Starting phenix.real_space_refine
on Wed Jul 30 20:18:49 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/5zal_6905/07_2025/5zal_6905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5zal_6905/07_2025/5zal_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/cci-nas-00/data/ceres_data/5zal_6905/07_2025/5zal_6905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5zal_6905/07_2025/5zal_6905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5zal_6905/07_2025/5zal_6905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5zal_6905/07_2025/5zal_6905.cif"
  }
  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. Time to flip 10 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.86, per 1000 atoms: 0.64
  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  - 3.00
        Amino acid           : True  - 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: 3.37
  Conformation dependent library (CDL) restraints added in 1.6 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: 4.98
  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: 5.14

  Time building geometry restraints manager: 4.01 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:
        0.00 -     3.22: 16795
        3.22 -     6.44: 552
        6.44 -     9.65: 93
        9.65 -    12.87: 21
       12.87 -    16.09: 7
  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 3.120
  nonbonded pdb=" OG1 THR B 331 "
            pdb=" O   PRO B 333 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   GLY A1568 "
            pdb=" OG1 THR A1572 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   VAL A  75 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OH  TYR A  47 "
            pdb=" OG1 THR A 238 "
     model   vdw
     2.248 3.040
  ... (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
Time spend for trying shortcut: 0.00
========== 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:                  0.010
  Normalize map: mean=0, sd=1:             0.300
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     36.840
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.210
-------------------------------------------------------------------------------
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  12712  Z= 0.409
  Angle     :  1.440  16.091  17470  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19850 (  439)
  hydrogen bonds       : angle       9.33078 ( 1207)
  SS BOND              : bond        0.00809 (    1)
  SS BOND              : angle       1.30399 (    2)
  covalent geometry    : bond        0.00832 (12711)
  covalent geometry    : angle       1.43958 (17468)

*********************** 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 to be fit.
    rotamer outliers: 12
    poor density    : 176
  time to evaluate  : 1.289 
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: 0.3415
  time to fit residues: 84.4994
Evaluate side-chains
  110 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 108 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9980
   chunk 43 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 129 optimal weight:   20.0000
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 140 GLN
A 279 ASN
A 356 HIS
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
A1339 HIS
A1660 ASN
A1693 HIS
** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.066730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.048413 restraints weight = 116067.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.049839 restraints weight = 85007.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.050951 restraints weight = 66792.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6111
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12712  Z= 0.190
  Angle     :  0.906  12.611  17470  Z= 0.475
  Chirality :  0.048   0.322   2036
  Planarity :  0.007   0.074   2012
  Dihedral  : 16.723  99.088   2404
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 25.66
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 15.34 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.51 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.38 %
    Twisted Proline : 1.43 %
    Twisted General : 0.53 %

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: -4.13 (0.20), residues: 1369
  helix: -2.13 (0.19), residues: 543
  sheet: -3.67 (0.44), residues: 92
  loop : -3.18 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 316 
 HIS   0.010   0.001   HIS A 116 
 PHE   0.029   0.002   PHE A 351 
 TYR   0.020   0.002   TYR A 387 
 ARG   0.011   0.001   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06651 (  439)
  hydrogen bonds       : angle       7.03723 ( 1207)
  SS BOND              : bond        0.00258 (    1)
  SS BOND              : angle       2.04740 (    2)
  covalent geometry    : bond        0.00384 (12711)
  covalent geometry    : angle       0.90607 (17468)

*********************** 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
  147 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 1.399 
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   61 ILE cc_start: 0.7950 (mp) cc_final: 0.7680 (mp)
REVERT: A  543 TYR cc_start: 0.8721 (p90) cc_final: 0.8338 (p90)
REVERT: A  579 TYR cc_start: 0.7754 (m-80) cc_final: 0.7527 (m-10)
REVERT: A  837 MET cc_start: 0.4573 (mmm) cc_final: 0.4348 (mmm)
REVERT: A 1687 PHE cc_start: 0.8733 (m-80) cc_final: 0.8507 (m-80)
REVERT: A 1812 PHE cc_start: 0.9057 (t80) cc_final: 0.8820 (t80)
REVERT: A 1848 ASN cc_start: 0.9412 (t0) cc_final: 0.9201 (p0)
REVERT: B  296 ARG cc_start: 0.7591 (tmm160) cc_final: 0.7326 (mmt180)
  outliers start: 3
  outliers final: 1
  residues processed: 146
  average time/residue: 0.3603
  time to fit residues: 69.4758
Evaluate side-chains
  96 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 96 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 49 optimal weight:   30.0000
   chunk 41 optimal weight:    5.9990
   chunk 137 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 75 optimal weight:    9.9990
   chunk 104 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 ASN
A 356 HIS
** A 648 HIS ** 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**
** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.064291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.046483 restraints weight = 121160.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.047866 restraints weight = 87975.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.048923 restraints weight = 68861.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6261
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12712  Z= 0.255
  Angle     :  0.952  12.026  17470  Z= 0.501
  Chirality :  0.050   0.293   2036
  Planarity :  0.007   0.063   2012
  Dihedral  : 16.758  96.030   2404
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 34.82
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 16.80 %
    Favored  : 82.91 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  5.15 %
    Favored  : 94.61 %
  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: -4.02 (0.21), residues: 1369
  helix: -1.91 (0.20), residues: 549
  sheet: -3.71 (0.44), residues: 90
  loop : -3.23 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 316 
 HIS   0.015   0.002   HIS A 116 
 PHE   0.026   0.003   PHE A1812 
 TYR   0.024   0.003   TYR A 637 
 ARG   0.013   0.001   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06779 (  439)
  hydrogen bonds       : angle       7.01412 ( 1207)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       1.89128 (    2)
  covalent geometry    : bond        0.00516 (12711)
  covalent geometry    : angle       0.95164 (17468)

*********************** 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
  116 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 1.308 
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: A  543 TYR cc_start: 0.8957 (p90) cc_final: 0.8577 (p90)
REVERT: A  579 TYR cc_start: 0.7961 (m-80) cc_final: 0.7667 (m-10)
REVERT: A  837 MET cc_start: 0.4613 (mmm) cc_final: 0.4345 (mmm)
REVERT: A 1688 THR cc_start: 0.6612 (OUTLIER) cc_final: 0.6112 (p)
REVERT: B  296 ARG cc_start: 0.7472 (tmm160) cc_final: 0.7165 (mmt180)
  outliers start: 3
  outliers final: 1
  residues processed: 115
  average time/residue: 0.3179
  time to fit residues: 50.7948
Evaluate side-chains
  86 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 112 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 133 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 137 optimal weight:    0.9980
   chunk 20 optimal weight:    8.9990
   overall best weight:    2.4786

-------------------------------------------------------------------------------
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 109 GLN
** 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 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1695 ASN ** 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 = 0.3766 r_free = 0.3766 target = 0.068204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.050955 restraints weight = 109017.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.052543 restraints weight = 75696.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.053744 restraints weight = 57102.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12712  Z= 0.167
  Angle     :  0.845  12.264  17470  Z= 0.445
  Chirality :  0.047   0.274   2036
  Planarity :  0.006   0.063   2012
  Dihedral  : 16.424  92.094   2404
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 26.24
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 14.76 %
    Favored  : 84.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  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: -3.78 (0.21), residues: 1369
  helix: -1.75 (0.20), residues: 570
  sheet: -3.57 (0.46), residues: 86
  loop : -3.08 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 316 
 HIS   0.005   0.001   HIS A1755 
 PHE   0.020   0.002   PHE A1374 
 TYR   0.022   0.002   TYR A 387 
 ARG   0.009   0.001   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05399 (  439)
  hydrogen bonds       : angle       6.50967 ( 1207)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       1.66312 (    2)
  covalent geometry    : bond        0.00351 (12711)
  covalent geometry    : angle       0.84508 (17468)

*********************** 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
  118 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.292 
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  543 TYR cc_start: 0.8842 (p90) cc_final: 0.8520 (p90)
REVERT: A  579 TYR cc_start: 0.7898 (m-80) cc_final: 0.7535 (m-10)
REVERT: A  837 MET cc_start: 0.4770 (mmm) cc_final: 0.4498 (mmm)
REVERT: A 1687 PHE cc_start: 0.8882 (m-80) cc_final: 0.8658 (m-80)
REVERT: A 1697 ILE cc_start: 0.0519 (mp) cc_final: -0.0268 (mp)
REVERT: B  296 ARG cc_start: 0.7541 (tmm160) cc_final: 0.7198 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.3026
  time to fit residues: 49.7987
Evaluate side-chains
  81 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 1 optimal weight:   30.0000
   chunk 90 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 128 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 134 optimal weight:   20.0000
   chunk 54 optimal weight:   30.0000
   chunk 0 optimal weight:    0.9980
   chunk 127 optimal weight:    6.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 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 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.066979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.048882 restraints weight = 116868.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.050349 restraints weight = 85466.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.051452 restraints weight = 66778.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6150
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12712  Z= 0.173
  Angle     :  0.841  12.018  17470  Z= 0.442
  Chirality :  0.047   0.284   2036
  Planarity :  0.006   0.061   2012
  Dihedral  : 16.246  90.234   2404
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 27.19
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 15.63 %
    Favored  : 84.15 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.62 %
    Favored  : 96.30 %
  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: -3.69 (0.21), residues: 1369
  helix: -1.63 (0.20), residues: 564
  sheet: -3.80 (0.45), residues: 84
  loop : -3.03 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 133 
 HIS   0.007   0.001   HIS A1755 
 PHE   0.028   0.002   PHE A 351 
 TYR   0.019   0.002   TYR A 387 
 ARG   0.011   0.001   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05352 (  439)
  hydrogen bonds       : angle       6.37861 ( 1207)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       1.58044 (    2)
  covalent geometry    : bond        0.00362 (12711)
  covalent geometry    : angle       0.84132 (17468)

*********************** 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
  110 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 1.473 
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: A  351 PHE cc_start: 0.9448 (m-80) cc_final: 0.9206 (m-80)
REVERT: A  543 TYR cc_start: 0.8905 (p90) cc_final: 0.8614 (p90)
REVERT: A  579 TYR cc_start: 0.7907 (m-80) cc_final: 0.7550 (m-10)
REVERT: A  837 MET cc_start: 0.4873 (mmm) cc_final: 0.4585 (mmm)
REVERT: B  296 ARG cc_start: 0.7543 (tmm160) cc_final: 0.7263 (mmt180)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.3560
  time to fit residues: 53.6583
Evaluate side-chains
  83 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 1.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 131 optimal weight:    0.0980
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 124 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
** 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 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1695 ASN ** 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 = 0.3817 r_free = 0.3817 target = 0.070158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.052577 restraints weight = 110209.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.054150 restraints weight = 77772.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.055390 restraints weight = 58900.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6194
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  12712  Z= 0.146
  Angle     :  0.820  12.150  17470  Z= 0.427
  Chirality :  0.047   0.257   2036
  Planarity :  0.006   0.064   2012
  Dihedral  : 15.976  91.583   2404
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 22.94
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 13.88 %
    Favored  : 85.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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: -3.47 (0.21), residues: 1369
  helix: -1.48 (0.20), residues: 580
  sheet: -3.25 (0.49), residues: 81
  loop : -2.97 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A1831 
 HIS   0.005   0.001   HIS A1719 
 PHE   0.020   0.002   PHE A 351 
 TYR   0.016   0.002   TYR A 387 
 ARG   0.015   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04836 (  439)
  hydrogen bonds       : angle       6.06467 ( 1207)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       1.46292 (    2)
  covalent geometry    : bond        0.00309 (12711)
  covalent geometry    : angle       0.81976 (17468)

*********************** 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
  112 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.346 
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: A  447 PHE cc_start: 0.9009 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  562 MET cc_start: 0.4962 (tpt) cc_final: 0.2520 (tpp)
REVERT: A  837 MET cc_start: 0.4871 (mmm) cc_final: 0.4588 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.3730
  time to fit residues: 58.1649
Evaluate side-chains
  77 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0970
   chunk 103 optimal weight:    0.8980
   chunk 100 optimal weight:   10.0000
   chunk 119 optimal weight:    0.7980
   chunk 133 optimal weight:   20.0000
   chunk 113 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 12 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 HIS
** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1028 GLN
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.080491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.067580 restraints weight = 126612.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.069024 restraints weight = 82928.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.069986 restraints weight = 60471.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12712  Z= 0.141
  Angle     :  0.800  12.118  17470  Z= 0.417
  Chirality :  0.046   0.249   2036
  Planarity :  0.006   0.061   2012
  Dihedral  : 15.747  93.900   2404
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 20.92
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 14.32 %
    Favored  : 85.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  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: -3.19 (0.22), residues: 1369
  helix: -1.25 (0.20), residues: 575
  sheet: -3.07 (0.53), residues: 77
  loop : -2.81 (0.23), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.004   TRP A 316 
 HIS   0.005   0.001   HIS A1661 
 PHE   0.022   0.002   PHE A 351 
 TYR   0.021   0.002   TYR A 579 
 ARG   0.012   0.000   ARG B 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04608 (  439)
  hydrogen bonds       : angle       5.87336 ( 1207)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       1.21457 (    2)
  covalent geometry    : bond        0.00300 (12711)
  covalent geometry    : angle       0.80014 (17468)

*********************** 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
  120 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.478 
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: A  196 CYS cc_start: 0.9399 (m) cc_final: 0.8727 (t)
REVERT: A  351 PHE cc_start: 0.9429 (m-80) cc_final: 0.9188 (m-80)
REVERT: A  356 HIS cc_start: 0.9252 (t-90) cc_final: 0.9050 (t-90)
REVERT: A  447 PHE cc_start: 0.8910 (m-80) cc_final: 0.8342 (m-80)
REVERT: A  562 MET cc_start: 0.6481 (tpt) cc_final: 0.4888 (tpp)
REVERT: A  837 MET cc_start: 0.4907 (mmm) cc_final: 0.4141 (mmm)
REVERT: A 1346 MET cc_start: 0.6516 (mtm) cc_final: 0.6191 (mtt)
REVERT: A 1687 PHE cc_start: 0.8974 (m-80) cc_final: 0.8708 (m-80)
REVERT: A 1821 MET cc_start: 0.8555 (tpt) cc_final: 0.8247 (tpt)
REVERT: A 1839 ARG cc_start: 0.9308 (ptt90) cc_final: 0.9017 (ptm-80)
REVERT: B  362 MET cc_start: 0.8468 (mmm) cc_final: 0.8244 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.3134
  time to fit residues: 51.8746
Evaluate side-chains
  82 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 125 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 132 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:   10.0000
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
A 116 HIS
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 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**
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.078166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.065193 restraints weight = 128573.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.066478 restraints weight = 85375.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.067382 restraints weight = 64406.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12712  Z= 0.162
  Angle     :  0.833  12.121  17470  Z= 0.434
  Chirality :  0.046   0.253   2036
  Planarity :  0.006   0.086   2012
  Dihedral  : 15.788  94.602   2404
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 25.04
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 13.81 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  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: -3.20 (0.22), residues: 1369
  helix: -1.27 (0.20), residues: 578
  sheet: -3.48 (0.47), residues: 79
  loop : -2.76 (0.23), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.004   TRP A 316 
 HIS   0.004   0.001   HIS A 648 
 PHE   0.022   0.002   PHE A1812 
 TYR   0.019   0.002   TYR A1721 
 ARG   0.010   0.001   ARG B 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04813 (  439)
  hydrogen bonds       : angle       5.88982 ( 1207)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       1.15582 (    2)
  covalent geometry    : bond        0.00341 (12711)
  covalent geometry    : angle       0.83294 (17468)

*********************** 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
  113 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.468 
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  196 CYS cc_start: 0.9397 (m) cc_final: 0.8726 (t)
REVERT: A  356 HIS cc_start: 0.9212 (t-90) cc_final: 0.8992 (t-90)
REVERT: A  562 MET cc_start: 0.6908 (tpt) cc_final: 0.5671 (tpp)
REVERT: A  805 LEU cc_start: 0.8933 (tp) cc_final: 0.8677 (tp)
REVERT: A  837 MET cc_start: 0.5013 (mmm) cc_final: 0.4153 (mmm)
REVERT: A 1308 ASP cc_start: 0.9093 (p0) cc_final: 0.8447 (t0)
REVERT: A 1346 MET cc_start: 0.6514 (mtm) cc_final: 0.6128 (mtt)
REVERT: A 1687 PHE cc_start: 0.9039 (m-80) cc_final: 0.8775 (m-80)
REVERT: A 1821 MET cc_start: 0.8565 (tpt) cc_final: 0.8289 (tpt)
REVERT: B  362 MET cc_start: 0.8544 (mmm) cc_final: 0.8229 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.3538
  time to fit residues: 55.0873
Evaluate side-chains
  83 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 127 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 82 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0870
   chunk 71 optimal weight:    4.9990
   overall best weight:    3.8166

-------------------------------------------------------------------------------
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 648 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**
A1028 GLN
** A1695 ASN ** 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 = 0.3860 r_free = 0.3860 target = 0.075774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.062882 restraints weight = 129807.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.064060 restraints weight = 86240.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.064973 restraints weight = 65103.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12712  Z= 0.197
  Angle     :  0.881  12.048  17470  Z= 0.459
  Chirality :  0.048   0.259   2036
  Planarity :  0.006   0.076   2012
  Dihedral  : 15.978  93.808   2404
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 29.54
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 15.27 %
    Favored  : 84.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  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: -3.31 (0.21), residues: 1369
  helix: -1.35 (0.20), residues: 581
  sheet: -3.59 (0.46), residues: 79
  loop : -2.82 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP A 316 
 HIS   0.005   0.002   HIS A 648 
 PHE   0.025   0.002   PHE A1812 
 TYR   0.020   0.002   TYR A1721 
 ARG   0.011   0.001   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05164 (  439)
  hydrogen bonds       : angle       6.09972 ( 1207)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       1.46076 (    2)
  covalent geometry    : bond        0.00409 (12711)
  covalent geometry    : angle       0.88083 (17468)

*********************** 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
  102 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.515 
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: A  196 CYS cc_start: 0.9340 (m) cc_final: 0.8582 (t)
REVERT: A  356 HIS cc_start: 0.9204 (t-90) cc_final: 0.8996 (t-90)
REVERT: A  579 TYR cc_start: 0.8977 (m-10) cc_final: 0.8742 (m-80)
REVERT: A  805 LEU cc_start: 0.8878 (tp) cc_final: 0.8654 (tp)
REVERT: A  837 MET cc_start: 0.5252 (mmm) cc_final: 0.4496 (mmm)
REVERT: A  897 MET cc_start: 0.9270 (ptp) cc_final: 0.8504 (ptp)
REVERT: A 1308 ASP cc_start: 0.9148 (p0) cc_final: 0.8593 (t0)
REVERT: A 1340 GLU cc_start: 0.8062 (pp20) cc_final: 0.7858 (pp20)
REVERT: A 1346 MET cc_start: 0.6514 (mtm) cc_final: 0.6069 (mtt)
REVERT: A 1687 PHE cc_start: 0.9196 (m-80) cc_final: 0.8946 (m-80)
REVERT: A 1821 MET cc_start: 0.8796 (tpt) cc_final: 0.8381 (tpt)
REVERT: A 1860 MET cc_start: 0.8959 (mpp) cc_final: 0.8699 (mpp)
REVERT: B  362 MET cc_start: 0.8746 (mmm) cc_final: 0.8405 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.3438
  time to fit residues: 49.4555
Evaluate side-chains
  78 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 108 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 116 optimal weight:    0.7980
   chunk 135 optimal weight:    0.3980
   overall best weight:    2.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 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**
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.069226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.051956 restraints weight = 111835.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.053511 restraints weight = 79218.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.054732 restraints weight = 60498.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6233
moved from start:          0.5010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12712  Z= 0.168
  Angle     :  0.856  12.174  17470  Z= 0.444
  Chirality :  0.047   0.250   2036
  Planarity :  0.006   0.079   2012
  Dihedral  : 15.939  93.371   2404
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 27.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.61 %
    Favored  : 85.32 %
  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: -3.32 (0.21), residues: 1369
  helix: -1.32 (0.20), residues: 578
  sheet: -3.47 (0.48), residues: 77
  loop : -2.89 (0.23), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 316 
 HIS   0.004   0.001   HIS A 703 
 PHE   0.021   0.002   PHE A1812 
 TYR   0.020   0.002   TYR A1757 
 ARG   0.011   0.001   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04815 (  439)
  hydrogen bonds       : angle       6.08361 ( 1207)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       1.51968 (    2)
  covalent geometry    : bond        0.00355 (12711)
  covalent geometry    : angle       0.85603 (17468)

********************** 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
  106 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.476 
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: A  190 MET cc_start: 0.9063 (tpp) cc_final: 0.8852 (mmm)
REVERT: A  356 HIS cc_start: 0.9443 (t-90) cc_final: 0.9203 (t-90)
REVERT: A  562 MET cc_start: 0.5163 (tpt) cc_final: 0.3031 (tpp)
REVERT: A  837 MET cc_start: 0.5026 (mmm) cc_final: 0.4713 (mmm)
REVERT: A  897 MET cc_start: 0.9442 (ptp) cc_final: 0.9099 (ptp)
REVERT: A 1687 PHE cc_start: 0.9063 (m-80) cc_final: 0.8779 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.3723
  time to fit residues: 54.8820
Evaluate side-chains
  76 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 113 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 50 optimal weight:   30.0000
   overall best weight:    2.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 ASN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 648 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**
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1695 ASN ** 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 = 0.3882 r_free = 0.3882 target = 0.076979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.064124 restraints weight = 129056.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.065422 restraints weight = 85088.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.066362 restraints weight = 62925.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12712  Z= 0.173
  Angle     :  0.865  16.817  17470  Z= 0.446
  Chirality :  0.047   0.250   2036
  Planarity :  0.006   0.083   2012
  Dihedral  : 15.916  94.344   2404
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 27.64
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.56 %
    Favored  : 84.37 %
  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 : 0.23 %

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: -3.28 (0.22), residues: 1369
  helix: -1.25 (0.20), residues: 582
  sheet: -3.45 (0.48), residues: 77
  loop : -2.91 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A 316 
 HIS   0.005   0.001   HIS A 703 
 PHE   0.022   0.002   PHE A1812 
 TYR   0.026   0.002   TYR A 668 
 ARG   0.027   0.001   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04776 (  439)
  hydrogen bonds       : angle       6.07526 ( 1207)
  SS BOND              : bond        0.00189 (    1)
  SS BOND              : angle       1.46954 (    2)
  covalent geometry    : bond        0.00365 (12711)
  covalent geometry    : angle       0.86505 (17468)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3963.13 seconds
wall clock time: 72 minutes 13.29 seconds (4333.29 seconds total)