Starting phenix.real_space_refine
on Wed Jul 30 03:25:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w41_37260/07_2025/8w41_37260.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w41_37260/07_2025/8w41_37260.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2025/8w41_37260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2025/8w41_37260.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2025/8w41_37260.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w41_37260/07_2025/8w41_37260.cif"
  }
  resolution = 3.54
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 28 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      68      5.16       5
     C    7417      2.51       5
     N    2071      2.21       5
     O    2295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11859
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 1156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1156
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 2, 'TRANS': 144}
    Chain: "I"
      Number of atoms: 1151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1151
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 2, 'TRANS': 143}
    Chain: "A"
      Number of atoms: 9515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1162, 9515
          Classifications: {'peptide': 1162}
          Link IDs: {'PTRANS': 37, 'TRANS': 1124}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 8.38, per 1000 atoms: 0.71
  Number of scatterers: 11859
  At special positions: 0
  Unit cell: (74.43, 102.548, 186.075, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      4     19.99
     S      68     16.00
     P       3     15.00
     Mg      1     11.99
     O    2295      8.00
     N    2071      7.00
     C    7417      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: 3.32
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2758

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 8 sheets defined
      63.5% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 21
    Processing helix  chain 'B' and resid 29 through 40
      removed outlier: 4.096A  pdb=" N   LEU B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 56
      removed outlier: 3.562A  pdb=" N   LEU B  49 " --> pdb=" O   THR B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 74
    Processing helix  chain 'B' and resid 80 through 94
    Processing helix  chain 'B' and resid 102 through 114
    Processing helix  chain 'B' and resid 118 through 130
      removed outlier: 3.661A  pdb=" N   ASP B 123 " --> pdb=" O   ASP B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 148
    Processing helix  chain 'I' and resid 6 through 20
    Processing helix  chain 'I' and resid 29 through 38
      removed outlier: 4.180A  pdb=" N   THR I  35 " --> pdb=" O   LYS I  31 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 45 through 57
    Processing helix  chain 'I' and resid 58 through 60
      No H-bonds generated for 'chain 'I' and resid 58 through 60'
    Processing helix  chain 'I' and resid 65 through 79
      removed outlier: 4.046A  pdb=" N   ASP I  79 " --> pdb=" O   ARG I  75 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 82 through 93
      removed outlier: 4.003A  pdb=" N   PHE I  93 " --> pdb=" O   ALA I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 102 through 113
    Processing helix  chain 'I' and resid 118 through 129
      removed outlier: 3.710A  pdb=" N   VAL I 122 " --> pdb=" O   THR I 118 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 139 through 148
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 69 through 83
      removed outlier: 3.520A  pdb=" N   SER A  82 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A  83 " --> pdb=" O   VAL A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 116
      removed outlier: 3.517A  pdb=" N   TYR A 115 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLN A 116 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 141
      removed outlier: 3.504A  pdb=" N   ILE A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
      removed outlier: 3.566A  pdb=" N   ASN A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 185
      removed outlier: 3.761A  pdb=" N   VAL A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 193
    Processing helix  chain 'A' and resid 246 through 255
      removed outlier: 3.883A  pdb=" N   CYS A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 267 through 270
    Processing helix  chain 'A' and resid 271 through 276
      removed outlier: 4.077A  pdb=" N   ARG A 276 " --> pdb=" O   ARG A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 291
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 312 through 327
    Processing helix  chain 'A' and resid 330 through 350
      removed outlier: 3.665A  pdb=" N   GLY A 348 " --> pdb=" O   VAL A 344 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE A 350 " --> pdb=" O   HIS A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 379
      removed outlier: 4.445A  pdb=" N   GLN A 370 " --> pdb=" O   ASN A 366 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER A 371 " --> pdb=" O   LYS A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 392
      removed outlier: 3.583A  pdb=" N   THR A 392 " --> pdb=" O   VAL A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 443
      removed outlier: 3.769A  pdb=" N   PHE A 443 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 489
    Processing helix  chain 'A' and resid 489 through 500
    Processing helix  chain 'A' and resid 511 through 520
    Processing helix  chain 'A' and resid 524 through 534
    Processing helix  chain 'A' and resid 539 through 551
    Processing helix  chain 'A' and resid 559 through 563
    Processing helix  chain 'A' and resid 567 through 571
    Processing helix  chain 'A' and resid 572 through 574
      No H-bonds generated for 'chain 'A' and resid 572 through 574'
    Processing helix  chain 'A' and resid 592 through 597
    Processing helix  chain 'A' and resid 602 through 611
      removed outlier: 3.549A  pdb=" N   GLU A 611 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 642 through 661
    Processing helix  chain 'A' and resid 681 through 692
      removed outlier: 3.518A  pdb=" N   ILE A 685 " --> pdb=" O   GLU A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 702
    Processing helix  chain 'A' and resid 711 through 720
      removed outlier: 3.879A  pdb=" N   LYS A 720 " --> pdb=" O   ASN A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 728
      removed outlier: 3.666A  pdb=" N   ARG A 728 " --> pdb=" O   ASP A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 742
      removed outlier: 3.561A  pdb=" N   PHE A 739 " --> pdb=" O   CYS A 735 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   LYS A 740 " --> pdb=" O   LYS A 736 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A 741 " --> pdb=" O   ALA A 737 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU A 742 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 770
      removed outlier: 3.750A  pdb=" N   GLN A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 829
      removed outlier: 3.994A  pdb=" N   VAL A 796 " --> pdb=" O   ARG A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 860
      removed outlier: 3.982A  pdb=" N   GLU A 855 " --> pdb=" O   ASP A 851 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   VAL A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 888
      removed outlier: 3.709A  pdb=" N   MET A 867 " --> pdb=" O   GLY A 863 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   THR A 888 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 920
      removed outlier: 3.558A  pdb=" N   LYS A 904 " --> pdb=" O   ASP A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 979
      removed outlier: 3.935A  pdb=" N   ARG A 928 " --> pdb=" O   GLU A 924 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS A 963 " --> pdb=" O   GLU A 959 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS A 979 " --> pdb=" O   GLU A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 1021
      removed outlier: 3.605A  pdb=" N   ARG A 991 " --> pdb=" O   ALA A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1088
      removed outlier: 3.511A  pdb=" N   LEU A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1095 through 1119
      removed outlier: 3.630A  pdb=" N   ALA A1100 " --> pdb=" O   GLU A1096 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1136
    Processing helix  chain 'A' and resid 1177 through 1181
      removed outlier: 3.888A  pdb=" N   GLN A1181 " --> pdb=" O   PRO A1178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1230 through 1235
    Processing helix  chain 'A' and resid 1245 through 1255
      removed outlier: 3.644A  pdb=" N   PHE A1249 " --> pdb=" O   LEU A1245 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A1250 " --> pdb=" O   PRO A1246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1268
    Processing sheet with id=AA1, first strand: chain 'I' and resid 100 through 101
      removed outlier: 3.530A  pdb=" N   VAL I 137 " --> pdb=" O   ILE I 101 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44
      removed outlier: 3.587A  pdb=" N   PHE A  41 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA A  43 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ASN A  20 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90
      removed outlier: 6.311A  pdb=" N   LEU A  94 " --> pdb=" O   ARG A 667 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ILE A 669 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ALA A  96 " --> pdb=" O   ILE A 669 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE A 666 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   GLN A 145 " --> pdb=" O   GLY A 453 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ILE A 147 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A 226 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 195
    Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354
    Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 558
    Processing sheet with id=AA7, first strand: chain 'A' and resid 707 through 710
      removed outlier: 3.588A  pdb=" N   SER A 707 " --> pdb=" O   PHE A 758 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1168 through 1174
      removed outlier: 5.751A  pdb=" N   TRP A1192 " --> pdb=" O   GLU A1207 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU A1207 " --> pdb=" O   TRP A1192 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   TYR A1194 " --> pdb=" O   GLN A1205 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   GLN A1205 " --> pdb=" O   TYR A1194 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   HIS A1196 " --> pdb=" O   ALA A1203 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TRP A1201 " --> pdb=" O   ASP A1198 " (cutoff:3.500A)

    670 hydrogen bonds defined for protein.
    1965 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: 3.82

  Time building geometry restraints manager: 3.90 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2139
        1.31 -     1.44: 2999
        1.44 -     1.56: 6802
        1.56 -     1.69: 3
        1.69 -     1.81: 112
  Bond restraints: 12055
  Sorted by residual:
  bond pdb=" CA  ILE A1244 "
       pdb=" C   ILE A1244 "
    ideal  model  delta    sigma   weight residual
    1.526  1.415  0.111 1.16e-02 7.43e+03 9.11e+01
  bond pdb=" CA  MET A1224 "
       pdb=" C   MET A1224 "
    ideal  model  delta    sigma   weight residual
    1.523  1.430  0.093 1.34e-02 5.57e+03 4.85e+01
  bond pdb=" CA  GLU A 152 "
       pdb=" C   GLU A 152 "
    ideal  model  delta    sigma   weight residual
    1.528  1.435  0.092 1.33e-02 5.65e+03 4.83e+01
  bond pdb=" CA  LYS A1221 "
       pdb=" C   LYS A1221 "
    ideal  model  delta    sigma   weight residual
    1.530  1.469  0.060 9.10e-03 1.21e+04 4.41e+01
  bond pdb=" CA  GLU A1104 "
       pdb=" C   GLU A1104 "
    ideal  model  delta    sigma   weight residual
    1.524  1.441  0.083 1.29e-02 6.01e+03 4.16e+01
  ... (remaining 12050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 16020
        3.82 -     7.65: 148
        7.65 -    11.47: 13
       11.47 -    15.29: 1
       15.29 -    19.12: 2
  Bond angle restraints: 16184
  Sorted by residual:
  angle pdb=" N   ILE A1089 "
        pdb=" CA  ILE A1089 "
        pdb=" C   ILE A1089 "
      ideal   model   delta    sigma   weight residual
     113.53   94.41   19.12 9.80e-01 1.04e+00 3.81e+02
  angle pdb=" N   LYS A1221 "
        pdb=" CA  LYS A1221 "
        pdb=" C   LYS A1221 "
      ideal   model   delta    sigma   weight residual
     108.49   89.98   18.51 1.15e+00 7.56e-01 2.59e+02
  angle pdb=" N   ARG A1102 "
        pdb=" CA  ARG A1102 "
        pdb=" C   ARG A1102 "
      ideal   model   delta    sigma   weight residual
     111.82  101.33   10.49 1.16e+00 7.43e-01 8.17e+01
  angle pdb=" N   GLU I 105 "
        pdb=" CA  GLU I 105 "
        pdb=" C   GLU I 105 "
      ideal   model   delta    sigma   weight residual
     111.36  102.39    8.97 1.09e+00 8.42e-01 6.77e+01
  angle pdb=" N   PHE A1249 "
        pdb=" CA  PHE A1249 "
        pdb=" C   PHE A1249 "
      ideal   model   delta    sigma   weight residual
     111.14  102.90    8.24 1.08e+00 8.57e-01 5.82e+01
  ... (remaining 16179 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.25: 7170
       31.25 -    62.51: 247
       62.51 -    93.76: 15
       93.76 -   125.01: 0
      125.01 -   156.27: 3
  Dihedral angle restraints: 7435
    sinusoidal: 3188
      harmonic: 4247
  Sorted by residual:
  dihedral pdb=" N   GLU A1103 "
           pdb=" C   GLU A1103 "
           pdb=" CA  GLU A1103 "
           pdb=" CB  GLU A1103 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  140.00  -17.20     0      2.50e+00 1.60e-01 4.73e+01
  dihedral pdb=" C5' ADP A2001 "
           pdb=" O5' ADP A2001 "
           pdb=" PA  ADP A2001 "
           pdb=" O2A ADP A2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   96.27 -156.27     1      2.00e+01 2.50e-03 4.60e+01
  dihedral pdb=" C   GLU A1103 "
           pdb=" N   GLU A1103 "
           pdb=" CA  GLU A1103 "
           pdb=" CB  GLU A1103 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.75   16.15     0      2.50e+00 1.60e-01 4.18e+01
  ... (remaining 7432 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.145: 1685
       0.145 -    0.289: 33
       0.289 -    0.434: 7
       0.434 -    0.579: 0
       0.579 -    0.724: 1
  Chirality restraints: 1726
  Sorted by residual:
  chirality pdb=" CA  GLU A1103 "
            pdb=" N   GLU A1103 "
            pdb=" C   GLU A1103 "
            pdb=" CB  GLU A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.79    0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" CA  ILE A1244 "
            pdb=" N   ILE A1244 "
            pdb=" C   ILE A1244 "
            pdb=" CB  ILE A1244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.04    0.40 2.00e-01 2.50e+01 3.92e+00
  chirality pdb=" CA  GLU A1254 "
            pdb=" N   GLU A1254 "
            pdb=" C   GLU A1254 "
            pdb=" CB  GLU A1254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.08e+00
  ... (remaining 1723 not shown)

  Planarity restraints: 2127
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 705 "   -0.063 5.00e-02 4.00e+02   9.58e-02 1.47e+01
        pdb=" N   PRO A 706 "    0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO A 706 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 706 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1082 "   -0.033 2.00e-02 2.50e+03   2.08e-02 8.66e+00
        pdb=" CG  TYR A1082 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1082 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1082 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1082 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1082 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1082 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A1082 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A1212 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A1213 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A1213 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A1213 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2124 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 129
        2.51 -     3.11: 9509
        3.11 -     3.71: 19529
        3.71 -     4.30: 26689
        4.30 -     4.90: 42974
  Nonbonded interactions: 98830
  Sorted by model distance:
  nonbonded pdb=" O1B ADP A2001 "
            pdb="MG    MG A2002 "
     model   vdw
     1.918 2.170
  nonbonded pdb="MG    MG A2002 "
            pdb=" O2  PO4 A2003 "
     model   vdw
     1.976 2.170
  nonbonded pdb=" OG  SER A 204 "
            pdb="MG    MG A2002 "
     model   vdw
     2.008 2.170
  nonbonded pdb=" N   LYS A1221 "
            pdb=" O   LYS A1221 "
     model   vdw
     2.105 2.496
  nonbonded pdb=" O   LEU A1231 "
            pdb=" OG1 THR A1234 "
     model   vdw
     2.127 3.040
  ... (remaining 98825 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 3 through 148)
  selection = chain 'I'
}

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:             5.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     31.600
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
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   0.111  12055  Z= 0.467
  Angle     :  0.912  19.118  16184  Z= 0.565
  Chirality :  0.060   0.724   1726
  Planarity :  0.005   0.096   2127
  Dihedral  : 15.405 156.268   4677
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 17.98
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.00 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  1.32 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.15 %
  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: -1.05 (0.21), residues: 1441
  helix: -0.00 (0.17), residues: 837
  sheet: -2.39 (0.47), residues: 107
  loop : -1.32 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A1253 
 HIS   0.009   0.001   HIS A 833 
 PHE   0.039   0.003   PHE I  66 
 TYR   0.047   0.002   TYR A1082 
 ARG   0.022   0.001   ARG A 387 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15433 (  670)
  hydrogen bonds       : angle       6.75064 ( 1965)
  covalent geometry    : bond        0.00784 (12055)
  covalent geometry    : angle       0.91226 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 311
  time to evaluate  : 1.320 
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: B   77 MET cc_start: 0.6807 (pmm) cc_final: 0.6389 (pmm)
REVERT: B   83 GLU cc_start: 0.7060 (tp30) cc_final: 0.6599 (tp30)
REVERT: I   38 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6616 (ttm110)
REVERT: I   42 GLN cc_start: 0.5856 (pp30) cc_final: 0.5120 (pp30)
REVERT: I   50 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6981 (tm-30)
REVERT: I   72 MET cc_start: 0.7568 (mmp) cc_final: 0.7363 (mmp)
REVERT: I   73 MET cc_start: 0.7331 (tpt) cc_final: 0.6782 (tpt)
REVERT: I  108 HIS cc_start: 0.7393 (m170) cc_final: 0.7191 (m170)
REVERT: I  124 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7247 (mm-30)
REVERT: I  141 GLU cc_start: 0.4241 (mm-30) cc_final: 0.3843 (mm-30)
REVERT: A    5 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8251 (ptpp)
REVERT: A   46 ASN cc_start: 0.7613 (p0) cc_final: 0.7408 (p0)
REVERT: A  132 ASP cc_start: 0.6276 (t70) cc_final: 0.5795 (t0)
REVERT: A  135 PHE cc_start: 0.7674 (t80) cc_final: 0.7359 (t80)
REVERT: A  138 MET cc_start: 0.7230 (tmm) cc_final: 0.6970 (tmm)
REVERT: A  176 GLN cc_start: 0.7550 (pm20) cc_final: 0.7230 (pm20)
REVERT: A  180 ASP cc_start: 0.7355 (m-30) cc_final: 0.7017 (m-30)
REVERT: A  196 LYS cc_start: 0.8249 (tttm) cc_final: 0.7905 (tttm)
REVERT: A  264 HIS cc_start: 0.7727 (m170) cc_final: 0.7376 (m170)
REVERT: A  327 ILE cc_start: 0.7967 (pt) cc_final: 0.7226 (pt)
REVERT: A  377 GLU cc_start: 0.7785 (tt0) cc_final: 0.7583 (tt0)
REVERT: A  387 ARG cc_start: 0.7443 (pmt170) cc_final: 0.6936 (pmt170)
REVERT: A  491 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7343 (tm-30)
REVERT: A  575 GLU cc_start: 0.6287 (mp0) cc_final: 0.6029 (mp0)
REVERT: A  596 LYS cc_start: 0.8142 (mptt) cc_final: 0.7883 (mptt)
REVERT: A  609 ILE cc_start: 0.8229 (tp) cc_final: 0.7966 (tp)
REVERT: A  611 GLU cc_start: 0.6973 (mp0) cc_final: 0.6766 (mp0)
REVERT: A  617 ILE cc_start: 0.8336 (mm) cc_final: 0.8065 (mm)
REVERT: A  619 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6555 (mt-10)
REVERT: A  701 MET cc_start: 0.7078 (mmt) cc_final: 0.6789 (mmt)
REVERT: A  732 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7778 (ttp80)
REVERT: A  765 GLU cc_start: 0.6707 (mp0) cc_final: 0.6396 (mp0)
REVERT: A  799 CYS cc_start: 0.6902 (t) cc_final: 0.6629 (t)
REVERT: A  802 SER cc_start: 0.7427 (t) cc_final: 0.7073 (p)
REVERT: A  956 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7416 (tmm)
REVERT: A  959 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7500 (tm-30)
REVERT: A  961 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6990 (mt-10)
REVERT: A 1104 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7577 (mm-30)
REVERT: A 1105 PHE cc_start: 0.8186 (t80) cc_final: 0.7926 (t80)
REVERT: A 1193 TRP cc_start: 0.8375 (t60) cc_final: 0.8087 (t60)
REVERT: A 1223 ASP cc_start: 0.7276 (t0) cc_final: 0.6716 (t0)
  outliers start: 21
  outliers final: 5
  residues processed: 323
  average time/residue: 0.2933
  time to fit residues: 128.1852
Evaluate side-chains
  305 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 297
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  956 MET
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1090 ASN
Chi-restraints excluded: chain A residue 1091 THR
Chi-restraints excluded: chain A residue 1095 ILE
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1222 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0370
   chunk 37 optimal weight:    0.4980
   chunk 73 optimal weight:    0.0980
   chunk 58 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 130 optimal weight:    0.5980
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 ASN
A 868 ASN
** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 988 GLN
** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1248 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.161844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.138642 restraints weight = 19132.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.143230 restraints weight = 9011.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.146239 restraints weight = 5336.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12055  Z= 0.156
  Angle     :  0.647  10.136  16184  Z= 0.342
  Chirality :  0.043   0.165   1726
  Planarity :  0.005   0.063   2127
  Dihedral  :  8.909 152.757   1611
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.26 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.68 %
    Favored  : 89.38 %
  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: -0.31 (0.21), residues: 1441
  helix:  0.59 (0.17), residues: 851
  sheet: -1.86 (0.48), residues: 112
  loop : -1.08 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A1253 
 HIS   0.003   0.001   HIS A 246 
 PHE   0.036   0.002   PHE A 853 
 TYR   0.014   0.002   TYR A 462 
 ARG   0.007   0.001   ARG A 387 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04674 (  670)
  hydrogen bonds       : angle       4.97285 ( 1965)
  covalent geometry    : bond        0.00330 (12055)
  covalent geometry    : angle       0.64665 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 302
  time to evaluate  : 1.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 MET cc_start: 0.8269 (mtp) cc_final: 0.7878 (mtm)
REVERT: B   73 MET cc_start: 0.6552 (mmt) cc_final: 0.6188 (mmp)
REVERT: B   77 MET cc_start: 0.6698 (pmm) cc_final: 0.6320 (pmm)
REVERT: B   83 GLU cc_start: 0.6909 (tp30) cc_final: 0.6501 (tp30)
REVERT: I   12 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: I   50 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: I   73 MET cc_start: 0.7270 (tpt) cc_final: 0.5832 (tpt)
REVERT: I   77 MET cc_start: 0.7677 (ptp) cc_final: 0.6424 (ptp)
REVERT: I  107 ARG cc_start: 0.7407 (ttt-90) cc_final: 0.7057 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7344 (m170) cc_final: 0.7070 (m170)
REVERT: I  110 MET cc_start: 0.7135 (mpp) cc_final: 0.6865 (mpp)
REVERT: I  120 GLU cc_start: 0.7400 (pm20) cc_final: 0.7062 (pm20)
REVERT: I  124 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7171 (mm-30)
REVERT: I  146 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6337 (mmm)
REVERT: A   16 PHE cc_start: 0.7974 (m-80) cc_final: 0.7393 (m-80)
REVERT: A   24 ILE cc_start: 0.7822 (mt) cc_final: 0.7559 (mt)
REVERT: A  125 PRO cc_start: 0.8376 (Cg_exo) cc_final: 0.8152 (Cg_endo)
REVERT: A  132 ASP cc_start: 0.6340 (t70) cc_final: 0.6125 (t0)
REVERT: A  146 SER cc_start: 0.8146 (p) cc_final: 0.7854 (m)
REVERT: A  171 SER cc_start: 0.8242 (m) cc_final: 0.8030 (p)
REVERT: A  228 TYR cc_start: 0.8519 (m-80) cc_final: 0.7910 (m-80)
REVERT: A  264 HIS cc_start: 0.7691 (m170) cc_final: 0.7410 (m170)
REVERT: A  327 ILE cc_start: 0.8026 (pt) cc_final: 0.7721 (pt)
REVERT: A  377 GLU cc_start: 0.7780 (tt0) cc_final: 0.7533 (tt0)
REVERT: A  448 SER cc_start: 0.8285 (p) cc_final: 0.8014 (m)
REVERT: A  575 GLU cc_start: 0.6276 (mp0) cc_final: 0.5862 (mp0)
REVERT: A  580 ARG cc_start: 0.6778 (mpp80) cc_final: 0.6533 (mpp80)
REVERT: A  603 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6870 (tpt)
REVERT: A  617 ILE cc_start: 0.8419 (mm) cc_final: 0.8210 (mm)
REVERT: A  619 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6597 (mt-10)
REVERT: A  701 MET cc_start: 0.7121 (mmt) cc_final: 0.6854 (mmt)
REVERT: A  732 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7131 (ttp80)
REVERT: A  736 LYS cc_start: 0.7946 (tppt) cc_final: 0.7494 (ttmm)
REVERT: A  765 GLU cc_start: 0.6805 (mp0) cc_final: 0.6417 (mp0)
REVERT: A  848 LYS cc_start: 0.7288 (mmtm) cc_final: 0.7059 (mmtm)
REVERT: A  870 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7440 (pp30)
REVERT: A  956 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7200 (ttp)
REVERT: A  959 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7610 (tp30)
REVERT: A  961 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7167 (mt-10)
REVERT: A 1091 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6574 (t)
REVERT: A 1104 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6737 (mm-30)
REVERT: A 1105 PHE cc_start: 0.8111 (t80) cc_final: 0.7664 (t80)
REVERT: A 1175 PHE cc_start: 0.8288 (m-80) cc_final: 0.8078 (m-80)
REVERT: A 1222 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.6696 (m-30)
REVERT: A 1223 ASP cc_start: 0.6744 (t0) cc_final: 0.6323 (t0)
  outliers start: 25
  outliers final: 7
  residues processed: 312
  average time/residue: 0.2777
  time to fit residues: 119.2029
Evaluate side-chains
  302 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 288
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  956 MET
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue 1091 THR
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1222 ASP
Chi-restraints excluded: chain A residue 1227 CYS
Chi-restraints excluded: chain A residue 1245 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0870
   chunk 59 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9980
   chunk 69 optimal weight:    0.2980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 GLN
** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1119 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 = 0.4069 r_free = 0.4069 target = 0.159726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.136366 restraints weight = 19186.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.140971 restraints weight = 9092.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.143933 restraints weight = 5384.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12055  Z= 0.189
  Angle     :  0.614   9.034  16184  Z= 0.325
  Chirality :  0.042   0.182   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  8.387 155.025   1607
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.40 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.33 %
    Favored  : 85.35 %
  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: -0.07 (0.21), residues: 1441
  helix:  0.84 (0.17), residues: 847
  sheet: -1.86 (0.48), residues: 114
  loop : -1.07 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A1253 
 HIS   0.006   0.001   HIS A 833 
 PHE   0.026   0.002   PHE I  90 
 TYR   0.013   0.002   TYR A 812 
 ARG   0.008   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04537 (  670)
  hydrogen bonds       : angle       4.82420 ( 1965)
  covalent geometry    : bond        0.00409 (12055)
  covalent geometry    : angle       0.61405 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 297
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.6552 (mmt) cc_final: 0.6149 (mmt)
REVERT: B   77 MET cc_start: 0.6681 (pmm) cc_final: 0.6285 (pmm)
REVERT: B   83 GLU cc_start: 0.6980 (tp30) cc_final: 0.6583 (tp30)
REVERT: B  128 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6394 (tm-30)
REVERT: I   12 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: I   50 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7220 (tm-30)
REVERT: I   73 MET cc_start: 0.7204 (tpt) cc_final: 0.5850 (tpt)
REVERT: I   77 MET cc_start: 0.7619 (ptp) cc_final: 0.6562 (ptp)
REVERT: I   92 VAL cc_start: 0.8402 (t) cc_final: 0.8181 (t)
REVERT: I  107 ARG cc_start: 0.7394 (ttt-90) cc_final: 0.7058 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7200 (m170) cc_final: 0.6980 (m170)
REVERT: I  120 GLU cc_start: 0.7538 (pm20) cc_final: 0.7240 (pm20)
REVERT: I  124 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7137 (mm-30)
REVERT: I  146 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6227 (mmm)
REVERT: A   24 ILE cc_start: 0.7886 (mt) cc_final: 0.7593 (mt)
REVERT: A   56 LYS cc_start: 0.8212 (mppt) cc_final: 0.7789 (mppt)
REVERT: A   61 ASP cc_start: 0.7178 (t70) cc_final: 0.6778 (t0)
REVERT: A  132 ASP cc_start: 0.6386 (t70) cc_final: 0.6108 (t0)
REVERT: A  138 MET cc_start: 0.7387 (tmm) cc_final: 0.7168 (ttp)
REVERT: A  264 HIS cc_start: 0.7676 (m170) cc_final: 0.7394 (m170)
REVERT: A  316 ASP cc_start: 0.6601 (m-30) cc_final: 0.5818 (m-30)
REVERT: A  327 ILE cc_start: 0.8093 (pt) cc_final: 0.7888 (pt)
REVERT: A  377 GLU cc_start: 0.7787 (tt0) cc_final: 0.7534 (tt0)
REVERT: A  415 GLN cc_start: 0.7893 (mt0) cc_final: 0.7076 (mp10)
REVERT: A  448 SER cc_start: 0.8215 (p) cc_final: 0.7970 (m)
REVERT: A  486 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6680 (tm-30)
REVERT: A  491 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: A  580 ARG cc_start: 0.7016 (mpp80) cc_final: 0.6792 (mtt-85)
REVERT: A  603 MET cc_start: 0.7289 (tpt) cc_final: 0.6800 (tpt)
REVERT: A  619 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6616 (mt-10)
REVERT: A  681 GLU cc_start: 0.7173 (tt0) cc_final: 0.6883 (tt0)
REVERT: A  701 MET cc_start: 0.7139 (mmt) cc_final: 0.6902 (mmt)
REVERT: A  732 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7741 (ttp80)
REVERT: A  733 LEU cc_start: 0.8368 (mt) cc_final: 0.8035 (mt)
REVERT: A  765 GLU cc_start: 0.6817 (mp0) cc_final: 0.6512 (mp0)
REVERT: A  848 LYS cc_start: 0.7379 (mmtm) cc_final: 0.7149 (mmtm)
REVERT: A  959 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7123 (tt0)
REVERT: A  960 MET cc_start: 0.7788 (mmm) cc_final: 0.7384 (mmm)
REVERT: A 1096 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6978 (pm20)
REVERT: A 1105 PHE cc_start: 0.8046 (t80) cc_final: 0.7805 (t80)
  outliers start: 30
  outliers final: 14
  residues processed: 307
  average time/residue: 0.3040
  time to fit residues: 127.1223
Evaluate side-chains
  303 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 286
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue   95 LYS
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  785 ASN
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1202 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 128 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 131 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 135 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
A 873 ASN
** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1119 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 = 0.4059 r_free = 0.4059 target = 0.158987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.135721 restraints weight = 18985.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.140250 restraints weight = 9094.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.143168 restraints weight = 5416.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12055  Z= 0.220
  Angle     :  0.634  11.329  16184  Z= 0.331
  Chirality :  0.043   0.193   1726
  Planarity :  0.004   0.053   2127
  Dihedral  :  8.159 161.196   1598
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.68 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.03 %
    Favored  : 83.49 %
  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: -0.05 (0.21), residues: 1441
  helix:  0.89 (0.17), residues: 847
  sheet: -1.94 (0.47), residues: 115
  loop : -1.10 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1253 
 HIS   0.008   0.001   HIS A 833 
 PHE   0.042   0.003   PHE A 853 
 TYR   0.015   0.002   TYR A 812 
 ARG   0.010   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  670)
  hydrogen bonds       : angle       4.83502 ( 1965)
  covalent geometry    : bond        0.00477 (12055)
  covalent geometry    : angle       0.63411 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 295
  time to evaluate  : 1.409 
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: B   73 MET cc_start: 0.6588 (mmt) cc_final: 0.6210 (mmt)
REVERT: B   77 MET cc_start: 0.6669 (pmm) cc_final: 0.6274 (pmm)
REVERT: B   83 GLU cc_start: 0.7006 (tp30) cc_final: 0.6580 (tp30)
REVERT: I   12 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7556 (tm-30)
REVERT: I   50 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7342 (tm-30)
REVERT: I   70 LEU cc_start: 0.8389 (tt) cc_final: 0.8118 (tt)
REVERT: I   73 MET cc_start: 0.7103 (tpt) cc_final: 0.5930 (tpt)
REVERT: I   77 MET cc_start: 0.7566 (ptp) cc_final: 0.6646 (ptp)
REVERT: I   92 VAL cc_start: 0.8419 (t) cc_final: 0.8197 (t)
REVERT: I  107 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.7156 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7223 (m170) cc_final: 0.7016 (m170)
REVERT: I  124 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7122 (mm-30)
REVERT: I  146 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6379 (mmm)
REVERT: A   24 ILE cc_start: 0.7849 (mt) cc_final: 0.7558 (mt)
REVERT: A   56 LYS cc_start: 0.8222 (mppt) cc_final: 0.7781 (mppt)
REVERT: A   61 ASP cc_start: 0.7114 (t70) cc_final: 0.6707 (t0)
REVERT: A  132 ASP cc_start: 0.6432 (t70) cc_final: 0.6020 (t0)
REVERT: A  137 ASP cc_start: 0.7252 (m-30) cc_final: 0.6565 (m-30)
REVERT: A  264 HIS cc_start: 0.7696 (m170) cc_final: 0.7454 (m170)
REVERT: A  327 ILE cc_start: 0.8184 (pt) cc_final: 0.7978 (pt)
REVERT: A  377 GLU cc_start: 0.7778 (tt0) cc_final: 0.7563 (tt0)
REVERT: A  448 SER cc_start: 0.8238 (p) cc_final: 0.8003 (m)
REVERT: A  603 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6826 (tpt)
REVERT: A  619 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6617 (mt-10)
REVERT: A  701 MET cc_start: 0.7150 (mmt) cc_final: 0.6940 (mmt)
REVERT: A  732 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7493 (ttp80)
REVERT: A  736 LYS cc_start: 0.7988 (tppt) cc_final: 0.7723 (ttmm)
REVERT: A  765 GLU cc_start: 0.6832 (mp0) cc_final: 0.6488 (mp0)
REVERT: A  848 LYS cc_start: 0.7362 (mmtm) cc_final: 0.7129 (mmtm)
REVERT: A  870 GLN cc_start: 0.7841 (pp30) cc_final: 0.7636 (tm-30)
REVERT: A  956 MET cc_start: 0.7785 (tpp) cc_final: 0.7063 (tpp)
REVERT: A  959 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7111 (tt0)
REVERT: A 1104 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7085 (mm-30)
REVERT: A 1206 MET cc_start: 0.7352 (tmm) cc_final: 0.7094 (tmm)
REVERT: A 1207 GLU cc_start: 0.7370 (pm20) cc_final: 0.7080 (mp0)
  outliers start: 32
  outliers final: 20
  residues processed: 307
  average time/residue: 0.2897
  time to fit residues: 121.8588
Evaluate side-chains
  308 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 285
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue   95 LYS
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1245 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 66 optimal weight:    0.1980
   chunk 24 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 35 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0170
   chunk 116 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
A 597 ASN
** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1119 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 = 0.4086 r_free = 0.4086 target = 0.160803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.137339 restraints weight = 19039.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.142001 restraints weight = 9061.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.145060 restraints weight = 5375.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12055  Z= 0.133
  Angle     :  0.590   8.992  16184  Z= 0.307
  Chirality :  0.040   0.172   1726
  Planarity :  0.004   0.051   2127
  Dihedral  :  7.967 170.900   1598
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.91 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.97 %
    Favored  : 81.55 %
  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:  0.44 (0.22), residues: 1441
  helix:  1.24 (0.17), residues: 850
  sheet: -1.04 (0.52), residues: 100
  loop : -1.04 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1253 
 HIS   0.004   0.001   HIS A 833 
 PHE   0.039   0.002   PHE A 853 
 TYR   0.014   0.001   TYR A 475 
 ARG   0.011   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  670)
  hydrogen bonds       : angle       4.56151 ( 1965)
  covalent geometry    : bond        0.00286 (12055)
  covalent geometry    : angle       0.58959 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 290
  time to evaluate  : 1.368 
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: B   77 MET cc_start: 0.6599 (pmm) cc_final: 0.6227 (pmm)
REVERT: B   83 GLU cc_start: 0.6987 (tp30) cc_final: 0.6565 (tp30)
REVERT: B  146 MET cc_start: 0.6686 (mmm) cc_final: 0.6348 (mmt)
REVERT: I   12 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7573 (tm-30)
REVERT: I   50 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: I   70 LEU cc_start: 0.8378 (tt) cc_final: 0.8110 (tt)
REVERT: I   72 MET cc_start: 0.6699 (mmt) cc_final: 0.6108 (mmt)
REVERT: I   73 MET cc_start: 0.7124 (tpt) cc_final: 0.6048 (tpt)
REVERT: I   77 MET cc_start: 0.7573 (ptp) cc_final: 0.6638 (ptp)
REVERT: I   92 VAL cc_start: 0.8396 (t) cc_final: 0.8171 (t)
REVERT: I  107 ARG cc_start: 0.7401 (ttt-90) cc_final: 0.7176 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7269 (m170) cc_final: 0.7043 (m170)
REVERT: I  124 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7021 (mm-30)
REVERT: I  146 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6309 (mmm)
REVERT: A   16 PHE cc_start: 0.8128 (m-80) cc_final: 0.7536 (m-80)
REVERT: A   24 ILE cc_start: 0.7834 (mt) cc_final: 0.7594 (mt)
REVERT: A   56 LYS cc_start: 0.8234 (mppt) cc_final: 0.7780 (mppt)
REVERT: A   57 LYS cc_start: 0.7360 (mtmt) cc_final: 0.7100 (mtmm)
REVERT: A   61 ASP cc_start: 0.7109 (t70) cc_final: 0.6709 (t0)
REVERT: A  132 ASP cc_start: 0.6415 (t70) cc_final: 0.5929 (t0)
REVERT: A  197 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7643 (p)
REVERT: A  231 GLU cc_start: 0.6890 (tt0) cc_final: 0.6499 (tt0)
REVERT: A  234 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7444 (mtt90)
REVERT: A  264 HIS cc_start: 0.7646 (m170) cc_final: 0.7383 (m170)
REVERT: A  377 GLU cc_start: 0.7769 (tt0) cc_final: 0.7458 (tt0)
REVERT: A  415 GLN cc_start: 0.7944 (mt0) cc_final: 0.7150 (mp10)
REVERT: A  448 SER cc_start: 0.8273 (p) cc_final: 0.8035 (m)
REVERT: A  596 LYS cc_start: 0.8047 (mptt) cc_final: 0.7560 (mmtp)
REVERT: A  603 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6805 (tpt)
REVERT: A  613 ARG cc_start: 0.7262 (ptp90) cc_final: 0.6663 (ptp90)
REVERT: A  732 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7116 (ttp80)
REVERT: A  736 LYS cc_start: 0.7834 (tppt) cc_final: 0.7247 (ttmm)
REVERT: A  765 GLU cc_start: 0.6826 (mp0) cc_final: 0.6415 (mp0)
REVERT: A  848 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7104 (mmtm)
REVERT: A  956 MET cc_start: 0.7750 (tpp) cc_final: 0.7253 (tpp)
REVERT: A  959 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7167 (tt0)
REVERT: A 1084 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7173 (tp30)
REVERT: A 1202 ILE cc_start: 0.8086 (tp) cc_final: 0.7807 (tt)
  outliers start: 32
  outliers final: 18
  residues processed: 304
  average time/residue: 0.2947
  time to fit residues: 122.1166
Evaluate side-chains
  307 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 284
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue   95 LYS
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  143 MET
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  785 ASN
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 125 optimal weight:   20.0000
   chunk 38 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0970
   chunk 116 optimal weight:    0.6980
   chunk 143 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 126 optimal weight:   20.0000
   chunk 113 optimal weight:    0.7980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1119 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 = 0.4071 r_free = 0.4071 target = 0.159646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.136140 restraints weight = 19222.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.140794 restraints weight = 9158.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.143791 restraints weight = 5418.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12055  Z= 0.181
  Angle     :  0.625  11.129  16184  Z= 0.323
  Chirality :  0.042   0.169   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  8.044 179.929   1598
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.26 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.52 %
    Favored  : 80.16 %
  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:  0.42 (0.22), residues: 1441
  helix:  1.23 (0.17), residues: 850
  sheet: -1.58 (0.49), residues: 113
  loop : -0.90 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1253 
 HIS   0.006   0.001   HIS A 833 
 PHE   0.023   0.002   PHE A1105 
 TYR   0.012   0.001   TYR A1082 
 ARG   0.006   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  670)
  hydrogen bonds       : angle       4.64546 ( 1965)
  covalent geometry    : bond        0.00394 (12055)
  covalent geometry    : angle       0.62487 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 290
  time to evaluate  : 1.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6628 (pmm) cc_final: 0.6237 (pmm)
REVERT: B   83 GLU cc_start: 0.7023 (tp30) cc_final: 0.6602 (tp30)
REVERT: B  146 MET cc_start: 0.6768 (mmm) cc_final: 0.6471 (mmt)
REVERT: I   12 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7552 (tm-30)
REVERT: I   50 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7366 (tm-30)
REVERT: I   70 LEU cc_start: 0.8385 (tt) cc_final: 0.8110 (tt)
REVERT: I   73 MET cc_start: 0.7197 (tpt) cc_final: 0.6070 (tpt)
REVERT: I   77 MET cc_start: 0.7625 (ptp) cc_final: 0.6594 (ptp)
REVERT: I   92 VAL cc_start: 0.8390 (t) cc_final: 0.8155 (t)
REVERT: I  107 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.7136 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7234 (m170) cc_final: 0.7006 (m170)
REVERT: I  120 GLU cc_start: 0.7767 (pm20) cc_final: 0.7497 (pm20)
REVERT: I  124 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7095 (mm-30)
REVERT: I  146 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6564 (mtm)
REVERT: A   24 ILE cc_start: 0.7852 (mt) cc_final: 0.7612 (mt)
REVERT: A   56 LYS cc_start: 0.8248 (mppt) cc_final: 0.7778 (mppt)
REVERT: A   61 ASP cc_start: 0.7129 (t70) cc_final: 0.6707 (t0)
REVERT: A  132 ASP cc_start: 0.6403 (t70) cc_final: 0.5939 (t0)
REVERT: A  197 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7629 (p)
REVERT: A  228 TYR cc_start: 0.8545 (m-80) cc_final: 0.8332 (m-80)
REVERT: A  231 GLU cc_start: 0.6900 (tt0) cc_final: 0.6501 (tt0)
REVERT: A  234 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7156 (mtt90)
REVERT: A  238 GLN cc_start: 0.6742 (tp-100) cc_final: 0.6201 (tp40)
REVERT: A  264 HIS cc_start: 0.7659 (m170) cc_final: 0.7366 (m170)
REVERT: A  319 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7062 (mtm-85)
REVERT: A  377 GLU cc_start: 0.7790 (tt0) cc_final: 0.7493 (tt0)
REVERT: A  415 GLN cc_start: 0.7928 (mt0) cc_final: 0.7137 (mp10)
REVERT: A  448 SER cc_start: 0.8246 (p) cc_final: 0.8027 (m)
REVERT: A  580 ARG cc_start: 0.6982 (mtt-85) cc_final: 0.6652 (mtt180)
REVERT: A  603 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.7060 (tpt)
REVERT: A  701 MET cc_start: 0.7094 (mmt) cc_final: 0.6880 (mmt)
REVERT: A  732 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7770 (ttp80)
REVERT: A  765 GLU cc_start: 0.6826 (mp0) cc_final: 0.6451 (mp0)
REVERT: A  848 LYS cc_start: 0.7353 (mmtm) cc_final: 0.7114 (mmtm)
REVERT: A  956 MET cc_start: 0.7687 (tpp) cc_final: 0.7361 (tpp)
REVERT: A  959 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7200 (tt0)
REVERT: A 1084 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7179 (tp30)
REVERT: A 1104 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6949 (mm-30)
REVERT: A 1202 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7666 (tt)
  outliers start: 30
  outliers final: 15
  residues processed: 302
  average time/residue: 0.2915
  time to fit residues: 120.8471
Evaluate side-chains
  305 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 284
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue   95 LYS
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1202 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 116 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 126 optimal weight:   40.0000
   chunk 41 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 141 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1119 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 = 0.4074 r_free = 0.4074 target = 0.160282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.136732 restraints weight = 19188.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.141383 restraints weight = 9165.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.144406 restraints weight = 5445.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12055  Z= 0.182
  Angle     :  0.626   8.843  16184  Z= 0.326
  Chirality :  0.042   0.172   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  7.740 169.772   1595
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.33 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.05 %
    Favored  : 80.00 %
  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:  0.43 (0.22), residues: 1441
  helix:  1.23 (0.17), residues: 850
  sheet: -1.62 (0.48), residues: 113
  loop : -0.86 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1253 
 HIS   0.006   0.001   HIS A 833 
 PHE   0.028   0.002   PHE A 445 
 TYR   0.013   0.002   TYR A1082 
 ARG   0.008   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04134 (  670)
  hydrogen bonds       : angle       4.64728 ( 1965)
  covalent geometry    : bond        0.00396 (12055)
  covalent geometry    : angle       0.62569 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 290
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6631 (pmm) cc_final: 0.6257 (pmm)
REVERT: B   83 GLU cc_start: 0.6985 (tp30) cc_final: 0.6561 (tp30)
REVERT: B  146 MET cc_start: 0.6710 (mmm) cc_final: 0.6473 (mmt)
REVERT: I   12 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: I   42 GLN cc_start: 0.5782 (pp30) cc_final: 0.5262 (pp30)
REVERT: I   50 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7397 (tm-30)
REVERT: I   70 LEU cc_start: 0.8406 (tt) cc_final: 0.8168 (tt)
REVERT: I   73 MET cc_start: 0.7175 (tpt) cc_final: 0.6044 (tpt)
REVERT: I   77 MET cc_start: 0.7622 (ptp) cc_final: 0.6594 (ptp)
REVERT: I   92 VAL cc_start: 0.8390 (t) cc_final: 0.8159 (t)
REVERT: I  101 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6475 (mm)
REVERT: I  107 ARG cc_start: 0.7422 (ttt-90) cc_final: 0.7110 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7245 (m170) cc_final: 0.7022 (m170)
REVERT: I  110 MET cc_start: 0.7219 (mpp) cc_final: 0.7006 (mpp)
REVERT: I  124 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7081 (mm-30)
REVERT: I  146 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6574 (mtm)
REVERT: A   24 ILE cc_start: 0.7841 (mt) cc_final: 0.7616 (mt)
REVERT: A   56 LYS cc_start: 0.8253 (mppt) cc_final: 0.7795 (mppt)
REVERT: A   57 LYS cc_start: 0.7399 (mtmt) cc_final: 0.7137 (mtmm)
REVERT: A   61 ASP cc_start: 0.7133 (t70) cc_final: 0.6716 (t0)
REVERT: A  132 ASP cc_start: 0.6424 (t70) cc_final: 0.6013 (t0)
REVERT: A  197 THR cc_start: 0.7996 (m) cc_final: 0.7674 (p)
REVERT: A  231 GLU cc_start: 0.6893 (tt0) cc_final: 0.6482 (tt0)
REVERT: A  234 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7410 (mtt90)
REVERT: A  238 GLN cc_start: 0.6749 (tp-100) cc_final: 0.6432 (tp40)
REVERT: A  264 HIS cc_start: 0.7644 (m170) cc_final: 0.7378 (m170)
REVERT: A  316 ASP cc_start: 0.6453 (OUTLIER) cc_final: 0.5051 (m-30)
REVERT: A  319 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.6580 (mtm-85)
REVERT: A  377 GLU cc_start: 0.7783 (tt0) cc_final: 0.7492 (tt0)
REVERT: A  415 GLN cc_start: 0.7942 (mt0) cc_final: 0.7125 (mp10)
REVERT: A  448 SER cc_start: 0.8250 (p) cc_final: 0.8042 (m)
REVERT: A  596 LYS cc_start: 0.8076 (mttm) cc_final: 0.7525 (mmtp)
REVERT: A  603 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6861 (tpt)
REVERT: A  701 MET cc_start: 0.7052 (mmt) cc_final: 0.6778 (mmt)
REVERT: A  702 GLN cc_start: 0.7750 (tt0) cc_final: 0.7536 (tt0)
REVERT: A  732 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7753 (ttp80)
REVERT: A  765 GLU cc_start: 0.6806 (mp0) cc_final: 0.6394 (mp0)
REVERT: A  848 LYS cc_start: 0.7368 (mmtm) cc_final: 0.7118 (mmtm)
REVERT: A  956 MET cc_start: 0.7667 (tpp) cc_final: 0.7368 (tpp)
REVERT: A  959 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7227 (tt0)
REVERT: A 1084 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7155 (tp30)
REVERT: A 1104 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6986 (mm-30)
REVERT: A 1202 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7644 (tt)
  outliers start: 38
  outliers final: 21
  residues processed: 308
  average time/residue: 0.2912
  time to fit residues: 123.5928
Evaluate side-chains
  311 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 283
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue    6 THR
Chi-restraints excluded: chain I residue   95 LYS
Chi-restraints excluded: chain I residue  101 ILE
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  785 ASN
Chi-restraints excluded: chain A residue  799 CYS
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1202 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0770
   chunk 143 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 117 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9990
   chunk 135 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1196 HIS ** 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 = 0.4078 r_free = 0.4078 target = 0.160090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.136912 restraints weight = 19019.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.141559 restraints weight = 9136.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.144443 restraints weight = 5411.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12055  Z= 0.171
  Angle     :  0.646  10.812  16184  Z= 0.331
  Chirality :  0.042   0.259   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  7.560 161.796   1595
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.47 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.37 %
    Favored  : 79.38 %
  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:  0.52 (0.22), residues: 1441
  helix:  1.31 (0.17), residues: 848
  sheet: -1.65 (0.48), residues: 113
  loop : -0.80 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1253 
 HIS   0.005   0.001   HIS A 833 
 PHE   0.025   0.002   PHE A1105 
 TYR   0.015   0.002   TYR A 172 
 ARG   0.007   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  670)
  hydrogen bonds       : angle       4.60418 ( 1965)
  covalent geometry    : bond        0.00375 (12055)
  covalent geometry    : angle       0.64612 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 291
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6628 (pmm) cc_final: 0.6265 (pmm)
REVERT: B   83 GLU cc_start: 0.6958 (tp30) cc_final: 0.6537 (tp30)
REVERT: B  146 MET cc_start: 0.6677 (mmm) cc_final: 0.6301 (mmt)
REVERT: I   70 LEU cc_start: 0.8384 (tt) cc_final: 0.8101 (tt)
REVERT: I   73 MET cc_start: 0.7175 (tpt) cc_final: 0.6053 (tpt)
REVERT: I   77 MET cc_start: 0.7626 (ptp) cc_final: 0.6614 (ptp)
REVERT: I   92 VAL cc_start: 0.8413 (t) cc_final: 0.8179 (t)
REVERT: I  107 ARG cc_start: 0.7410 (ttt-90) cc_final: 0.7039 (ttt-90)
REVERT: I  110 MET cc_start: 0.7253 (mpp) cc_final: 0.6944 (mpp)
REVERT: I  124 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6999 (mm-30)
REVERT: I  146 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6512 (mtm)
REVERT: A   23 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.6916 (t70)
REVERT: A   24 ILE cc_start: 0.7817 (mt) cc_final: 0.7425 (mt)
REVERT: A   56 LYS cc_start: 0.8256 (mppt) cc_final: 0.7962 (mmtm)
REVERT: A   57 LYS cc_start: 0.7473 (mtmt) cc_final: 0.7195 (mtmm)
REVERT: A   61 ASP cc_start: 0.7124 (t70) cc_final: 0.6723 (t0)
REVERT: A  132 ASP cc_start: 0.6444 (t70) cc_final: 0.6144 (t0)
REVERT: A  197 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7628 (p)
REVERT: A  231 GLU cc_start: 0.6921 (tt0) cc_final: 0.6632 (tt0)
REVERT: A  264 HIS cc_start: 0.7619 (m170) cc_final: 0.7343 (m170)
REVERT: A  316 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.5635 (m-30)
REVERT: A  377 GLU cc_start: 0.7775 (tt0) cc_final: 0.7487 (tt0)
REVERT: A  383 GLN cc_start: 0.7952 (mt0) cc_final: 0.7744 (mt0)
REVERT: A  415 GLN cc_start: 0.7929 (mt0) cc_final: 0.7085 (mp10)
REVERT: A  448 SER cc_start: 0.8206 (p) cc_final: 0.7985 (m)
REVERT: A  603 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6700 (tpt)
REVERT: A  701 MET cc_start: 0.7046 (mmt) cc_final: 0.6784 (mmt)
REVERT: A  732 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7790 (ttp80)
REVERT: A  739 PHE cc_start: 0.7634 (m-10) cc_final: 0.7273 (m-10)
REVERT: A  765 GLU cc_start: 0.6790 (mp0) cc_final: 0.6394 (mp0)
REVERT: A  848 LYS cc_start: 0.7350 (mmtm) cc_final: 0.7118 (mmtm)
REVERT: A  956 MET cc_start: 0.7633 (tpp) cc_final: 0.7361 (tpp)
REVERT: A  959 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7266 (tt0)
REVERT: A 1084 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7084 (tp30)
REVERT: A 1104 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6995 (mm-30)
  outliers start: 29
  outliers final: 18
  residues processed: 304
  average time/residue: 0.2809
  time to fit residues: 118.2062
Evaluate side-chains
  310 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 285
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue    6 THR
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  785 ASN
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 141 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0970
   chunk 31 optimal weight:    0.2980
   chunk 127 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 108 HIS
A 176 GLN
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1090 ASN
** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.160701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.137591 restraints weight = 18877.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.142198 restraints weight = 9050.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145175 restraints weight = 5367.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6764
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12055  Z= 0.150
  Angle     :  0.639  10.411  16184  Z= 0.328
  Chirality :  0.042   0.206   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  7.316 151.503   1595
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.12 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.60 %
    Favored  : 78.84 %
  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:  0.63 (0.22), residues: 1441
  helix:  1.38 (0.17), residues: 851
  sheet: -1.55 (0.49), residues: 112
  loop : -0.75 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1253 
 HIS   0.020   0.001   HIS I 108 
 PHE   0.028   0.002   PHE A1105 
 TYR   0.018   0.001   TYR A 172 
 ARG   0.009   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  670)
  hydrogen bonds       : angle       4.50165 ( 1965)
  covalent geometry    : bond        0.00329 (12055)
  covalent geometry    : angle       0.63866 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 290
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6575 (pmm) cc_final: 0.6197 (pmm)
REVERT: B   83 GLU cc_start: 0.6948 (tp30) cc_final: 0.6501 (tp30)
REVERT: B  146 MET cc_start: 0.6620 (mmm) cc_final: 0.6250 (mmt)
REVERT: I   70 LEU cc_start: 0.8410 (tt) cc_final: 0.8118 (tt)
REVERT: I   73 MET cc_start: 0.7159 (tpt) cc_final: 0.6087 (tpt)
REVERT: I   77 MET cc_start: 0.7637 (ptp) cc_final: 0.6705 (ptp)
REVERT: I   92 VAL cc_start: 0.8383 (t) cc_final: 0.8148 (t)
REVERT: I  101 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6305 (mm)
REVERT: I  107 ARG cc_start: 0.7411 (ttt-90) cc_final: 0.7073 (ttt-90)
REVERT: I  110 MET cc_start: 0.7256 (mpp) cc_final: 0.6921 (mpp)
REVERT: I  146 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6367 (mtm)
REVERT: A   23 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.6785 (t70)
REVERT: A   24 ILE cc_start: 0.7790 (mt) cc_final: 0.7402 (mt)
REVERT: A   56 LYS cc_start: 0.8277 (mppt) cc_final: 0.7977 (mmtm)
REVERT: A   61 ASP cc_start: 0.7114 (t70) cc_final: 0.6734 (t0)
REVERT: A   88 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7782 (t)
REVERT: A  113 LYS cc_start: 0.7794 (ptpt) cc_final: 0.7572 (ptpt)
REVERT: A  132 ASP cc_start: 0.6457 (t70) cc_final: 0.6028 (t0)
REVERT: A  197 THR cc_start: 0.7993 (m) cc_final: 0.7692 (p)
REVERT: A  228 TYR cc_start: 0.8523 (m-80) cc_final: 0.8220 (m-80)
REVERT: A  231 GLU cc_start: 0.6938 (tt0) cc_final: 0.6659 (tt0)
REVERT: A  264 HIS cc_start: 0.7593 (m170) cc_final: 0.7310 (m170)
REVERT: A  316 ASP cc_start: 0.6381 (OUTLIER) cc_final: 0.5568 (m-30)
REVERT: A  383 GLN cc_start: 0.7945 (mt0) cc_final: 0.7636 (mt0)
REVERT: A  387 ARG cc_start: 0.7572 (ptt180) cc_final: 0.7254 (ptt180)
REVERT: A  415 GLN cc_start: 0.7920 (mt0) cc_final: 0.7102 (mp10)
REVERT: A  603 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6722 (tpt)
REVERT: A  701 MET cc_start: 0.7031 (mmt) cc_final: 0.6779 (mmt)
REVERT: A  732 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7805 (ttp80)
REVERT: A  765 GLU cc_start: 0.6781 (mp0) cc_final: 0.6363 (mp0)
REVERT: A  956 MET cc_start: 0.7643 (tpp) cc_final: 0.7332 (tpp)
REVERT: A  959 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7301 (tt0)
REVERT: A 1104 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6991 (mm-30)
  outliers start: 33
  outliers final: 22
  residues processed: 305
  average time/residue: 0.2847
  time to fit residues: 120.2806
Evaluate side-chains
  306 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 277
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue    6 THR
Chi-restraints excluded: chain I residue  101 ILE
Chi-restraints excluded: chain I residue  108 HIS
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  145 MET
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  785 ASN
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0170
   chunk 31 optimal weight:    0.0270
   chunk 52 optimal weight:    0.3980
   chunk 83 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 117 optimal weight:    0.6980
   chunk 136 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 17 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.3076

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

Flipped N/Q/H residues before XYZ refinement:
** I  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 108 HIS
A 176 GLN
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1260 GLN
A1264 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.161499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.138086 restraints weight = 19171.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.142656 restraints weight = 9246.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.145710 restraints weight = 5541.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12055  Z= 0.137
  Angle     :  0.655  11.088  16184  Z= 0.336
  Chirality :  0.042   0.185   1726
  Planarity :  0.004   0.051   2127
  Dihedral  :  7.161 144.979   1595
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.85 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.53 %
    Favored  : 78.06 %
  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:  0.74 (0.22), residues: 1441
  helix:  1.44 (0.17), residues: 853
  sheet: -1.39 (0.50), residues: 110
  loop : -0.69 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1253 
 HIS   0.018   0.001   HIS I 108 
 PHE   0.030   0.002   PHE A 445 
 TYR   0.021   0.001   TYR A 172 
 ARG   0.009   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  670)
  hydrogen bonds       : angle       4.44947 ( 1965)
  covalent geometry    : bond        0.00299 (12055)
  covalent geometry    : angle       0.65523 (16184)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 281
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6569 (pmm) cc_final: 0.6182 (pmm)
REVERT: B   83 GLU cc_start: 0.6932 (tp30) cc_final: 0.6516 (tp30)
REVERT: B  146 MET cc_start: 0.6610 (mmm) cc_final: 0.6254 (mmt)
REVERT: I   70 LEU cc_start: 0.8442 (tt) cc_final: 0.8156 (tt)
REVERT: I   73 MET cc_start: 0.7176 (tpt) cc_final: 0.6137 (tpt)
REVERT: I   77 MET cc_start: 0.7647 (ptp) cc_final: 0.6787 (ptp)
REVERT: I   92 VAL cc_start: 0.8367 (t) cc_final: 0.8138 (t)
REVERT: I  101 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6305 (mm)
REVERT: I  107 ARG cc_start: 0.7431 (ttt-90) cc_final: 0.7080 (ttt-90)
REVERT: I  110 MET cc_start: 0.7236 (mpp) cc_final: 0.6987 (mpp)
REVERT: I  146 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6336 (mtm)
REVERT: A   16 PHE cc_start: 0.8152 (m-80) cc_final: 0.7577 (m-80)
REVERT: A   23 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7101 (t70)
REVERT: A   24 ILE cc_start: 0.7847 (mt) cc_final: 0.7527 (mt)
REVERT: A   56 LYS cc_start: 0.8288 (mppt) cc_final: 0.7951 (mmtm)
REVERT: A   57 LYS cc_start: 0.7390 (mtmt) cc_final: 0.7096 (mtmm)
REVERT: A   60 GLU cc_start: 0.6213 (mt-10) cc_final: 0.5989 (mt-10)
REVERT: A   61 ASP cc_start: 0.7101 (t70) cc_final: 0.6738 (t0)
REVERT: A   88 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7786 (t)
REVERT: A  132 ASP cc_start: 0.6448 (t70) cc_final: 0.6121 (t0)
REVERT: A  197 THR cc_start: 0.8026 (m) cc_final: 0.7702 (p)
REVERT: A  228 TYR cc_start: 0.8482 (m-80) cc_final: 0.8271 (m-80)
REVERT: A  231 GLU cc_start: 0.6907 (tt0) cc_final: 0.6595 (tt0)
REVERT: A  237 VAL cc_start: 0.8215 (t) cc_final: 0.7811 (p)
REVERT: A  264 HIS cc_start: 0.7635 (m170) cc_final: 0.7311 (m170)
REVERT: A  319 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.6957 (mtt-85)
REVERT: A  383 GLN cc_start: 0.7961 (mt0) cc_final: 0.7587 (mt0)
REVERT: A  387 ARG cc_start: 0.7595 (ptt180) cc_final: 0.7269 (ptt180)
REVERT: A  415 GLN cc_start: 0.7933 (mt0) cc_final: 0.7101 (mp10)
REVERT: A  603 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6742 (tpt)
REVERT: A  613 ARG cc_start: 0.7367 (ptp90) cc_final: 0.6963 (ptp90)
REVERT: A  701 MET cc_start: 0.7042 (mmt) cc_final: 0.6815 (mmt)
REVERT: A  732 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7287 (ttp80)
REVERT: A  736 LYS cc_start: 0.7894 (tppt) cc_final: 0.7315 (ttmm)
REVERT: A  739 PHE cc_start: 0.7605 (m-10) cc_final: 0.7289 (m-10)
REVERT: A  765 GLU cc_start: 0.6774 (mp0) cc_final: 0.6376 (mp0)
REVERT: A  956 MET cc_start: 0.7678 (tpp) cc_final: 0.7426 (tpp)
REVERT: A  959 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7377 (tt0)
REVERT: A 1084 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7186 (tp30)
REVERT: A 1104 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6975 (mm-30)
REVERT: A 1207 GLU cc_start: 0.7409 (pm20) cc_final: 0.6916 (mp0)
  outliers start: 31
  outliers final: 21
  residues processed: 296
  average time/residue: 0.2872
  time to fit residues: 117.6095
Evaluate side-chains
  304 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 276
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain I residue    6 THR
Chi-restraints excluded: chain I residue  101 ILE
Chi-restraints excluded: chain I residue  108 HIS
Chi-restraints excluded: chain I residue  137 VAL
Chi-restraints excluded: chain I residue  145 MET
Chi-restraints excluded: chain I residue  146 MET
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  170 GLU
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  597 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  785 ASN
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  959 GLU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 120 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0370
   chunk 31 optimal weight:    0.0980
   chunk 86 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
I 108 HIS
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 GLN
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1196 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 = 0.4097 r_free = 0.4097 target = 0.161841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.138579 restraints weight = 19214.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.143197 restraints weight = 9252.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.146256 restraints weight = 5519.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  12055  Z= 0.166
  Angle     :  0.680  10.406  16184  Z= 0.350
  Chirality :  0.043   0.185   1726
  Planarity :  0.004   0.051   2127
  Dihedral  :  7.166 139.436   1595
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.33 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.61 %
    Favored  : 77.91 %
  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:  0.65 (0.22), residues: 1441
  helix:  1.36 (0.17), residues: 853
  sheet: -1.49 (0.49), residues: 111
  loop : -0.68 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1253 
 HIS   0.012   0.001   HIS I 108 
 PHE   0.029   0.002   PHE A 445 
 TYR   0.031   0.002   TYR A 172 
 ARG   0.009   0.000   ARG I  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  670)
  hydrogen bonds       : angle       4.47266 ( 1965)
  covalent geometry    : bond        0.00371 (12055)
  covalent geometry    : angle       0.68049 (16184)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4530.13 seconds
wall clock time: 79 minutes 9.88 seconds (4749.88 seconds total)