Starting phenix.real_space_refine
on Mon Dec 30 05:07:45 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xw3_33490/12_2024/7xw3_33490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xw3_33490/12_2024/7xw3_33490.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xw3_33490/12_2024/7xw3_33490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xw3_33490/12_2024/7xw3_33490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xw3_33490/12_2024/7xw3_33490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xw3_33490/12_2024/7xw3_33490.cif"
  }
  resolution = 4.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
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: 4
    Type Number    sf(0)   Gaussians
     S      67      5.16       5
     C    7694      2.51       5
     N    2060      2.21       5
     O    2260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 12081
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1502, 12081
          Classifications: {'peptide': 1502}
          Link IDs: {'PTRANS': 89, 'TRANS': 1412}
          Chain breaks: 5
  Time building chain proxies: 7.52, per 1000 atoms: 0.62
  Number of scatterers: 12081
  At special positions: 0
  Unit cell: (101.384, 106.894, 160.892, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      67     16.00
     O    2260      8.00
     N    2060      7.00
     C    7694      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.17
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2878

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 12 sheets defined
      43.7% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 50
      removed outlier: 4.268A  pdb=" N   GLU A  50 " --> pdb=" O   TYR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 58
      removed outlier: 4.271A  pdb=" N   ALA A  55 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASP A  57 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 79
      removed outlier: 4.912A  pdb=" N   LEU A  76 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU A  77 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 85
      removed outlier: 5.387A  pdb=" N   TYR A  83 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLN A  84 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 115
      removed outlier: 3.698A  pdb=" N   THR A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 133
      removed outlier: 3.873A  pdb=" N   TRP A 133 " --> pdb=" O   ASN A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 151 through 161
    Processing helix  chain 'A' and resid 176 through 182
      removed outlier: 3.544A  pdb=" N   LEU A 179 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 196
      removed outlier: 4.338A  pdb=" N   GLU A 188 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 231
    Processing helix  chain 'A' and resid 266 through 282
    Processing helix  chain 'A' and resid 295 through 313
    Processing helix  chain 'A' and resid 314 through 336
      removed outlier: 3.969A  pdb=" N   ALA A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLY A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   MET A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 363
    Processing helix  chain 'A' and resid 374 through 385
      removed outlier: 3.748A  pdb=" N   ILE A 378 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 468 through 473
      removed outlier: 3.625A  pdb=" N   TYR A 473 " --> pdb=" O   PRO A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 510
      removed outlier: 3.669A  pdb=" N   ALA A 510 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 567 through 588
      removed outlier: 4.429A  pdb=" N   SER A 571 " --> pdb=" O   ASP A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
      removed outlier: 3.770A  pdb=" N   ILE A 631 " --> pdb=" O   ILE A 627 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   CYS A 638 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 705
    Processing helix  chain 'A' and resid 754 through 758
    Processing helix  chain 'A' and resid 839 through 857
    Processing helix  chain 'A' and resid 893 through 903
      removed outlier: 3.745A  pdb=" N   MET A 897 " --> pdb=" O   ASP A 893 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   SER A 903 " --> pdb=" O   ASP A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 974
      removed outlier: 3.598A  pdb=" N   TYR A 971 " --> pdb=" O   THR A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1036
      No H-bonds generated for 'chain 'A' and resid 1034 through 1036'
    Processing helix  chain 'A' and resid 1044 through 1053
      removed outlier: 3.963A  pdb=" N   CYS A1053 " --> pdb=" O   ARG A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1078
    Processing helix  chain 'A' and resid 1293 through 1302
      removed outlier: 3.748A  pdb=" N   ILE A1297 " --> pdb=" O   ASN A1293 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLN A1299 " --> pdb=" O   GLY A1295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1312 through 1333
      removed outlier: 3.894A  pdb=" N   MET A1317 " --> pdb=" O   GLU A1313 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU A1318 " --> pdb=" O   ARG A1314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1351
      removed outlier: 5.487A  pdb=" N   LYS A1349 " --> pdb=" O   TYR A1345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1352 through 1361
      removed outlier: 3.777A  pdb=" N   ARG A1358 " --> pdb=" O   CYS A1354 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU A1359 " --> pdb=" O   ASN A1355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1364 through 1369
      removed outlier: 3.595A  pdb=" N   MET A1369 " --> pdb=" O   PRO A1366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1375 through 1380
      removed outlier: 3.502A  pdb=" N   ASN A1379 " --> pdb=" O   ASP A1375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1452
      removed outlier: 4.120A  pdb=" N   ILE A1450 " --> pdb=" O   ASP A1446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1556 through 1587
      removed outlier: 4.234A  pdb=" N   ALA A1560 " --> pdb=" O   ASP A1556 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY A1568 " --> pdb=" O   GLU A1564 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   GLU A1576 " --> pdb=" O   THR A1572 " (cutoff:3.500A)
      removed outlier: 10.132A  pdb=" N   ARG A1577 " --> pdb=" O   SER A1573 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ALA A1578 " --> pdb=" O   CYS A1574 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU A1586 " --> pdb=" O   PHE A1582 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLY A1587 " --> pdb=" O   LEU A1583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1595 through 1601
      removed outlier: 3.533A  pdb=" N   ARG A1599 " --> pdb=" O   LYS A1595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1656 through 1668
      removed outlier: 4.418A  pdb=" N   ASN A1668 " --> pdb=" O   SER A1664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1680 through 1688
      removed outlier: 4.344A  pdb=" N   PHE A1687 " --> pdb=" O   LEU A1683 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR A1688 " --> pdb=" O   LEU A1684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1701 through 1722
      removed outlier: 3.759A  pdb=" N   ALA A1710 " --> pdb=" O   PHE A1706 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   ILE A1711 " --> pdb=" O   LEU A1707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1741 through 1752
    Processing helix  chain 'A' and resid 1762 through 1778
      removed outlier: 3.955A  pdb=" N   PHE A1766 " --> pdb=" O   SER A1762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1801
    Processing helix  chain 'A' and resid 1807 through 1823
      removed outlier: 3.564A  pdb=" N   ILE A1811 " --> pdb=" O   ALA A1807 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   SER A1823 " --> pdb=" O   ILE A1819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1826 through 1846
      removed outlier: 3.981A  pdb=" N   VAL A1830 " --> pdb=" O   SER A1826 " (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 1916
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
      removed outlier: 3.685A  pdb=" N   THR A  60 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY A 204 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99
      removed outlier: 5.514A  pdb=" N   PHE A  98 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 256
      removed outlier: 5.844A  pdb=" N   SER A 558 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   CYS A 251 " --> pdb=" O   SER A 558 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 560 " --> pdb=" O   CYS A 251 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE A 253 " --> pdb=" O   TYR A 560 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET A 562 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 534 " --> pdb=" O   ASN A 559 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU A 563 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 445 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   GLY A 444 " --> pdb=" O   LEU A 516 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ALA A 518 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ILE A 446 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 589 through 590
    Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 657
    Processing sheet with id=AA6, first strand: chain 'A' and resid 746 through 750
      removed outlier: 4.133A  pdb=" N   GLN A 747 " --> pdb=" O   ILE A1554 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE A1554 " --> pdb=" O   GLN A 747 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 806
      removed outlier: 3.617A  pdb=" N   THR A 806 " --> pdb=" O   TYR A 769 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE A 836 " --> pdb=" O   CYS A 768 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU A 770 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   SER A 834 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 8.638A  pdb=" N   VAL A 772 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   LYS A 832 " --> pdb=" O   VAL A 772 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 777
      removed outlier: 3.673A  pdb=" N   VAL A 776 " --> pdb=" O   THR A 826 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY A 823 " --> pdb=" O   THR A 820 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR A 820 " --> pdb=" O   GLY A 823 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 801 through 802
    Processing sheet with id=AB1, first strand: chain 'A' and resid 865 through 867
      removed outlier: 3.711A  pdb=" N   GLU A 866 " --> pdb=" O   VAL A1386 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A1386 " --> pdb=" O   GLU A 866 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 988 through 991
      removed outlier: 5.702A  pdb=" N   ASP A 991 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   VAL A 947 " --> pdb=" O   ASP A 991 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE A 945 " --> pdb=" O   ILE A 932 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   VAL A 931 " --> pdb=" O   HIS A1041 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1878 through 1881
      removed outlier: 3.611A  pdb=" N   VAL A1878 " --> pdb=" O   GLY A1894 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A1894 " --> pdb=" O   VAL A1878 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLY A1892 " --> pdb=" O   VAL A1880 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1275 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.61

  Time building geometry restraints manager: 3.66 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.32: 2063
        1.32 -     1.44: 3116
        1.44 -     1.57: 7070
        1.57 -     1.69: 0
        1.69 -     1.82: 95
  Bond restraints: 12344
  Sorted by residual:
  bond pdb=" N   ARG A 763 "
       pdb=" CA  ARG A 763 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 7.00e-03 2.04e+04 1.88e+01
  bond pdb=" C   VAL A 129 "
       pdb=" O   VAL A 129 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.23e-02 6.61e+03 1.28e+01
  bond pdb=" N   VAL A 113 "
       pdb=" CA  VAL A 113 "
    ideal  model  delta    sigma   weight residual
    1.456  1.500 -0.044 1.30e-02 5.92e+03 1.13e+01
  bond pdb=" N   ILE A 813 "
       pdb=" CA  ILE A 813 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.031 9.10e-03 1.21e+04 1.13e+01
  bond pdb=" N   GLN A 488 "
       pdb=" CA  GLN A 488 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.04e-02 9.25e+03 1.12e+01
  ... (remaining 12339 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 15541
        2.38 -     4.77: 1050
        4.77 -     7.15: 102
        7.15 -     9.53: 14
        9.53 -    11.91: 5
  Bond angle restraints: 16712
  Sorted by residual:
  angle pdb=" N   ILE A  73 "
        pdb=" CA  ILE A  73 "
        pdb=" C   ILE A  73 "
      ideal   model   delta    sigma   weight residual
     113.43  103.09   10.34 1.09e+00 8.42e-01 9.00e+01
  angle pdb=" N   PRO A1376 "
        pdb=" CA  PRO A1376 "
        pdb=" C   PRO A1376 "
      ideal   model   delta    sigma   weight residual
     110.70  121.51  -10.81 1.22e+00 6.72e-01 7.85e+01
  angle pdb=" N   THR A  71 "
        pdb=" CA  THR A  71 "
        pdb=" C   THR A  71 "
      ideal   model   delta    sigma   weight residual
     111.28  103.06    8.22 1.09e+00 8.42e-01 5.69e+01
  angle pdb=" N   MET A1346 "
        pdb=" CA  MET A1346 "
        pdb=" C   MET A1346 "
      ideal   model   delta    sigma   weight residual
     112.72  103.16    9.56 1.28e+00 6.10e-01 5.58e+01
  angle pdb=" N   ASN A1455 "
        pdb=" CA  ASN A1455 "
        pdb=" C   ASN A1455 "
      ideal   model   delta    sigma   weight residual
     112.87  105.22    7.65 1.20e+00 6.94e-01 4.07e+01
  ... (remaining 16707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 6709
       17.66 -    35.32: 681
       35.32 -    52.98: 124
       52.98 -    70.64: 53
       70.64 -    88.29: 27
  Dihedral angle restraints: 7594
    sinusoidal: 3153
      harmonic: 4441
  Sorted by residual:
  dihedral pdb=" C   ASP A1753 "
           pdb=" N   ASP A1753 "
           pdb=" CA  ASP A1753 "
           pdb=" CB  ASP A1753 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.23   18.63     0      2.50e+00 1.60e-01 5.56e+01
  dihedral pdb=" N   ASP A1753 "
           pdb=" C   ASP A1753 "
           pdb=" CA  ASP A1753 "
           pdb=" CB  ASP A1753 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.98  -17.18     0      2.50e+00 1.60e-01 4.72e+01
  dihedral pdb=" C   TYR A1752 "
           pdb=" N   TYR A1752 "
           pdb=" CA  TYR A1752 "
           pdb=" CB  TYR A1752 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.92   13.32     0      2.50e+00 1.60e-01 2.84e+01
  ... (remaining 7591 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1754
       0.139 -    0.279: 103
       0.279 -    0.418: 7
       0.418 -    0.558: 1
       0.558 -    0.697: 1
  Chirality restraints: 1866
  Sorted by residual:
  chirality pdb=" CA  ASP A1753 "
            pdb=" N   ASP A1753 "
            pdb=" C   ASP A1753 "
            pdb=" CB  ASP A1753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.81    0.70 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" CA  PHE A  72 "
            pdb=" N   PHE A  72 "
            pdb=" C   PHE A  72 "
            pdb=" CB  PHE A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.27e+00
  chirality pdb=" CA  TYR A1752 "
            pdb=" N   TYR A1752 "
            pdb=" C   TYR A1752 "
            pdb=" CB  TYR A1752 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.83e+00
  ... (remaining 1863 not shown)

  Planarity restraints: 2158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 553 "   -0.021 2.00e-02 2.50e+03   4.31e-02 1.86e+01
        pdb=" C   ALA A 553 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ALA A 553 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ARG A 554 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1667 "   -0.019 2.00e-02 2.50e+03   3.93e-02 1.55e+01
        pdb=" C   GLU A1667 "    0.068 2.00e-02 2.50e+03
        pdb=" O   GLU A1667 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ASN A1668 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1778 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   GLU A1778 "    0.059 2.00e-02 2.50e+03
        pdb=" O   GLU A1778 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LYS A1779 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2155 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1908
        2.75 -     3.29: 12432
        3.29 -     3.83: 19617
        3.83 -     4.36: 23741
        4.36 -     4.90: 38336
  Nonbonded interactions: 96034
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 319 "
            pdb=" NZ  LYS A 320 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" O   HIS A 145 "
            pdb=" NE2 GLN A 146 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   HIS A 856 "
            pdb=" NH2 ARG A 944 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" N   GLU A 188 "
            pdb=" OE1 GLU A 188 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   SER A1287 "
            pdb=" OG  SER A1287 "
     model   vdw
     2.256 3.040
  ... (remaining 96029 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.670
  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:             0.020
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     30.370
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6348
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.119  12344  Z= 0.620
  Angle     :  1.242  11.914  16712  Z= 0.820
  Chirality :  0.074   0.697   1866
  Planarity :  0.007   0.078   2158
  Dihedral  : 16.199  88.294   4716
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.39 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 10.78 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.18), residues: 1490
  helix: -2.80 (0.16), residues: 615
  sheet: -3.97 (0.38), residues: 120
  loop : -2.36 (0.20), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP A 133 
 HIS   0.014   0.003   HIS A1325 
 PHE   0.055   0.003   PHE A1812 
 TYR   0.031   0.003   TYR A1546 
 ARG   0.010   0.001   ARG A 821 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 1.513 
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: A  116 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8194 (m-70)
REVERT: A  324 MET cc_start: -0.0902 (mmm) cc_final: -0.1326 (mmm)
REVERT: A  713 MET cc_start: 0.2126 (ptm) cc_final: 0.1451 (ptm)
REVERT: A  747 GLN cc_start: 0.7972 (mt0) cc_final: 0.7592 (mp10)
REVERT: A  842 MET cc_start: 0.7944 (mmt) cc_final: 0.7237 (mmt)
REVERT: A 1090 ARG cc_start: 0.3420 (OUTLIER) cc_final: 0.2659 (tmt170)
REVERT: A 1559 ILE cc_start: 0.7451 (tp) cc_final: 0.7233 (tp)
REVERT: A 1860 MET cc_start: 0.3830 (tpt) cc_final: 0.2510 (mtt)
  outliers start: 34
  outliers final: 11
  residues processed: 179
  average time/residue: 0.2820
  time to fit residues: 71.2602
Evaluate side-chains
  119 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    8.9990
   chunk 117 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   chunk 136 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN
A  65 ASN
A  84 GLN
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 249 GLN
A 356 HIS
A 362 HIS
A 588 ASN
A 628 ASN
A 850 HIS
A 885 ASN
A1004 HIS
A1028 GLN
A1041 HIS
A1339 HIS
A1355 ASN
A1668 ASN
A1727 HIS
A1780 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6215
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12344  Z= 0.243
  Angle     :  0.679   7.419  16712  Z= 0.362
  Chirality :  0.045   0.166   1866
  Planarity :  0.006   0.050   2158
  Dihedral  :  6.304  28.432   1653
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.90 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.55 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.20), residues: 1490
  helix: -1.21 (0.19), residues: 627
  sheet: -3.40 (0.37), residues: 144
  loop : -2.00 (0.21), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1831 
 HIS   0.008   0.001   HIS A 511 
 PHE   0.027   0.002   PHE A1812 
 TYR   0.026   0.002   TYR A1757 
 ARG   0.011   0.001   ARG A1049 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 1.439 
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: A  145 HIS cc_start: 0.6535 (m-70) cc_final: 0.6131 (m90)
REVERT: A  163 TYR cc_start: 0.6651 (m-80) cc_final: 0.6332 (m-10)
REVERT: A  559 ASN cc_start: 0.7027 (t0) cc_final: 0.6798 (t0)
REVERT: A  713 MET cc_start: 0.3122 (ppp) cc_final: 0.2696 (ppp)
REVERT: A  747 GLN cc_start: 0.7681 (mt0) cc_final: 0.7407 (mp10)
REVERT: A  842 MET cc_start: 0.7959 (mmt) cc_final: 0.7337 (mmt)
REVERT: A 1021 LYS cc_start: 0.5492 (mmtt) cc_final: 0.4599 (tttt)
REVERT: A 1049 ARG cc_start: 0.7277 (mpp-170) cc_final: 0.6633 (mtm-85)
REVERT: A 1751 LYS cc_start: 0.7483 (mmtp) cc_final: 0.7237 (tttm)
REVERT: A 1860 MET cc_start: 0.4069 (tpt) cc_final: 0.2599 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 155
  average time/residue: 0.2686
  time to fit residues: 59.5231
Evaluate side-chains
  100 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 136 optimal weight:    2.9990
   chunk 147 optimal weight:   20.0000
   chunk 121 optimal weight:    7.9990
   chunk 135 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 GLN
A 532 ASN
A1742 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6373
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  12344  Z= 0.342
  Angle     :  0.735  10.417  16712  Z= 0.382
  Chirality :  0.047   0.208   1866
  Planarity :  0.006   0.056   2158
  Dihedral  :  6.244  37.863   1653
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.85 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.20), residues: 1490
  helix: -0.97 (0.19), residues: 633
  sheet: -3.48 (0.35), residues: 144
  loop : -1.87 (0.22), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1831 
 HIS   0.010   0.002   HIS A1727 
 PHE   0.040   0.003   PHE A1812 
 TYR   0.026   0.003   TYR A1692 
 ARG   0.006   0.001   ARG A 587 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.500 
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: A 1069 GLU cc_start: 0.6878 (tp30) cc_final: 0.6632 (tm-30)
REVERT: A 1765 LEU cc_start: 0.5622 (mp) cc_final: 0.5381 (mt)
REVERT: A 1860 MET cc_start: 0.4577 (tpt) cc_final: 0.2689 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2452
  time to fit residues: 47.8160
Evaluate side-chains
  91 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 102 optimal weight:    0.1980
   chunk 70 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 136 optimal weight:    0.8980
   chunk 144 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 129 optimal weight:    0.5980
   chunk 39 optimal weight:   40.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1353 ASN
A1660 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6193
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12344  Z= 0.164
  Angle     :  0.582   6.835  16712  Z= 0.306
  Chirality :  0.043   0.208   1866
  Planarity :  0.005   0.048   2158
  Dihedral  :  5.438  28.493   1653
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.43 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.21), residues: 1490
  helix: -0.18 (0.21), residues: 616
  sheet: -3.34 (0.40), residues: 119
  loop : -1.69 (0.22), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1048 
 HIS   0.006   0.001   HIS A 145 
 PHE   0.014   0.001   PHE A1812 
 TYR   0.016   0.001   TYR A 972 
 ARG   0.006   0.000   ARG A1049 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 MET cc_start: -0.0840 (mmp) cc_final: -0.1303 (mmm)
REVERT: A  773 ILE cc_start: 0.6999 (mt) cc_final: 0.6195 (mm)
REVERT: A 1069 GLU cc_start: 0.6968 (tp30) cc_final: 0.6764 (tm-30)
REVERT: A 1860 MET cc_start: 0.4689 (tpt) cc_final: 0.2748 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2217
  time to fit residues: 47.7056
Evaluate side-chains
  101 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 123 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9990
   chunk 130 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 532 ASN
A1353 ASN
A1832 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  12344  Z= 0.283
  Angle     :  0.674  10.015  16712  Z= 0.347
  Chirality :  0.046   0.243   1866
  Planarity :  0.005   0.048   2158
  Dihedral  :  5.655  36.115   1653
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.44 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.21), residues: 1490
  helix: -0.35 (0.20), residues: 621
  sheet: -3.29 (0.42), residues: 104
  loop : -1.79 (0.22), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1831 
 HIS   0.014   0.002   HIS A1449 
 PHE   0.026   0.002   PHE A  72 
 TYR   0.026   0.002   TYR A1546 
 ARG   0.004   0.000   ARG A1049 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  773 ILE cc_start: 0.6687 (mt) cc_final: 0.5949 (mm)
REVERT: A 1802 ILE cc_start: 0.7889 (tt) cc_final: 0.7619 (mt)
REVERT: A 1860 MET cc_start: 0.4391 (tpt) cc_final: 0.2628 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2168
  time to fit residues: 44.0422
Evaluate side-chains
  91 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0070
   chunk 145 optimal weight:   10.0000
   chunk 120 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 139 optimal weight:    0.5980
   overall best weight:    0.8400

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 532 ASN
** A1449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6219
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12344  Z= 0.176
  Angle     :  0.592   8.051  16712  Z= 0.306
  Chirality :  0.043   0.237   1866
  Planarity :  0.005   0.050   2158
  Dihedral  :  5.226  29.628   1653
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.57 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.21), residues: 1490
  helix: -0.05 (0.21), residues: 632
  sheet: -3.44 (0.40), residues: 106
  loop : -1.67 (0.22), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1048 
 HIS   0.005   0.001   HIS A1727 
 PHE   0.029   0.001   PHE A 280 
 TYR   0.031   0.001   TYR A 186 
 ARG   0.004   0.000   ARG A 944 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 MET cc_start: 0.8837 (mmm) cc_final: 0.8490 (mmm)
REVERT: A 1069 GLU cc_start: 0.6986 (tp30) cc_final: 0.6652 (tm-30)
REVERT: A 1785 MET cc_start: 0.0030 (ptp) cc_final: -0.0740 (pmm)
REVERT: A 1860 MET cc_start: 0.4480 (tpt) cc_final: 0.2688 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2379
  time to fit residues: 47.3921
Evaluate side-chains
  94 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 105 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0870
   chunk 144 optimal weight:    5.9990
   chunk 90 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 89 optimal weight:   20.0000
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.5562

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 493 GLN
A 532 ASN
A 982 ASN
** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1447 GLN
** A1449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6301
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12344  Z= 0.245
  Angle     :  0.643   9.856  16712  Z= 0.329
  Chirality :  0.045   0.236   1866
  Planarity :  0.005   0.048   2158
  Dihedral  :  5.391  33.541   1653
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.11 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.21), residues: 1490
  helix: -0.12 (0.21), residues: 629
  sheet: -3.40 (0.40), residues: 118
  loop : -1.61 (0.23), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1831 
 HIS   0.007   0.001   HIS A1727 
 PHE   0.026   0.002   PHE A 174 
 TYR   0.024   0.002   TYR A 186 
 ARG   0.004   0.000   ARG A 944 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  773 ILE cc_start: 0.6664 (mt) cc_final: 0.5974 (mm)
REVERT: A  837 MET cc_start: 0.7303 (tpp) cc_final: 0.6914 (tpp)
REVERT: A 1069 GLU cc_start: 0.7032 (tp30) cc_final: 0.6684 (tm-30)
REVERT: A 1359 LEU cc_start: 0.7151 (tp) cc_final: 0.6908 (tt)
REVERT: A 1785 MET cc_start: 0.0084 (ptp) cc_final: -0.0829 (pmm)
REVERT: A 1860 MET cc_start: 0.4558 (tpt) cc_final: 0.2773 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2311
  time to fit residues: 49.3101
Evaluate side-chains
  101 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   chunk 91 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 138 optimal weight:    1.9990
   chunk 126 optimal weight:    0.6980
   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 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 532 ASN
** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12344  Z= 0.180
  Angle     :  0.595   8.843  16712  Z= 0.305
  Chirality :  0.043   0.213   1866
  Planarity :  0.005   0.049   2158
  Dihedral  :  5.084  29.415   1653
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.17 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.22), residues: 1490
  helix:  0.07 (0.21), residues: 625
  sheet: -3.22 (0.40), residues: 120
  loop : -1.48 (0.23), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1831 
 HIS   0.005   0.001   HIS A1727 
 PHE   0.022   0.001   PHE A 347 
 TYR   0.020   0.001   TYR A 186 
 ARG   0.004   0.000   ARG A 944 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 MET cc_start: 0.8674 (mmm) cc_final: 0.8351 (mmm)
REVERT: A  571 SER cc_start: 0.8757 (m) cc_final: 0.8552 (p)
REVERT: A  713 MET cc_start: 0.3113 (ppp) cc_final: 0.2875 (ppp)
REVERT: A  837 MET cc_start: 0.7474 (tpp) cc_final: 0.7065 (tpp)
REVERT: A  842 MET cc_start: 0.8066 (mmt) cc_final: 0.7402 (mmt)
REVERT: A 1069 GLU cc_start: 0.6953 (tp30) cc_final: 0.6583 (tm-30)
REVERT: A 1785 MET cc_start: -0.0343 (ptp) cc_final: -0.0966 (pmm)
REVERT: A 1860 MET cc_start: 0.4565 (tpt) cc_final: 0.2756 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2120
  time to fit residues: 44.7568
Evaluate side-chains
  100 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    0.7980
   chunk 138 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 121 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 142 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0470
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 GLN
A 532 ASN
** A1449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1767 HIS
A1832 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6188
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12344  Z= 0.159
  Angle     :  0.579   9.081  16712  Z= 0.294
  Chirality :  0.042   0.200   1866
  Planarity :  0.005   0.050   2158
  Dihedral  :  4.781  24.114   1653
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.77 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.22), residues: 1490
  helix:  0.26 (0.21), residues: 628
  sheet: -3.13 (0.39), residues: 119
  loop : -1.36 (0.23), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1380 
 HIS   0.004   0.001   HIS A 356 
 PHE   0.022   0.001   PHE A 347 
 TYR   0.018   0.001   TYR A1570 
 ARG   0.003   0.000   ARG A 944 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 MET cc_start: 0.8620 (mmm) cc_final: 0.8377 (mmm)
REVERT: A  713 MET cc_start: 0.3095 (ppp) cc_final: 0.2795 (ppp)
REVERT: A  837 MET cc_start: 0.7549 (tpp) cc_final: 0.7142 (tpp)
REVERT: A 1069 GLU cc_start: 0.6834 (tp30) cc_final: 0.6437 (tm-30)
REVERT: A 1785 MET cc_start: -0.0110 (ptp) cc_final: -0.0861 (pmm)
REVERT: A 1860 MET cc_start: 0.4374 (tpt) cc_final: 0.2580 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2107
  time to fit residues: 43.7587
Evaluate side-chains
  99 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 149 optimal weight:   10.0000
   chunk 137 optimal weight:   30.0000
   chunk 118 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 126 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 532 ASN
** A1449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6197
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12344  Z= 0.171
  Angle     :  0.586   9.281  16712  Z= 0.299
  Chirality :  0.043   0.180   1866
  Planarity :  0.005   0.050   2158
  Dihedral  :  4.728  27.766   1653
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.70 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.22), residues: 1490
  helix:  0.25 (0.21), residues: 631
  sheet: -3.01 (0.40), residues: 119
  loop : -1.26 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 138 
 HIS   0.005   0.001   HIS A1727 
 PHE   0.025   0.001   PHE A 347 
 TYR   0.026   0.001   TYR A1834 
 ARG   0.011   0.000   ARG A 137 

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

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

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2980 Ramachandran restraints generated.
    1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 MET cc_start: 0.3144 (ppp) cc_final: 0.2748 (ppp)
REVERT: A  837 MET cc_start: 0.7569 (tpp) cc_final: 0.7152 (tpp)
REVERT: A 1069 GLU cc_start: 0.6882 (tp30) cc_final: 0.6384 (tm-30)
REVERT: A 1073 GLN cc_start: 0.8096 (pm20) cc_final: 0.7871 (pm20)
REVERT: A 1785 MET cc_start: -0.0015 (ptp) cc_final: -0.0768 (pmm)
REVERT: A 1860 MET cc_start: 0.4335 (tpt) cc_final: 0.2465 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2189
  time to fit residues: 44.2762
Evaluate side-chains
  97 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 119 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 122 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0010
   chunk 104 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0470
   overall best weight:    0.4484

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 HIS
A 488 GLN
A 532 ASN
** A1449 HIS ** 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 = 0.4653 r_free = 0.4653 target = 0.187226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.154451 restraints weight = 30722.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.155290 restraints weight = 26295.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.156375 restraints weight = 22617.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6221
moved from start:          0.5422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12344  Z= 0.147
  Angle     :  0.573   8.800  16712  Z= 0.291
  Chirality :  0.042   0.168   1866
  Planarity :  0.005   0.052   2158
  Dihedral  :  4.560  24.146   1653
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.22), residues: 1490
  helix:  0.49 (0.21), residues: 626
  sheet: -2.96 (0.39), residues: 119
  loop : -1.16 (0.24), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1831 
 HIS   0.006   0.001   HIS A1767 
 PHE   0.010   0.001   PHE A1845 
 TYR   0.018   0.001   TYR A1834 
 ARG   0.008   0.000   ARG A 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2317.00 seconds
wall clock time: 43 minutes 26.21 seconds (2606.21 seconds total)