Starting phenix.real_space_refine
on Sat Aug 23 14:37:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5zal_6905/08_2025/5zal_6905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5zal_6905/08_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_6905/08_2025/5zal_6905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5zal_6905/08_2025/5zal_6905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5zal_6905/08_2025/5zal_6905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5zal_6905/08_2025/5zal_6905.cif"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.24, per 1000 atoms: 0.18
  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: 0.92
  Conformation dependent library (CDL) restraints added in 388.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 1.58
  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: 1.79

  Time building geometry restraints manager: 1.17 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:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.540
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.250
-------------------------------------------------------------------------------
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 : 18.94
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.015   0.002   ARG A 636 
 TYR   0.037   0.005   TYR A 876 
 PHE   0.038   0.005   PHE A1812 
 TRP   0.030   0.006   TRP A1048 
 HIS   0.018   0.003   HIS A 116 

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

*********************** 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  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  494 MET cc_start: 0.6770 (mtm) cc_final: 0.6273 (ttm)
REVERT: A  509 ARG cc_start: 0.9273 (mtt180) cc_final: 0.8887 (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: 0.8885 (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: 0.8122 (t70)
REVERT: A 1825 MET cc_start: 0.8600 (mpt) cc_final: 0.7970 (mpt)
REVERT: A 1895 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7946 (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: 0.1289
  time to fit residues: 32.0536
Evaluate side-chains
  107 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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
A1355 ASN
A1660 ASN
A1693 HIS
** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 305 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.067699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.050524 restraints weight = 110415.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.052155 restraints weight = 75444.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.053398 restraints weight = 56416.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.054373 restraints weight = 44694.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.055115 restraints weight = 36965.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6173
moved from start:          0.2297

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= 0.183
  Angle     :  0.916  12.654  17470  Z= 0.478
  Chirality :  0.048   0.316   2036
  Planarity :  0.007   0.075   2012
  Dihedral  : 16.763  98.516   2404
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 25.04
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 15.41 %
    Favored  : 84.15 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.35 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.38 %
    Twisted Proline : 1.43 %
    Twisted General : 0.53 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.22 (0.20), residues: 1369
  helix: -2.21 (0.18), residues: 549
  sheet: -3.71 (0.43), residues: 92
  loop : -3.22 (0.22), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 187 
 TYR   0.019   0.002   TYR A 387 
 PHE   0.033   0.002   PHE A 351 
 TRP   0.032   0.003   TRP A 316 
 HIS   0.010   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12711)
  covalent geometry    : angle       0.91544 (17468)
  SS BOND              : bond        0.00188 (    1)
  SS BOND              : angle       2.19030 (    2)
  hydrogen bonds       : bond        0.06804 (  439)
  hydrogen bonds       : angle       7.12093 ( 1207)

*********************** 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  : 0.397 
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: A   61 ILE cc_start: 0.7851 (mp) cc_final: 0.7563 (mp)
REVERT: A  494 MET cc_start: 0.7715 (mtm) cc_final: 0.7506 (ttp)
REVERT: A  543 TYR cc_start: 0.8742 (p90) cc_final: 0.8344 (p90)
REVERT: A  579 TYR cc_start: 0.7708 (m-80) cc_final: 0.7410 (m-10)
REVERT: A  837 MET cc_start: 0.4576 (mmm) cc_final: 0.4339 (mmm)
REVERT: A 1687 PHE cc_start: 0.8679 (m-80) cc_final: 0.8446 (m-80)
REVERT: A 1812 PHE cc_start: 0.9064 (t80) cc_final: 0.8810 (t80)
REVERT: A 1848 ASN cc_start: 0.9383 (t0) cc_final: 0.9168 (p0)
REVERT: B  296 ARG cc_start: 0.7610 (tmm160) cc_final: 0.7323 (mmt180)
  outliers start: 3
  outliers final: 1
  residues processed: 146
  average time/residue: 0.1384
  time to fit residues: 26.7584
Evaluate side-chains
  99 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 78 optimal weight:    2.9990
   chunk 127 optimal weight:    0.0570
   chunk 106 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 103 optimal weight:    7.9990
   chunk 120 optimal weight:    0.2980
   chunk 101 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.2702

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
A 109 GLN
A 195 ASN
A 282 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**
** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1028 GLN
** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1668 ASN
** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.070063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.051947 restraints weight = 107206.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.053589 restraints weight = 74542.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.054865 restraints weight = 56159.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.055832 restraints weight = 44783.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.056608 restraints weight = 37219.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.3252

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= 0.152
  Angle     :  0.836  12.231  17470  Z= 0.438
  Chirality :  0.047   0.283   2036
  Planarity :  0.006   0.064   2012
  Dihedral  : 16.228  94.541   2404
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 22.24
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 14.10 %
    Favored  : 85.54 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.51 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.30 %
    Twisted Proline : 1.43 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.81 (0.21), residues: 1369
  helix: -1.79 (0.19), residues: 574
  sheet: -3.42 (0.45), residues: 86
  loop : -3.13 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 187 
 TYR   0.018   0.002   TYR A 387 
 PHE   0.019   0.002   PHE A 351 
 TRP   0.019   0.002   TRP A 316 
 HIS   0.007   0.001   HIS A1755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12711)
  covalent geometry    : angle       0.83613 (17468)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       1.57151 (    2)
  hydrogen bonds       : bond        0.05379 (  439)
  hydrogen bonds       : angle       6.50811 ( 1207)

*********************** 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
  141 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  543 TYR cc_start: 0.8928 (p90) cc_final: 0.8393 (p90)
REVERT: A  562 MET cc_start: 0.6130 (tpt) cc_final: 0.3907 (tpp)
REVERT: A  579 TYR cc_start: 0.8189 (m-80) cc_final: 0.7648 (m-10)
REVERT: A  837 MET cc_start: 0.4732 (mmm) cc_final: 0.4320 (mmm)
REVERT: A 1323 LEU cc_start: 0.8086 (pp) cc_final: 0.7742 (pp)
REVERT: A 1848 ASN cc_start: 0.9408 (t0) cc_final: 0.9193 (p0)
REVERT: B  296 ARG cc_start: 0.7723 (tmm160) cc_final: 0.7403 (mmt180)
  outliers start: 1
  outliers final: 1
  residues processed: 141
  average time/residue: 0.1106
  time to fit residues: 21.1042
Evaluate side-chains
  89 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 140 optimal weight:   30.0000
   chunk 7 optimal weight:    3.9990
   chunk 109 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 118 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 114 optimal weight:    0.0970
   chunk 86 optimal weight:   30.0000
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    2.4186

-------------------------------------------------------------------------------
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 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**
** 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 = 0.3773 r_free = 0.3773 target = 0.068394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.049866 restraints weight = 114258.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.051317 restraints weight = 84099.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.052412 restraints weight = 66124.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.053272 restraints weight = 54563.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.053967 restraints weight = 46601.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6124
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  12712  Z= 0.167
  Angle     :  0.834  12.047  17470  Z= 0.437
  Chirality :  0.046   0.276   2036
  Planarity :  0.006   0.062   2012
  Dihedral  : 16.058  91.840   2404
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 24.47
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 13.88 %
    Favored  : 85.83 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.66 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.30 %
    Twisted Proline : 1.43 %
    Twisted General : 0.38 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.64 (0.21), residues: 1369
  helix: -1.65 (0.20), residues: 581
  sheet: -3.34 (0.47), residues: 90
  loop : -3.02 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 187 
 TYR   0.027   0.002   TYR A 668 
 PHE   0.020   0.002   PHE A1812 
 TRP   0.010   0.002   TRP A 316 
 HIS   0.006   0.001   HIS A1755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (12711)
  covalent geometry    : angle       0.83426 (17468)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       1.54223 (    2)
  hydrogen bonds       : bond        0.05239 (  439)
  hydrogen bonds       : angle       6.26937 ( 1207)

*********************** 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
  123 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.278 
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  543 TYR cc_start: 0.8815 (p90) cc_final: 0.8441 (p90)
REVERT: A  562 MET cc_start: 0.4418 (tpt) cc_final: 0.2501 (tpp)
REVERT: A  579 TYR cc_start: 0.7845 (m-80) cc_final: 0.7366 (m-10)
REVERT: A  837 MET cc_start: 0.4709 (mmm) cc_final: 0.4402 (mmm)
REVERT: A 1848 ASN cc_start: 0.9394 (t0) cc_final: 0.9184 (p0)
REVERT: B  296 ARG cc_start: 0.7666 (tmm160) cc_final: 0.7373 (mmt180)
  outliers start: 1
  outliers final: 1
  residues processed: 122
  average time/residue: 0.1160
  time to fit residues: 19.2868
Evaluate side-chains
  88 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 138 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 41 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 81 optimal weight:    8.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 356 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 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1028 GLN
A1355 ASN
** 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 = 0.3718 r_free = 0.3718 target = 0.066011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.047993 restraints weight = 120167.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.049408 restraints weight = 88010.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.050478 restraints weight = 69045.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.051331 restraints weight = 56898.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.051985 restraints weight = 48581.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6200
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12712  Z= 0.207
  Angle     :  0.870  11.893  17470  Z= 0.457
  Chirality :  0.047   0.285   2036
  Planarity :  0.006   0.063   2012
  Dihedral  : 16.204  91.247   2404
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 30.08
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 15.49 %
    Favored  : 84.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.30 %
    Twisted Proline : 1.43 %
    Twisted General : 0.38 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.58 (0.21), residues: 1369
  helix: -1.51 (0.20), residues: 569
  sheet: -3.19 (0.47), residues: 95
  loop : -3.07 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 187 
 TYR   0.021   0.002   TYR A1757 
 PHE   0.024   0.002   PHE A1812 
 TRP   0.026   0.003   TRP A 133 
 HIS   0.009   0.002   HIS A1755 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (12711)
  covalent geometry    : angle       0.87013 (17468)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       1.62294 (    2)
  hydrogen bonds       : bond        0.05622 (  439)
  hydrogen bonds       : angle       6.31949 ( 1207)

*********************** 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
  111 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 PHE cc_start: 0.9454 (m-80) cc_final: 0.9224 (m-80)
REVERT: A  543 TYR cc_start: 0.8945 (p90) cc_final: 0.8590 (p90)
REVERT: A  579 TYR cc_start: 0.7866 (m-80) cc_final: 0.7513 (m-10)
REVERT: A  837 MET cc_start: 0.4829 (mmm) cc_final: 0.4536 (mmm)
REVERT: A 1668 ASN cc_start: 0.8570 (t0) cc_final: 0.8224 (t0)
REVERT: A 1687 PHE cc_start: 0.8880 (m-80) cc_final: 0.8677 (m-80)
REVERT: B  296 ARG cc_start: 0.7617 (tmm160) cc_final: 0.7297 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1202
  time to fit residues: 18.1683
Evaluate side-chains
  85 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 127 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 125 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 63 optimal weight:    9.9990
   chunk 136 optimal weight:   20.0000
   chunk 15 optimal weight:    0.2980
   chunk 101 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    2.4184

-------------------------------------------------------------------------------
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 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 = 0.3784 r_free = 0.3784 target = 0.068810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.051647 restraints weight = 110713.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.053227 restraints weight = 77414.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.054430 restraints weight = 58603.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.055361 restraints weight = 46744.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.056110 restraints weight = 38830.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12712  Z= 0.162
  Angle     :  0.837  12.568  17470  Z= 0.436
  Chirality :  0.047   0.260   2036
  Planarity :  0.006   0.061   2012
  Dihedral  : 16.044  91.859   2404
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 26.12
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 14.54 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.30 %
    Twisted Proline : 1.43 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.44 (0.22), residues: 1369
  helix: -1.39 (0.20), residues: 574
  sheet: -3.41 (0.47), residues: 89
  loop : -2.97 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 187 
 TYR   0.025   0.002   TYR A1757 
 PHE   0.021   0.002   PHE A 351 
 TRP   0.010   0.002   TRP A1831 
 HIS   0.006   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (12711)
  covalent geometry    : angle       0.83727 (17468)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       1.59545 (    2)
  hydrogen bonds       : bond        0.04978 (  439)
  hydrogen bonds       : angle       6.13336 ( 1207)

*********************** 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
  115 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  543 TYR cc_start: 0.9103 (p90) cc_final: 0.8769 (p90)
REVERT: A  579 TYR cc_start: 0.8241 (m-80) cc_final: 0.7806 (m-10)
REVERT: A  837 MET cc_start: 0.4935 (mmm) cc_final: 0.4582 (mmm)
REVERT: A 1687 PHE cc_start: 0.9095 (m-80) cc_final: 0.8797 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1115
  time to fit residues: 17.8508
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  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 105 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 52 optimal weight:   20.0000
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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**
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.069138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.050617 restraints weight = 113482.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.052078 restraints weight = 83577.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.053197 restraints weight = 65823.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.054098 restraints weight = 54314.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.054801 restraints weight = 46327.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6127
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12712  Z= 0.145
  Angle     :  0.800  12.339  17470  Z= 0.418
  Chirality :  0.046   0.247   2036
  Planarity :  0.006   0.082   2012
  Dihedral  : 15.803  93.863   2404
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 22.78
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 14.32 %
    Favored  : 85.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.30 %
    Twisted Proline : 1.43 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.22), residues: 1369
  helix: -1.29 (0.20), residues: 580
  sheet: -3.16 (0.50), residues: 81
  loop : -2.88 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 187 
 TYR   0.014   0.002   TYR A 387 
 PHE   0.017   0.002   PHE A1812 
 TRP   0.013   0.002   TRP A1831 
 HIS   0.004   0.001   HIS A1661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12711)
  covalent geometry    : angle       0.79977 (17468)
  SS BOND              : bond        0.00217 (    1)
  SS BOND              : angle       1.44013 (    2)
  hydrogen bonds       : bond        0.04643 (  439)
  hydrogen bonds       : angle       5.87237 ( 1207)

*********************** 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
  122 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 HIS cc_start: 0.9426 (t-90) cc_final: 0.9184 (t-90)
REVERT: A  447 PHE cc_start: 0.8924 (m-80) cc_final: 0.8573 (m-80)
REVERT: A  562 MET cc_start: 0.4164 (tpt) cc_final: 0.1499 (tpt)
REVERT: A  837 MET cc_start: 0.4827 (mmm) cc_final: 0.4505 (mmm)
REVERT: A 1687 PHE cc_start: 0.9130 (m-80) cc_final: 0.8869 (m-80)
REVERT: A 1754 TYR cc_start: 0.9261 (m-10) cc_final: 0.9043 (m-10)
REVERT: A 1812 PHE cc_start: 0.9045 (t80) cc_final: 0.8828 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1196
  time to fit residues: 20.2354
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  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 127 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 142 optimal weight:   20.0000
   chunk 112 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 50 optimal weight:    0.3980
   chunk 38 optimal weight:   20.0000
   chunk 60 optimal weight:    8.9990
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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**
** 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 = 0.3843 r_free = 0.3843 target = 0.071334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.053505 restraints weight = 110033.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.055109 restraints weight = 77655.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.056382 restraints weight = 59003.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.057357 restraints weight = 47228.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.058112 restraints weight = 39376.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.4955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12712  Z= 0.139
  Angle     :  0.801  12.285  17470  Z= 0.416
  Chirality :  0.046   0.245   2036
  Planarity :  0.006   0.096   2012
  Dihedral  : 15.675  94.488   2404
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 21.17
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 13.81 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.30 %
    Twisted Proline : 1.43 %
    Twisted General : 0.38 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.13 (0.22), residues: 1369
  helix: -1.15 (0.21), residues: 588
  sheet: -3.05 (0.51), residues: 81
  loop : -2.84 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 187 
 TYR   0.013   0.002   TYR A1721 
 PHE   0.015   0.002   PHE A1812 
 TRP   0.069   0.004   TRP A 316 
 HIS   0.005   0.001   HIS A1661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12711)
  covalent geometry    : angle       0.80138 (17468)
  SS BOND              : bond        0.00192 (    1)
  SS BOND              : angle       1.27645 (    2)
  hydrogen bonds       : bond        0.04500 (  439)
  hydrogen bonds       : angle       5.83000 ( 1207)

*********************** 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
  119 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  447 PHE cc_start: 0.8929 (m-80) cc_final: 0.8530 (m-80)
REVERT: A  562 MET cc_start: 0.4775 (tpt) cc_final: 0.2372 (tpt)
REVERT: A  837 MET cc_start: 0.4832 (mmm) cc_final: 0.4518 (mmm)
REVERT: A 1050 LYS cc_start: 0.9126 (ptmt) cc_final: 0.8917 (mmtt)
REVERT: A 1571 LEU cc_start: 0.7649 (tp) cc_final: 0.7442 (mt)
REVERT: A 1687 PHE cc_start: 0.9193 (m-80) cc_final: 0.8917 (m-80)
REVERT: A 1754 TYR cc_start: 0.9257 (m-10) cc_final: 0.8997 (m-10)
REVERT: A 1838 MET cc_start: 0.8910 (tpp) cc_final: 0.8688 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1020
  time to fit residues: 16.8645
Evaluate side-chains
  84 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 91 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 109 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0010
   chunk 13 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.8988

-------------------------------------------------------------------------------
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 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 = 0.3863 r_free = 0.3863 target = 0.072430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.054469 restraints weight = 107858.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.056100 restraints weight = 75979.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.057404 restraints weight = 57787.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.058399 restraints weight = 46254.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.059207 restraints weight = 38490.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6138
moved from start:          0.5309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12712  Z= 0.137
  Angle     :  0.784  12.092  17470  Z= 0.408
  Chirality :  0.045   0.243   2036
  Planarity :  0.006   0.066   2012
  Dihedral  : 15.509  95.934   2404
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 20.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.00 %
    Favored  : 86.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.57 %
    Cis-general     : 1.30 %
    Twisted Proline : 1.43 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.04 (0.22), residues: 1369
  helix: -1.04 (0.21), residues: 587
  sheet: -2.96 (0.51), residues: 81
  loop : -2.83 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 187 
 TYR   0.017   0.002   TYR A1820 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.050   0.004   TRP A 316 
 HIS   0.007   0.001   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12711)
  covalent geometry    : angle       0.78396 (17468)
  SS BOND              : bond        0.00218 (    1)
  SS BOND              : angle       1.12505 (    2)
  hydrogen bonds       : bond        0.04405 (  439)
  hydrogen bonds       : angle       5.64664 ( 1207)

*********************** 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
  123 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 MET cc_start: 0.7779 (ptp) cc_final: 0.7323 (ptp)
REVERT: A  356 HIS cc_start: 0.9397 (t-90) cc_final: 0.9183 (t-90)
REVERT: A  447 PHE cc_start: 0.8993 (m-80) cc_final: 0.8615 (m-80)
REVERT: A  562 MET cc_start: 0.4715 (tpt) cc_final: 0.2722 (tpt)
REVERT: A  837 MET cc_start: 0.4810 (mmm) cc_final: 0.4494 (mmm)
REVERT: A 1050 LYS cc_start: 0.9085 (ptmt) cc_final: 0.8883 (mmtt)
REVERT: A 1312 LEU cc_start: 0.8959 (tp) cc_final: 0.7596 (tp)
REVERT: A 1687 PHE cc_start: 0.9202 (m-80) cc_final: 0.8868 (m-80)
REVERT: A 1754 TYR cc_start: 0.9171 (m-10) cc_final: 0.8704 (m-10)
REVERT: A 1812 PHE cc_start: 0.9059 (t80) cc_final: 0.8778 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1053
  time to fit residues: 17.8989
Evaluate side-chains
  85 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 132 optimal weight:   10.0000
   chunk 115 optimal weight:    0.7980
   chunk 16 optimal weight:    8.9990
   chunk 123 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0570
   chunk 89 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    1.3302

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

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** 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 = 0.3846 r_free = 0.3846 target = 0.072195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.054621 restraints weight = 108831.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.056283 restraints weight = 76221.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.057583 restraints weight = 57577.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.058604 restraints weight = 45818.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.059376 restraints weight = 37851.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6199
moved from start:          0.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12712  Z= 0.139
  Angle     :  0.798  12.037  17470  Z= 0.414
  Chirality :  0.045   0.242   2036
  Planarity :  0.006   0.073   2012
  Dihedral  : 15.443  96.393   2404
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 20.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.93 %
    Favored  : 87.07 %
  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 : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.95 (0.22), residues: 1369
  helix: -0.95 (0.20), residues: 591
  sheet: -2.92 (0.51), residues: 81
  loop : -2.81 (0.23), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 187 
 TYR   0.014   0.002   TYR A  83 
 PHE   0.030   0.002   PHE A1758 
 TRP   0.051   0.004   TRP A 316 
 HIS   0.007   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12711)
  covalent geometry    : angle       0.79790 (17468)
  SS BOND              : bond        0.00206 (    1)
  SS BOND              : angle       1.17906 (    2)
  hydrogen bonds       : bond        0.04286 (  439)
  hydrogen bonds       : angle       5.61718 ( 1207)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 LEU cc_start: 0.8793 (mt) cc_final: 0.8512 (tt)
REVERT: A  324 MET cc_start: 0.7876 (ptp) cc_final: 0.7500 (ptp)
REVERT: A  356 HIS cc_start: 0.9389 (t-90) cc_final: 0.9175 (t-90)
REVERT: A  447 PHE cc_start: 0.9019 (m-80) cc_final: 0.8630 (m-80)
REVERT: A  562 MET cc_start: 0.5025 (tpt) cc_final: 0.3011 (tpt)
REVERT: A  837 MET cc_start: 0.4989 (mmm) cc_final: 0.4665 (mmm)
REVERT: A 1050 LYS cc_start: 0.9173 (ptmt) cc_final: 0.8966 (mmtt)
REVERT: A 1687 PHE cc_start: 0.9271 (m-80) cc_final: 0.8984 (m-80)
REVERT: A 1754 TYR cc_start: 0.9220 (m-10) cc_final: 0.8618 (m-10)
REVERT: A 1812 PHE cc_start: 0.8939 (t80) cc_final: 0.8728 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1239
  time to fit residues: 19.7173
Evaluate side-chains
  84 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 141 optimal weight:   20.0000
   chunk 119 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
** A 145 HIS ** 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 = 0.3811 r_free = 0.3811 target = 0.070940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.052186 restraints weight = 113956.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.053740 restraints weight = 83099.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.054955 restraints weight = 64722.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.055921 restraints weight = 52973.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.056665 restraints weight = 44836.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6049
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12712  Z= 0.140
  Angle     :  0.804  12.094  17470  Z= 0.417
  Chirality :  0.045   0.241   2036
  Planarity :  0.006   0.063   2012
  Dihedral  : 15.408  96.390   2404
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 21.08
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.78 %
    Favored  : 87.14 %
  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 : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.97 (0.22), residues: 1369
  helix: -1.02 (0.20), residues: 597
  sheet: -3.08 (0.48), residues: 89
  loop : -2.73 (0.23), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 506 
 TYR   0.015   0.002   TYR A 452 
 PHE   0.018   0.002   PHE A1812 
 TRP   0.047   0.003   TRP A 316 
 HIS   0.006   0.001   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12711)
  covalent geometry    : angle       0.80401 (17468)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       1.15131 (    2)
  hydrogen bonds       : bond        0.04305 (  439)
  hydrogen bonds       : angle       5.63897 ( 1207)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1807.12 seconds
wall clock time: 32 minutes 19.98 seconds (1939.98 seconds total)