Starting phenix.real_space_refine on Fri Mar 15 17:35:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/03_2024/5zal_6905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/03_2024/5zal_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_6905/03_2024/5zal_6905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/03_2024/5zal_6905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/03_2024/5zal_6905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zal_6905/03_2024/5zal_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-dev-5265/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: 6.57, per 1000 atoms: 0.53 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: 5.79 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: 3.27 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: 4.41 Time building geometry restraints manager: 6.09 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: 7167 18.18 - 36.37: 492 36.37 - 54.55: 113 54.55 - 72.74: 75 72.74 - 90.92: 14 Dihedral angle restraints: 7861 sinusoidal: 3758 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 7858 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: 0.290 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: 1.980 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 37.010 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- 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 : 15.070 90.922 5192 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 : 1.241 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 REVERT: A 509 ARG cc_start: 0.9273 (mtt180) cc_final: 0.8886 (ptp-110) REVERT: A 528 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6413 (tp) REVERT: A 562 MET cc_start: 0.7700 (tpt) cc_final: 0.7240 (tpt) REVERT: A 573 GLU cc_start: 0.9293 (tt0) cc_final: 0.9027 (tt0) REVERT: A 579 TYR cc_start: 0.9081 (m-80) cc_final: 0.8346 (m-10) REVERT: A 589 LYS cc_start: 0.9428 (mptt) cc_final: 0.9226 (mmtm) REVERT: A 858 LEU cc_start: 0.9197 (mt) cc_final: 0.8750 (tt) REVERT: A 977 ASN cc_start: 0.9637 (m-40) cc_final: 0.9420 (t0) REVERT: A 1313 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8883 (mp0) REVERT: A 1687 PHE cc_start: 0.9401 (m-80) cc_final: 0.8980 (m-80) REVERT: A 1767 HIS cc_start: 0.8375 (t-170) cc_final: 0.8121 (t70) REVERT: A 1825 MET cc_start: 0.8600 (mpt) cc_final: 0.7969 (mpt) REVERT: A 1895 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7948 (mpp-170) REVERT: B 296 ARG cc_start: 0.7766 (tmm160) cc_final: 0.7336 (mmt180) outliers start: 12 outliers final: 2 residues processed: 187 average time/residue: 0.3347 time to fit residues: 82.6406 Evaluate side-chains 110 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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: 5.9990 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: 8.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 356 HIS A 514 ASN A 548 GLN ** 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 ** A1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 ASN A1693 HIS ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2114 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= 0.283 Angle : 0.935 12.336 17468 Z= 0.488 Chirality : 0.048 0.326 2036 Planarity : 0.007 0.080 2012 Dihedral : 16.913 98.097 2404 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 33.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.70 % Favored : 84.00 % Rotamer: Outliers : 0.32 % Allowed : 5.07 % Favored : 94.61 % 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: -4.28 (0.20), residues: 1369 helix: -2.23 (0.19), residues: 543 sheet: -3.80 (0.43), residues: 90 loop : -3.28 (0.21), residues: 736 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 0.033 0.002 PHE A 351 TYR 0.024 0.002 TYR A 637 ARG 0.011 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: 4 poor density : 137 time to evaluate : 1.367 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: A 503 GLU cc_start: 0.7456 (tt0) cc_final: 0.7070 (tm-30) REVERT: A 509 ARG cc_start: 0.9288 (mtt180) cc_final: 0.8932 (ptp-110) REVERT: A 562 MET cc_start: 0.7115 (tpt) cc_final: 0.6873 (tpt) REVERT: A 572 PHE cc_start: 0.9482 (m-10) cc_final: 0.9267 (m-10) REVERT: A 579 TYR cc_start: 0.8991 (m-80) cc_final: 0.8193 (m-10) REVERT: A 837 MET cc_start: 0.4729 (mmm) cc_final: 0.3892 (mmm) REVERT: A 858 LEU cc_start: 0.9139 (mt) cc_final: 0.8703 (tt) REVERT: A 1687 PHE cc_start: 0.9272 (m-80) cc_final: 0.9059 (m-80) REVERT: A 1767 HIS cc_start: 0.8192 (t-170) cc_final: 0.7980 (t70) REVERT: B 296 ARG cc_start: 0.7521 (tmm160) cc_final: 0.7097 (mmt180) outliers start: 4 outliers final: 2 residues processed: 140 average time/residue: 0.3440 time to fit residues: 64.1714 Evaluate side-chains 97 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 140 optimal weight: 30.0000 chunk 115 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 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: 0.7452 moved from start: 0.2866 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= 0.246 Angle : 0.860 11.960 17468 Z= 0.453 Chirality : 0.047 0.256 2036 Planarity : 0.006 0.075 2012 Dihedral : 16.589 95.254 2404 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 33.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.63 % Favored : 84.08 % Rotamer: Outliers : 0.16 % Allowed : 5.15 % 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: -3.86 (0.21), residues: 1369 helix: -1.74 (0.20), residues: 545 sheet: -3.51 (0.47), residues: 90 loop : -3.18 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 316 HIS 0.008 0.001 HIS A1755 PHE 0.028 0.002 PHE A 351 TYR 0.021 0.002 TYR A 387 ARG 0.013 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 127 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.480 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: A 351 PHE cc_start: 0.9402 (m-80) cc_final: 0.9175 (m-80) REVERT: A 509 ARG cc_start: 0.9291 (mtt180) cc_final: 0.8951 (ptp-110) REVERT: A 562 MET cc_start: 0.7115 (tpt) cc_final: 0.6887 (tpt) REVERT: A 579 TYR cc_start: 0.9048 (m-80) cc_final: 0.8294 (m-10) REVERT: A 837 MET cc_start: 0.4943 (mmm) cc_final: 0.4189 (mmm) REVERT: A 858 LEU cc_start: 0.9150 (mt) cc_final: 0.8809 (tt) REVERT: A 1337 ASP cc_start: 0.9018 (t0) cc_final: 0.8724 (t70) REVERT: A 1767 HIS cc_start: 0.8012 (t-170) cc_final: 0.7771 (t70) REVERT: B 296 ARG cc_start: 0.7526 (tmm160) cc_final: 0.7046 (mmt180) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.3173 time to fit residues: 55.2240 Evaluate side-chains 93 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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: 8.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 711 HIS ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 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: 0.7468 moved from start: 0.3321 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= 0.256 Angle : 0.856 11.492 17468 Z= 0.449 Chirality : 0.047 0.240 2036 Planarity : 0.006 0.066 2012 Dihedral : 16.494 92.525 2404 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 35.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.00 % Favored : 83.71 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.31 % 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: -3.75 (0.21), residues: 1369 helix: -1.53 (0.20), residues: 557 sheet: -3.58 (0.46), residues: 90 loop : -3.23 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 138 HIS 0.006 0.001 HIS A1755 PHE 0.023 0.002 PHE A1812 TYR 0.021 0.002 TYR A 387 ARG 0.013 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: 0 poor density : 114 time to evaluate : 1.021 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: A 98 PHE cc_start: 0.8713 (m-10) cc_final: 0.8392 (m-80) REVERT: A 572 PHE cc_start: 0.9251 (m-10) cc_final: 0.9047 (m-80) REVERT: A 579 TYR cc_start: 0.9074 (m-80) cc_final: 0.8398 (m-10) REVERT: A 837 MET cc_start: 0.5040 (mmm) cc_final: 0.4263 (mmm) REVERT: A 858 LEU cc_start: 0.9200 (mt) cc_final: 0.8892 (tt) REVERT: A 1337 ASP cc_start: 0.9077 (t0) cc_final: 0.8786 (t70) REVERT: A 1687 PHE cc_start: 0.9092 (m-80) cc_final: 0.8863 (m-80) REVERT: A 1768 VAL cc_start: 0.8521 (t) cc_final: 0.8218 (t) REVERT: A 1851 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7144 (ptt90) REVERT: B 296 ARG cc_start: 0.7500 (tmm160) cc_final: 0.6943 (mmt180) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2674 time to fit residues: 41.8085 Evaluate side-chains 90 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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: 0.7980 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 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** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 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: 0.7429 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12711 Z= 0.226 Angle : 0.826 11.682 17468 Z= 0.431 Chirality : 0.046 0.280 2036 Planarity : 0.006 0.068 2012 Dihedral : 16.303 89.835 2404 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 32.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.29 % Favored : 83.49 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -3.56 (0.21), residues: 1369 helix: -1.38 (0.20), residues: 555 sheet: -3.53 (0.45), residues: 92 loop : -3.10 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 138 HIS 0.005 0.001 HIS A1755 PHE 0.020 0.002 PHE A1812 TYR 0.020 0.002 TYR A 387 ARG 0.005 0.000 ARG A1855 *********************** 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 114 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.301 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: A 66 THR cc_start: 0.7694 (m) cc_final: 0.7238 (p) REVERT: A 351 PHE cc_start: 0.9370 (m-80) cc_final: 0.9160 (m-80) REVERT: A 562 MET cc_start: 0.6816 (tpt) cc_final: 0.5487 (tpp) REVERT: A 579 TYR cc_start: 0.9022 (m-80) cc_final: 0.8177 (m-10) REVERT: A 837 MET cc_start: 0.5011 (mmm) cc_final: 0.4263 (mmm) REVERT: A 858 LEU cc_start: 0.9224 (mt) cc_final: 0.8959 (tt) REVERT: A 1346 MET cc_start: 0.6955 (mtm) cc_final: 0.6555 (mtt) REVERT: A 1768 VAL cc_start: 0.8444 (t) cc_final: 0.8138 (t) REVERT: A 1837 MET cc_start: 0.8037 (mtp) cc_final: 0.7762 (mtp) REVERT: A 1851 ARG cc_start: 0.7427 (mmm160) cc_final: 0.7120 (ptt90) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3079 time to fit residues: 48.4901 Evaluate side-chains 90 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 0.0000 chunk 34 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 0.0010 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 3.7996 ------------------------------------------------------------------------------- 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** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 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: 0.7468 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12711 Z= 0.271 Angle : 0.867 15.165 17468 Z= 0.452 Chirality : 0.047 0.231 2036 Planarity : 0.006 0.064 2012 Dihedral : 16.340 91.080 2404 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 37.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.95 % Favored : 82.83 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.31 % 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: -3.53 (0.21), residues: 1369 helix: -1.35 (0.21), residues: 550 sheet: -3.33 (0.47), residues: 85 loop : -3.12 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 133 HIS 0.010 0.002 HIS A1719 PHE 0.025 0.002 PHE A1812 TYR 0.022 0.002 TYR A 637 ARG 0.017 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 119 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.335 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: A 66 THR cc_start: 0.7763 (m) cc_final: 0.7347 (p) REVERT: A 351 PHE cc_start: 0.9368 (m-80) cc_final: 0.9147 (m-80) REVERT: A 562 MET cc_start: 0.6958 (tpt) cc_final: 0.5846 (tpp) REVERT: A 579 TYR cc_start: 0.9003 (m-80) cc_final: 0.8190 (m-10) REVERT: A 805 LEU cc_start: 0.8878 (tp) cc_final: 0.8615 (tp) REVERT: A 837 MET cc_start: 0.4896 (mmm) cc_final: 0.4332 (mmm) REVERT: A 897 MET cc_start: 0.9172 (ptp) cc_final: 0.8374 (ptp) REVERT: A 1317 MET cc_start: 0.6109 (mmp) cc_final: 0.4746 (mmt) REVERT: A 1340 GLU cc_start: 0.8128 (pp20) cc_final: 0.7885 (pp20) REVERT: A 1346 MET cc_start: 0.7005 (mtm) cc_final: 0.6567 (mtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3035 time to fit residues: 50.2791 Evaluate side-chains 85 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 137 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 116 HIS 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** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 GLN ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7374 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12711 Z= 0.200 Angle : 0.810 13.786 17468 Z= 0.419 Chirality : 0.045 0.220 2036 Planarity : 0.006 0.068 2012 Dihedral : 16.071 91.403 2404 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 29.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.56 % Favored : 84.15 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.31 % 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: -3.18 (0.22), residues: 1369 helix: -0.99 (0.21), residues: 547 sheet: -3.11 (0.49), residues: 81 loop : -2.98 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 133 HIS 0.004 0.001 HIS A 850 PHE 0.024 0.002 PHE A1669 TYR 0.016 0.002 TYR A 387 ARG 0.008 0.000 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 118 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.379 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: A 52 LEU cc_start: 0.9646 (mt) cc_final: 0.9444 (mt) REVERT: A 66 THR cc_start: 0.7890 (m) cc_final: 0.7485 (p) REVERT: A 351 PHE cc_start: 0.9360 (m-80) cc_final: 0.9114 (m-80) REVERT: A 503 GLU cc_start: 0.8333 (pp20) cc_final: 0.8056 (mp0) REVERT: A 562 MET cc_start: 0.6972 (tpt) cc_final: 0.5476 (tpp) REVERT: A 579 TYR cc_start: 0.9013 (m-80) cc_final: 0.8162 (m-10) REVERT: A 837 MET cc_start: 0.5048 (mmm) cc_final: 0.4290 (mmm) REVERT: A 897 MET cc_start: 0.9176 (ptp) cc_final: 0.8318 (ptp) REVERT: A 1317 MET cc_start: 0.5757 (mmp) cc_final: 0.4376 (mmt) REVERT: A 1346 MET cc_start: 0.6956 (mtm) cc_final: 0.6572 (mtt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2959 time to fit residues: 48.6382 Evaluate side-chains 85 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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: 10.0000 chunk 82 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 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** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 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: 0.7335 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12711 Z= 0.192 Angle : 0.799 12.941 17468 Z= 0.412 Chirality : 0.045 0.207 2036 Planarity : 0.006 0.066 2012 Dihedral : 15.792 93.080 2404 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.24 % Favored : 85.46 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: -3.05 (0.22), residues: 1369 helix: -0.92 (0.21), residues: 564 sheet: -2.98 (0.50), residues: 81 loop : -2.92 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP A 316 HIS 0.004 0.001 HIS A 850 PHE 0.015 0.002 PHE A1812 TYR 0.018 0.002 TYR A1570 ARG 0.005 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 128 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.339 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: A 52 LEU cc_start: 0.9654 (mt) cc_final: 0.9442 (mt) REVERT: A 66 THR cc_start: 0.8258 (m) cc_final: 0.7852 (p) REVERT: A 351 PHE cc_start: 0.9380 (m-80) cc_final: 0.9134 (m-80) REVERT: A 447 PHE cc_start: 0.8789 (m-80) cc_final: 0.8115 (m-80) REVERT: A 562 MET cc_start: 0.6913 (tpt) cc_final: 0.5807 (tpt) REVERT: A 579 TYR cc_start: 0.8979 (m-80) cc_final: 0.8648 (m-80) REVERT: A 805 LEU cc_start: 0.8786 (tp) cc_final: 0.8516 (tp) REVERT: A 837 MET cc_start: 0.4943 (mmm) cc_final: 0.4132 (mmm) REVERT: A 897 MET cc_start: 0.9169 (ptp) cc_final: 0.8292 (ptp) REVERT: A 1308 ASP cc_start: 0.8886 (p0) cc_final: 0.8154 (t0) REVERT: A 1317 MET cc_start: 0.5622 (mmp) cc_final: 0.5148 (mmt) REVERT: A 1346 MET cc_start: 0.6980 (mtm) cc_final: 0.6649 (mtt) REVERT: A 1860 MET cc_start: 0.8882 (mpp) cc_final: 0.8550 (mpp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2994 time to fit residues: 52.5793 Evaluate side-chains 88 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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: 6.9990 chunk 120 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 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** A1028 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 ASN ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7338 moved from start: 0.4855 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= 0.203 Angle : 0.805 12.361 17468 Z= 0.416 Chirality : 0.045 0.209 2036 Planarity : 0.006 0.066 2012 Dihedral : 15.702 94.286 2404 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.88 % Favored : 85.83 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -2.97 (0.22), residues: 1369 helix: -0.75 (0.21), residues: 564 sheet: -3.14 (0.49), residues: 88 loop : -2.93 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 316 HIS 0.004 0.001 HIS A 850 PHE 0.017 0.002 PHE A1812 TYR 0.047 0.002 TYR A 668 ARG 0.013 0.000 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 116 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.357 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: A 52 LEU cc_start: 0.9672 (mt) cc_final: 0.9469 (mt) REVERT: A 66 THR cc_start: 0.8389 (m) cc_final: 0.8000 (p) REVERT: A 351 PHE cc_start: 0.9380 (m-80) cc_final: 0.9130 (m-80) REVERT: A 356 HIS cc_start: 0.9137 (t-90) cc_final: 0.8937 (t-90) REVERT: A 579 TYR cc_start: 0.8971 (m-80) cc_final: 0.8669 (m-80) REVERT: A 805 LEU cc_start: 0.8806 (tp) cc_final: 0.8542 (tp) REVERT: A 837 MET cc_start: 0.4955 (mmm) cc_final: 0.4166 (mmm) REVERT: A 897 MET cc_start: 0.9142 (ptp) cc_final: 0.8277 (ptp) REVERT: A 1050 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8800 (mmtt) REVERT: A 1308 ASP cc_start: 0.8877 (p0) cc_final: 0.8120 (t0) REVERT: A 1346 MET cc_start: 0.7019 (mtm) cc_final: 0.6603 (mtt) REVERT: A 1837 MET cc_start: 0.8275 (mtp) cc_final: 0.8002 (ttm) REVERT: A 1860 MET cc_start: 0.8855 (mpp) cc_final: 0.8630 (mpp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3002 time to fit residues: 48.2883 Evaluate side-chains 85 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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: 20.0000 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 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 116 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** A1028 GLN ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7365 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12711 Z= 0.217 Angle : 0.815 12.187 17468 Z= 0.422 Chirality : 0.045 0.209 2036 Planarity : 0.006 0.091 2012 Dihedral : 15.708 94.902 2404 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.10 % Favored : 85.68 % 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: -2.96 (0.22), residues: 1369 helix: -0.79 (0.21), residues: 563 sheet: -3.18 (0.48), residues: 88 loop : -2.87 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 316 HIS 0.004 0.001 HIS A 850 PHE 0.019 0.002 PHE A1812 TYR 0.034 0.002 TYR A 668 ARG 0.015 0.001 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 114 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.414 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: A 66 THR cc_start: 0.8286 (m) cc_final: 0.7897 (p) REVERT: A 351 PHE cc_start: 0.9387 (m-80) cc_final: 0.9146 (m-80) REVERT: A 356 HIS cc_start: 0.9118 (t-90) cc_final: 0.8892 (t-90) REVERT: A 562 MET cc_start: 0.6931 (tpt) cc_final: 0.5784 (tpt) REVERT: A 579 TYR cc_start: 0.8980 (m-80) cc_final: 0.8676 (m-80) REVERT: A 837 MET cc_start: 0.4957 (mmm) cc_final: 0.4186 (mmm) REVERT: A 897 MET cc_start: 0.8964 (ptp) cc_final: 0.8256 (ptp) REVERT: A 1340 GLU cc_start: 0.7815 (pp20) cc_final: 0.7582 (pp20) REVERT: A 1346 MET cc_start: 0.6972 (mtm) cc_final: 0.6537 (mtt) REVERT: A 1860 MET cc_start: 0.8811 (mpp) cc_final: 0.8586 (mpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3045 time to fit residues: 48.3270 Evaluate side-chains 84 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 99 optimal weight: 0.0270 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 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** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3810 r_free = 0.3810 target = 0.070611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.053135 restraints weight = 109827.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.054765 restraints weight = 77216.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.056008 restraints weight = 58952.934| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.5179 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= 0.195 Angle : 0.793 12.339 17468 Z= 0.409 Chirality : 0.045 0.200 2036 Planarity : 0.006 0.083 2012 Dihedral : 15.591 94.887 2404 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.51 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: -2.86 (0.22), residues: 1369 helix: -0.71 (0.21), residues: 564 sheet: -3.08 (0.49), residues: 88 loop : -2.82 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 316 HIS 0.004 0.001 HIS A 850 PHE 0.016 0.002 PHE A1374 TYR 0.030 0.002 TYR A 668 ARG 0.011 0.000 ARG A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.55 seconds wall clock time: 42 minutes 12.90 seconds (2532.90 seconds total)