z= 0.782 Chirality : 0.068 0.479 2036 Planarity : 0.010 0.091 2012 Dihedral : 14.252 90.922 5114 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.14 % Favored : 83.20 % Rotamer: Outliers : 0.97 % Allowed : 3.46 % Favored : 95.57 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.22 % Twisted Proline : 5.71 % Twisted General : 1.22 % 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: -5.19 (0.18), residues: 1369 helix: -3.37 (0.15), residues: 544 sheet: -3.71 (0.44), residues: 78 loop : -3.57 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP A1048 HIS 0.018 0.003 HIS A 116 PHE 0.038 0.005 PHE A1812 TYR 0.037 0.005 TYR A 876 ARG 0.015 0.002 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 187 average time/residue: 0.3456 time to fit residues: 85.2669 Evaluate side-chains 102 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1140 time to fit residues: 2.3290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 116 HIS A 140 GLN A 157 ASN A 195 ASN A 279 ASN A 514 ASN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 GLN A1293 ASN A1339 HIS A1660 ASN A1693 HIS ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12711 Z= 0.264 Angle : 0.912 12.247 17468 Z= 0.476 Chirality : 0.048 0.333 2036 Planarity : 0.007 0.078 2012 Dihedral : 15.423 98.015 2326 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 33.59 Ramachandran Plot: Outliers : 0.37 % Allowed : 15.34 % Favored : 84.30 % Rotamer: Outliers : 0.40 % Allowed : 4.75 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.38 % Twisted Proline : 1.43 % Twisted General : 0.76 % 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: -4.19 (0.20), residues: 1369 helix: -2.15 (0.19), residues: 536 sheet: -3.73 (0.44), residues: 90 loop : -3.24 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 316 HIS 0.011 0.002 HIS A 116 PHE 0.030 0.002 PHE A 351 TYR 0.023 0.002 TYR A 637 ARG 0.014 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 140 average time/residue: 0.3327 time to fit residues: 62.5612 Evaluate side-chains 93 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1214 time to fit residues: 2.3802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 35 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 140 optimal weight: 30.0000 chunk 115 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12711 Z= 0.258 Angle : 0.869 11.848 17468 Z= 0.457 Chirality : 0.047 0.257 2036 Planarity : 0.007 0.076 2012 Dihedral : 15.236 94.713 2326 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 34.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 15.12 % Favored : 84.51 % Rotamer: Outliers : 0.40 % Allowed : 4.91 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.46 % 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: -3.76 (0.21), residues: 1369 helix: -1.65 (0.20), residues: 543 sheet: -3.49 (0.47), residues: 90 loop : -3.12 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 316 HIS 0.009 0.002 HIS A1755 PHE 0.031 0.002 PHE A 351 TYR 0.021 0.002 TYR A 387 ARG 0.011 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 127 average time/residue: 0.2990 time to fit residues: 52.7618 Evaluate side-chains 87 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1397 time to fit residues: 2.4336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12711 Z= 0.319 Angle : 0.916 11.454 17468 Z= 0.481 Chirality : 0.048 0.247 2036 Planarity : 0.007 0.076 2012 Dihedral : 15.405 92.621 2326 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 43.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 17.02 % Favored : 82.76 % Rotamer: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.38 % 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: -3.80 (0.21), residues: 1369 helix: -1.64 (0.20), residues: 548 sheet: -3.67 (0.44), residues: 90 loop : -3.18 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 138 HIS 0.009 0.002 HIS A1755 PHE 0.030 0.003 PHE A1374 TYR 0.025 0.003 TYR A 387 ARG 0.012 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.3104 time to fit residues: 49.3691 Evaluate side-chains 77 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 2 optimal weight: 0.0870 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.0670 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12711 Z= 0.197 Angle : 0.803 11.952 17468 Z= 0.421 Chirality : 0.046 0.283 2036 Planarity : 0.006 0.069 2012 Dihedral : 14.813 87.629 2326 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.10 % Favored : 85.61 % Rotamer: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.38 % 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: -3.44 (0.21), residues: 1369 helix: -1.34 (0.20), residues: 571 sheet: -3.31 (0.50), residues: 76 loop : -3.05 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 138 HIS 0.005 0.001 HIS A 850 PHE 0.034 0.002 PHE A 351 TYR 0.024 0.002 TYR A 163 ARG 0.006 0.000 ARG A1879 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.3171 time to fit residues: 56.9937 Evaluate side-chains 88 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12711 Z= 0.282 Angle : 0.874 13.561 17468 Z= 0.456 Chirality : 0.048 0.253 2036 Planarity : 0.007 0.071 2012 Dihedral : 15.002 89.889 2326 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 37.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.44 % Favored : 83.35 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.23 % 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: -3.43 (0.21), residues: 1369 helix: -1.31 (0.21), residues: 547 sheet: -3.49 (0.48), residues: 80 loop : -3.00 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 316 HIS 0.011 0.002 HIS A 116 PHE 0.028 0.002 PHE A 351 TYR 0.020 0.002 TYR A 637 ARG 0.018 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3135 time to fit residues: 50.3586 Evaluate side-chains 81 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 63 optimal weight: 0.1980 chunk 85 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12711 Z= 0.291 Angle : 0.896 11.660 17468 Z= 0.467 Chirality : 0.049 0.229 2036 Planarity : 0.006 0.065 2012 Dihedral : 15.154 89.715 2326 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 38.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.73 % Favored : 83.05 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.23 % 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: -3.54 (0.21), residues: 1369 helix: -1.49 (0.20), residues: 563 sheet: -3.59 (0.47), residues: 80 loop : -2.99 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 316 HIS 0.009 0.002 HIS A1755 PHE 0.032 0.003 PHE A 351 TYR 0.023 0.002 TYR A 637 ARG 0.009 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3235 time to fit residues: 48.4180 Evaluate side-chains 79 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12711 Z= 0.214 Angle : 0.825 12.280 17468 Z= 0.428 Chirality : 0.047 0.211 2036 Planarity : 0.006 0.081 2012 Dihedral : 14.864 91.599 2326 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 29.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.34 % Favored : 84.37 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.23 % 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: -3.17 (0.22), residues: 1369 helix: -1.15 (0.20), residues: 557 sheet: -3.21 (0.48), residues: 81 loop : -2.83 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 316 HIS 0.004 0.001 HIS A 850 PHE 0.033 0.002 PHE A 351 TYR 0.022 0.002 TYR A1570 ARG 0.012 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3471 time to fit residues: 52.1500 Evaluate side-chains 79 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 0.0060 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 0.0040 chunk 84 optimal weight: 4.9990 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 HIS A1028 GLN A1293 ASN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12711 Z= 0.194 Angle : 0.807 12.729 17468 Z= 0.419 Chirality : 0.046 0.200 2036 Planarity : 0.006 0.083 2012 Dihedral : 14.415 93.751 2326 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.44 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.15 % 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: -3.02 (0.22), residues: 1369 helix: -0.95 (0.21), residues: 562 sheet: -3.01 (0.47), residues: 93 loop : -2.82 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 316 HIS 0.004 0.001 HIS A1661 PHE 0.031 0.002 PHE A 351 TYR 0.018 0.002 TYR A 473 ARG 0.013 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3177 time to fit residues: 53.5988 Evaluate side-chains 79 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12711 Z= 0.202 Angle : 0.802 12.267 17468 Z= 0.414 Chirality : 0.045 0.205 2036 Planarity : 0.006 0.083 2012 Dihedral : 14.343 94.800 2326 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.39 % Favored : 85.39 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.15 % 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: -2.93 (0.22), residues: 1369 helix: -0.78 (0.21), residues: 558 sheet: -3.27 (0.42), residues: 110 loop : -2.77 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 316 HIS 0.005 0.001 HIS A 703 PHE 0.028 0.002 PHE A 351 TYR 0.027 0.002 TYR A1570 ARG 0.009 0.000 ARG A 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3358 time to fit residues: 51.2632 Evaluate side-chains 75 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 GLN ** B 305 GLN ** 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 = 0.3894 r_free = 0.3894 target = 0.075702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.057020 restraints weight = 116657.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.058682 restraints weight = 80350.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.059942 restraints weight = 60844.120| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12711 Z= 0.210 Angle : 0.806 12.203 17468 Z= 0.418 Chirality : 0.046 0.212 2036 Planarity : 0.006 0.080 2012 Dihedral : 14.360 95.074 2326 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 29.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.32 % Favored : 85.46 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.15 % 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: -2.95 (0.22), residues: 1369 helix: -0.88 (0.21), residues: 563 sheet: -3.30 (0.42), residues: 110 loop : -2.70 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 316 HIS 0.004 0.001 HIS A 850 PHE 0.021 0.002 PHE A 351 TYR 0.019 0.002 TYR A1757 ARG 0.009 0.000 ARG A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.30 seconds wall clock time: 42 minutes 28.91 seconds (2548.91 seconds total)