Starting phenix.real_space_refine
on Sat Aug 23 12:04:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w41_37260/08_2025/8w41_37260.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w41_37260/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w41_37260/08_2025/8w41_37260.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w41_37260/08_2025/8w41_37260.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w41_37260/08_2025/8w41_37260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w41_37260/08_2025/8w41_37260.map"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.88, per 1000 atoms: 0.24
  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: 1.12
  Conformation dependent library (CDL) restraints added in 546.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.39
  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: 2.24

  Time building geometry restraints manager: 1.40 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:             5.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.330
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.410
-------------------------------------------------------------------------------
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 : 17.89
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.022   0.001   ARG A 387 
 TYR   0.047   0.002   TYR A1082 
 PHE   0.039   0.003   PHE I  66 
 TRP   0.028   0.003   TRP A1253 
 HIS   0.009   0.001   HIS A 833 

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

*********************** 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  : 0.454 
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: 0.1337
  time to fit residues: 58.5746
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  : 0.467 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0270
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:   40.0000
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.5980
   chunk 55 optimal weight:    0.3980
   overall best weight:    0.4438

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.161486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.138264 restraints weight = 19193.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.142876 restraints weight = 9053.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.145884 restraints weight = 5345.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.147794 restraints weight = 3669.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.149050 restraints weight = 2822.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12055  Z= 0.164
  Angle     :  0.650  10.470  16184  Z= 0.343
  Chirality :  0.043   0.166   1726
  Planarity :  0.005   0.062   2127
  Dihedral  :  8.902 152.226   1611
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.40 %
    Favored  : 96.53 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.21), residues: 1441
  helix:  0.57 (0.17), residues: 851
  sheet: -1.88 (0.48), residues: 112
  loop : -1.09 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 387 
 TYR   0.014   0.002   TYR A1082 
 PHE   0.037   0.002   PHE A 853 
 TRP   0.039   0.002   TRP A1253 
 HIS   0.004   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12055)
  covalent geometry    : angle       0.64958 (16184)
  hydrogen bonds       : bond        0.04678 (  670)
  hydrogen bonds       : angle       4.98706 ( 1965)

*********************** 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
  325 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 300
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 MET cc_start: 0.8270 (mtp) cc_final: 0.7987 (mtm)
REVERT: B   73 MET cc_start: 0.6572 (mmt) cc_final: 0.6215 (mmp)
REVERT: B   77 MET cc_start: 0.6697 (pmm) cc_final: 0.6308 (pmm)
REVERT: B   83 GLU cc_start: 0.6903 (tp30) cc_final: 0.6502 (tp30)
REVERT: I   12 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7533 (tm-30)
REVERT: I   50 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7201 (tm-30)
REVERT: I   73 MET cc_start: 0.7217 (tpt) cc_final: 0.5793 (tpt)
REVERT: I   77 MET cc_start: 0.7633 (ptp) cc_final: 0.6389 (ptp)
REVERT: I  108 HIS cc_start: 0.7325 (m170) cc_final: 0.7064 (m170)
REVERT: I  110 MET cc_start: 0.7111 (mpp) cc_final: 0.6896 (mpp)
REVERT: I  120 GLU cc_start: 0.7397 (pm20) cc_final: 0.7068 (pm20)
REVERT: I  146 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6327 (mmm)
REVERT: A   16 PHE cc_start: 0.7987 (m-80) cc_final: 0.7420 (m-80)
REVERT: A   24 ILE cc_start: 0.7836 (mt) cc_final: 0.7563 (mt)
REVERT: A  132 ASP cc_start: 0.6310 (t70) cc_final: 0.6094 (t0)
REVERT: A  146 SER cc_start: 0.8128 (p) cc_final: 0.7834 (m)
REVERT: A  228 TYR cc_start: 0.8500 (m-80) cc_final: 0.7903 (m-80)
REVERT: A  264 HIS cc_start: 0.7661 (m170) cc_final: 0.7368 (m170)
REVERT: A  316 ASP cc_start: 0.6666 (m-30) cc_final: 0.6011 (m-30)
REVERT: A  327 ILE cc_start: 0.8024 (pt) cc_final: 0.7727 (pt)
REVERT: A  377 GLU cc_start: 0.7758 (tt0) cc_final: 0.7521 (tt0)
REVERT: A  448 SER cc_start: 0.8284 (p) cc_final: 0.8013 (m)
REVERT: A  479 LYS cc_start: 0.7783 (mttm) cc_final: 0.7505 (mttp)
REVERT: A  575 GLU cc_start: 0.6264 (mp0) cc_final: 0.5884 (mp0)
REVERT: A  580 ARG cc_start: 0.6812 (mpp80) cc_final: 0.6219 (mpp80)
REVERT: A  603 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6807 (tpt)
REVERT: A  617 ILE cc_start: 0.8424 (mm) cc_final: 0.8220 (mm)
REVERT: A  619 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6575 (mt-10)
REVERT: A  701 MET cc_start: 0.7144 (mmt) cc_final: 0.6863 (mmt)
REVERT: A  732 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7141 (ttp80)
REVERT: A  736 LYS cc_start: 0.7943 (tppt) cc_final: 0.7510 (ttmm)
REVERT: A  765 GLU cc_start: 0.6773 (mp0) cc_final: 0.6400 (mp0)
REVERT: A  848 LYS cc_start: 0.7301 (mmtm) cc_final: 0.7078 (mmtm)
REVERT: A  870 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7452 (pp30)
REVERT: A  956 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7172 (ttp)
REVERT: A  959 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7561 (tp30)
REVERT: A  961 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7169 (mt-10)
REVERT: A 1091 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6563 (t)
REVERT: A 1104 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6765 (mm-30)
REVERT: A 1105 PHE cc_start: 0.8108 (t80) cc_final: 0.7663 (t80)
REVERT: A 1175 PHE cc_start: 0.8282 (m-80) cc_final: 0.8076 (m-80)
REVERT: A 1222 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.6664 (m-30)
REVERT: A 1223 ASP cc_start: 0.6751 (t0) cc_final: 0.6333 (t0)
  outliers start: 25
  outliers final: 7
  residues processed: 310
  average time/residue: 0.1110
  time to fit residues: 47.5824
Evaluate side-chains
  299 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 285
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 LYS
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  557 LEU
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 103 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
** A  11 HIS ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.159803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.136479 restraints weight = 19141.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.141079 restraints weight = 9112.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.143953 restraints weight = 5399.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.145885 restraints weight = 3757.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.147130 restraints weight = 2884.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12055  Z= 0.203
  Angle     :  0.626   9.124  16184  Z= 0.331
  Chirality :  0.043   0.183   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  8.437 153.602   1607
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.61 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.40 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.21), residues: 1441
  helix:  0.80 (0.17), residues: 847
  sheet: -1.90 (0.47), residues: 115
  loop : -1.10 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I  87 
 TYR   0.014   0.002   TYR A 812 
 PHE   0.025   0.002   PHE I  90 
 TRP   0.026   0.002   TRP A1253 
 HIS   0.007   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (12055)
  covalent geometry    : angle       0.62553 (16184)
  hydrogen bonds       : bond        0.04620 (  670)
  hydrogen bonds       : angle       4.89690 ( 1965)

*********************** 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
  329 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 298
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.6566 (mmt) cc_final: 0.6189 (mmt)
REVERT: B   77 MET cc_start: 0.6686 (pmm) cc_final: 0.6300 (pmm)
REVERT: B   83 GLU cc_start: 0.6951 (tp30) cc_final: 0.6561 (tp30)
REVERT: B  128 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6370 (tm-30)
REVERT: I   12 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: I   38 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6930 (ttm110)
REVERT: I   50 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7233 (tm-30)
REVERT: I   73 MET cc_start: 0.7107 (tpt) cc_final: 0.5867 (tpt)
REVERT: I   77 MET cc_start: 0.7577 (ptp) cc_final: 0.6557 (ptp)
REVERT: I   92 VAL cc_start: 0.8388 (t) cc_final: 0.8185 (t)
REVERT: I  107 ARG cc_start: 0.7419 (ttt-90) cc_final: 0.7133 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7232 (m170) cc_final: 0.6998 (m170)
REVERT: I  146 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6405 (mmm)
REVERT: A   24 ILE cc_start: 0.7890 (mt) cc_final: 0.7604 (mt)
REVERT: A   56 LYS cc_start: 0.8205 (mppt) cc_final: 0.7799 (mppt)
REVERT: A  132 ASP cc_start: 0.6367 (t70) cc_final: 0.6082 (t0)
REVERT: A  138 MET cc_start: 0.7342 (tmm) cc_final: 0.7119 (ttp)
REVERT: A  171 SER cc_start: 0.8220 (m) cc_final: 0.7995 (p)
REVERT: A  264 HIS cc_start: 0.7659 (m170) cc_final: 0.7375 (m170)
REVERT: A  316 ASP cc_start: 0.6586 (m-30) cc_final: 0.5842 (m-30)
REVERT: A  327 ILE cc_start: 0.8131 (pt) cc_final: 0.7910 (pt)
REVERT: A  377 GLU cc_start: 0.7758 (tt0) cc_final: 0.7513 (tt0)
REVERT: A  415 GLN cc_start: 0.7893 (mt0) cc_final: 0.7084 (mp10)
REVERT: A  448 SER cc_start: 0.8222 (p) cc_final: 0.7970 (m)
REVERT: A  479 LYS cc_start: 0.7788 (mttm) cc_final: 0.7454 (mttp)
REVERT: A  580 ARG cc_start: 0.7014 (mpp80) cc_final: 0.6774 (mtt-85)
REVERT: A  603 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6770 (tpt)
REVERT: A  619 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6585 (mt-10)
REVERT: A  701 MET cc_start: 0.7159 (mmt) cc_final: 0.6919 (mmt)
REVERT: A  732 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7749 (ttp80)
REVERT: A  733 LEU cc_start: 0.8340 (mt) cc_final: 0.8020 (mt)
REVERT: A  765 GLU cc_start: 0.6800 (mp0) cc_final: 0.6489 (mp0)
REVERT: A  848 LYS cc_start: 0.7390 (mmtm) cc_final: 0.7166 (mmtm)
REVERT: A  872 LYS cc_start: 0.8642 (mttp) cc_final: 0.8298 (mttp)
REVERT: A  956 MET cc_start: 0.7661 (ttm) cc_final: 0.7435 (tpp)
REVERT: A  958 LEU cc_start: 0.8432 (mm) cc_final: 0.8115 (mm)
REVERT: A  959 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7146 (tt0)
REVERT: A  960 MET cc_start: 0.7828 (mmm) cc_final: 0.7293 (mmm)
REVERT: A 1096 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6890 (pm20)
REVERT: A 1104 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6879 (tp30)
REVERT: A 1105 PHE cc_start: 0.8057 (t80) cc_final: 0.7759 (t80)
REVERT: A 1221 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7235 (mttt)
REVERT: A 1223 ASP cc_start: 0.6809 (t0) cc_final: 0.6580 (t0)
  outliers start: 31
  outliers final: 14
  residues processed: 308
  average time/residue: 0.1226
  time to fit residues: 51.5031
Evaluate side-chains
  308 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 289
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
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   42 GLN
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  603 MET
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 1221 LYS
Chi-restraints excluded: chain A residue 1245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 131 optimal weight:    1.9990
   chunk 138 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0570
   chunk 120 optimal weight:    0.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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  11 HIS ** 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 = 0.4070 r_free = 0.4070 target = 0.159860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.136355 restraints weight = 19139.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.140971 restraints weight = 9109.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.143903 restraints weight = 5405.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145834 restraints weight = 3751.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.146897 restraints weight = 2883.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12055  Z= 0.189
  Angle     :  0.618  10.806  16184  Z= 0.323
  Chirality :  0.042   0.191   1726
  Planarity :  0.004   0.049   2127
  Dihedral  :  8.105 160.256   1598
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.47 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.57 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.21), residues: 1441
  helix:  0.96 (0.17), residues: 849
  sheet: -1.82 (0.48), residues: 113
  loop : -1.04 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I  87 
 TYR   0.013   0.002   TYR A 812 
 PHE   0.041   0.002   PHE A 853 
 TRP   0.023   0.002   TRP A1253 
 HIS   0.006   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (12055)
  covalent geometry    : angle       0.61791 (16184)
  hydrogen bonds       : bond        0.04344 (  670)
  hydrogen bonds       : angle       4.75859 ( 1965)

*********************** 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
  321 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 289
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 MET cc_start: 0.6586 (mmt) cc_final: 0.6162 (mmt)
REVERT: B   77 MET cc_start: 0.6654 (pmm) cc_final: 0.6256 (pmm)
REVERT: B   83 GLU cc_start: 0.6966 (tp30) cc_final: 0.6581 (tp30)
REVERT: B  146 MET cc_start: 0.6722 (mmm) cc_final: 0.6360 (mmt)
REVERT: I   12 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7557 (tm-30)
REVERT: I   38 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6767 (ttm110)
REVERT: I   50 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7293 (tm-30)
REVERT: I   70 LEU cc_start: 0.8375 (tt) cc_final: 0.8132 (tt)
REVERT: I   73 MET cc_start: 0.7043 (tpt) cc_final: 0.5954 (tpt)
REVERT: I   77 MET cc_start: 0.7559 (ptp) cc_final: 0.6704 (ptp)
REVERT: I   92 VAL cc_start: 0.8400 (t) cc_final: 0.8177 (t)
REVERT: I  107 ARG cc_start: 0.7405 (ttt-90) cc_final: 0.7051 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7243 (m170) cc_final: 0.7011 (m170)
REVERT: I  146 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6315 (mmm)
REVERT: A   24 ILE cc_start: 0.7866 (mt) cc_final: 0.7561 (mt)
REVERT: A   56 LYS cc_start: 0.8221 (mppt) cc_final: 0.7785 (mppt)
REVERT: A   61 ASP cc_start: 0.7108 (t70) cc_final: 0.6715 (t0)
REVERT: A  132 ASP cc_start: 0.6388 (t70) cc_final: 0.5936 (t0)
REVERT: A  171 SER cc_start: 0.8196 (m) cc_final: 0.7992 (p)
REVERT: A  264 HIS cc_start: 0.7679 (m170) cc_final: 0.7400 (m170)
REVERT: A  377 GLU cc_start: 0.7749 (tt0) cc_final: 0.7524 (tt0)
REVERT: A  448 SER cc_start: 0.8238 (p) cc_final: 0.7986 (m)
REVERT: A  479 LYS cc_start: 0.7777 (mttm) cc_final: 0.7411 (mttm)
REVERT: A  580 ARG cc_start: 0.7061 (mpp80) cc_final: 0.6834 (mtt-85)
REVERT: A  603 MET cc_start: 0.7271 (tpt) cc_final: 0.6760 (tpt)
REVERT: A  619 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6574 (mt-10)
REVERT: A  701 MET cc_start: 0.7160 (mmt) cc_final: 0.6933 (mmt)
REVERT: A  732 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7119 (ttp80)
REVERT: A  736 LYS cc_start: 0.7926 (tppt) cc_final: 0.7401 (ttmm)
REVERT: A  765 GLU cc_start: 0.6790 (mp0) cc_final: 0.6398 (mp0)
REVERT: A  848 LYS cc_start: 0.7401 (mmtm) cc_final: 0.7164 (mmtm)
REVERT: A  870 GLN cc_start: 0.7840 (pp30) cc_final: 0.7637 (tm-30)
REVERT: A  872 LYS cc_start: 0.8662 (mttp) cc_final: 0.8231 (mptp)
REVERT: A  958 LEU cc_start: 0.8466 (mm) cc_final: 0.8086 (mm)
REVERT: A  959 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7006 (tt0)
REVERT: A 1089 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7273 (pt)
REVERT: A 1094 ASP cc_start: 0.6563 (m-30) cc_final: 0.6289 (m-30)
REVERT: A 1096 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6683 (pm20)
REVERT: A 1171 PHE cc_start: 0.7922 (m-80) cc_final: 0.7677 (m-80)
REVERT: A 1206 MET cc_start: 0.7338 (tmm) cc_final: 0.7066 (tmm)
REVERT: A 1207 GLU cc_start: 0.7415 (pm20) cc_final: 0.7079 (mp0)
REVERT: A 1221 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7230 (mttt)
  outliers start: 32
  outliers final: 14
  residues processed: 304
  average time/residue: 0.1233
  time to fit residues: 51.3358
Evaluate side-chains
  305 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 286
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 PHE
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  326 LYS
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  597 ASN
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 1089 ILE
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1202 ILE
Chi-restraints excluded: chain A residue 1221 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 127 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0040
   chunk 114 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 105 optimal weight:    0.6980
   chunk 48 optimal weight:    0.3980
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.4992

-------------------------------------------------------------------------------
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  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
** 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 = 0.4079 r_free = 0.4079 target = 0.160230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.136588 restraints weight = 19182.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.141284 restraints weight = 9153.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.144324 restraints weight = 5429.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.146239 restraints weight = 3734.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.147383 restraints weight = 2874.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.2266

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= 0.163
  Angle     :  0.605   9.037  16184  Z= 0.315
  Chirality :  0.041   0.176   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  8.041 169.080   1598
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.26 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.43 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.21), residues: 1441
  helix:  1.18 (0.17), residues: 848
  sheet: -1.14 (0.52), residues: 100
  loop : -1.08 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG I  87 
 TYR   0.011   0.001   TYR A1082 
 PHE   0.041   0.002   PHE A 853 
 TRP   0.022   0.001   TRP A1253 
 HIS   0.005   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (12055)
  covalent geometry    : angle       0.60463 (16184)
  hydrogen bonds       : bond        0.04131 (  670)
  hydrogen bonds       : angle       4.65272 ( 1965)

*********************** 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: 34
    poor density    : 288
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6612 (pmm) cc_final: 0.6239 (pmm)
REVERT: B   83 GLU cc_start: 0.6955 (tp30) cc_final: 0.6555 (tp30)
REVERT: B  146 MET cc_start: 0.6770 (mmm) cc_final: 0.6443 (mmt)
REVERT: I   12 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: I   38 ARG cc_start: 0.6977 (ttm-80) cc_final: 0.6756 (ttm110)
REVERT: I   50 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7295 (tm-30)
REVERT: I   70 LEU cc_start: 0.8320 (tt) cc_final: 0.8059 (tt)
REVERT: I   72 MET cc_start: 0.6605 (mmt) cc_final: 0.6083 (mmt)
REVERT: I   73 MET cc_start: 0.6938 (tpt) cc_final: 0.6044 (tpt)
REVERT: I   77 MET cc_start: 0.7546 (ptp) cc_final: 0.6732 (ptp)
REVERT: I   92 VAL cc_start: 0.8387 (t) cc_final: 0.8162 (t)
REVERT: I  107 ARG cc_start: 0.7391 (ttt-90) cc_final: 0.7020 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7252 (m170) cc_final: 0.7020 (m170)
REVERT: I  146 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6336 (mmm)
REVERT: A   16 PHE cc_start: 0.8098 (m-80) cc_final: 0.7537 (m-80)
REVERT: A   24 ILE cc_start: 0.7834 (mt) cc_final: 0.7594 (mt)
REVERT: A   56 LYS cc_start: 0.8240 (mppt) cc_final: 0.7795 (mppt)
REVERT: A   57 LYS cc_start: 0.7370 (mtmt) cc_final: 0.7119 (mtmm)
REVERT: A   61 ASP cc_start: 0.7103 (t70) cc_final: 0.6708 (t0)
REVERT: A  132 ASP cc_start: 0.6360 (t70) cc_final: 0.5925 (t0)
REVERT: A  197 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7653 (p)
REVERT: A  264 HIS cc_start: 0.7633 (m170) cc_final: 0.7359 (m170)
REVERT: A  377 GLU cc_start: 0.7723 (tt0) cc_final: 0.7496 (tt0)
REVERT: A  415 GLN cc_start: 0.7942 (mt0) cc_final: 0.7159 (mp10)
REVERT: A  448 SER cc_start: 0.8214 (p) cc_final: 0.7984 (m)
REVERT: A  479 LYS cc_start: 0.7802 (mttm) cc_final: 0.7385 (mttm)
REVERT: A  580 ARG cc_start: 0.7039 (mpp80) cc_final: 0.6753 (mtt-85)
REVERT: A  596 LYS cc_start: 0.8122 (mptt) cc_final: 0.7863 (mttm)
REVERT: A  603 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6752 (tpt)
REVERT: A  701 MET cc_start: 0.7120 (mmt) cc_final: 0.6917 (mmt)
REVERT: A  732 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7137 (ttp80)
REVERT: A  736 LYS cc_start: 0.7851 (tppt) cc_final: 0.7438 (ttmm)
REVERT: A  765 GLU cc_start: 0.6807 (mp0) cc_final: 0.6376 (mp0)
REVERT: A  807 LYS cc_start: 0.7562 (tttt) cc_final: 0.7357 (ttpt)
REVERT: A  848 LYS cc_start: 0.7405 (mmtm) cc_final: 0.7163 (mmtm)
REVERT: A  958 LEU cc_start: 0.8468 (mm) cc_final: 0.8051 (mm)
REVERT: A  959 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7197 (tt0)
REVERT: A 1104 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6843 (mm-30)
REVERT: A 1221 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7056 (mttt)
  outliers start: 34
  outliers final: 18
  residues processed: 302
  average time/residue: 0.1457
  time to fit residues: 59.7805
Evaluate side-chains
  303 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 280
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
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  308 ASP
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  507 HIS
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  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
Chi-restraints excluded: chain A residue 1221 LYS
Chi-restraints excluded: chain A residue 1227 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 139 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 121 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 ASN
** 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 = 0.4078 r_free = 0.4078 target = 0.160272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.136783 restraints weight = 19047.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.141446 restraints weight = 9143.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.144492 restraints weight = 5418.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.146492 restraints weight = 3710.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.147688 restraints weight = 2833.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6716
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12055  Z= 0.165
  Angle     :  0.612  10.968  16184  Z= 0.316
  Chirality :  0.042   0.168   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  7.914 179.329   1595
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.33 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.29 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.22), residues: 1441
  helix:  1.24 (0.17), residues: 850
  sheet: -1.70 (0.48), residues: 114
  loop : -0.89 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG I  87 
 TYR   0.012   0.001   TYR A1082 
 PHE   0.036   0.002   PHE A 451 
 TRP   0.021   0.001   TRP A1253 
 HIS   0.005   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (12055)
  covalent geometry    : angle       0.61221 (16184)
  hydrogen bonds       : bond        0.04056 (  670)
  hydrogen bonds       : angle       4.60861 ( 1965)

*********************** 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: 31
    poor density    : 289
  time to evaluate  : 0.475 
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: 0.6622 (pmm) cc_final: 0.6218 (pmm)
REVERT: B   83 GLU cc_start: 0.6968 (tp30) cc_final: 0.6563 (tp30)
REVERT: B  146 MET cc_start: 0.6808 (mmm) cc_final: 0.6524 (mmt)
REVERT: I   38 ARG cc_start: 0.6914 (ttm-80) cc_final: 0.6689 (ttm110)
REVERT: I   50 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7293 (tm-30)
REVERT: I   70 LEU cc_start: 0.8311 (tt) cc_final: 0.8047 (tt)
REVERT: I   73 MET cc_start: 0.7105 (tpt) cc_final: 0.6180 (tpt)
REVERT: I   77 MET cc_start: 0.7594 (ptp) cc_final: 0.6841 (ptp)
REVERT: I   92 VAL cc_start: 0.8386 (t) cc_final: 0.8153 (t)
REVERT: I  107 ARG cc_start: 0.7395 (ttt-90) cc_final: 0.7149 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7254 (m170) cc_final: 0.7010 (m170)
REVERT: I  110 MET cc_start: 0.7168 (mpp) cc_final: 0.6938 (mpp)
REVERT: I  146 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6506 (mtm)
REVERT: A   24 ILE cc_start: 0.7857 (mt) cc_final: 0.7615 (mt)
REVERT: A   56 LYS cc_start: 0.8250 (mppt) cc_final: 0.7797 (mppt)
REVERT: A   61 ASP cc_start: 0.7114 (t70) cc_final: 0.6713 (t0)
REVERT: A  132 ASP cc_start: 0.6370 (t70) cc_final: 0.6006 (t0)
REVERT: A  231 GLU cc_start: 0.6895 (tt0) cc_final: 0.6619 (tt0)
REVERT: A  264 HIS cc_start: 0.7613 (m170) cc_final: 0.7314 (m170)
REVERT: A  377 GLU cc_start: 0.7736 (tt0) cc_final: 0.7501 (tt0)
REVERT: A  415 GLN cc_start: 0.7915 (mt0) cc_final: 0.7162 (mp10)
REVERT: A  448 SER cc_start: 0.8274 (p) cc_final: 0.8033 (m)
REVERT: A  475 TYR cc_start: 0.7663 (t80) cc_final: 0.7178 (t80)
REVERT: A  479 LYS cc_start: 0.7802 (mttm) cc_final: 0.7317 (mttm)
REVERT: A  580 ARG cc_start: 0.7071 (mpp80) cc_final: 0.6820 (mtt-85)
REVERT: A  596 LYS cc_start: 0.8071 (mptt) cc_final: 0.7858 (mttm)
REVERT: A  603 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7023 (tpt)
REVERT: A  701 MET cc_start: 0.7129 (mmt) cc_final: 0.6909 (mmt)
REVERT: A  732 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7786 (ttp80)
REVERT: A  765 GLU cc_start: 0.6818 (mp0) cc_final: 0.6374 (mp0)
REVERT: A  848 LYS cc_start: 0.7401 (mmtm) cc_final: 0.7153 (mmtm)
REVERT: A  872 LYS cc_start: 0.8652 (mttp) cc_final: 0.8350 (mptt)
REVERT: A  956 MET cc_start: 0.7689 (tpp) cc_final: 0.7236 (tpp)
REVERT: A  958 LEU cc_start: 0.8476 (mm) cc_final: 0.8031 (mm)
REVERT: A  959 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7185 (tt0)
REVERT: A 1084 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7109 (tp30)
REVERT: A 1089 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7447 (mm)
REVERT: A 1104 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6882 (mm-30)
REVERT: A 1202 ILE cc_start: 0.8081 (tp) cc_final: 0.7666 (tt)
REVERT: A 1221 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7022 (mttt)
  outliers start: 31
  outliers final: 17
  residues processed: 303
  average time/residue: 0.1346
  time to fit residues: 55.6810
Evaluate side-chains
  304 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 281
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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   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  308 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  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 1084 GLU
Chi-restraints excluded: chain A residue 1089 ILE
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1221 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 81 optimal weight:    0.0010
   chunk 79 optimal weight:    0.9990
   chunk 47 optimal weight:    0.3980
   chunk 59 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0980
   overall best weight:    0.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 597 ASN
** 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 = 0.4091 r_free = 0.4091 target = 0.161128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.137711 restraints weight = 19055.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.142405 restraints weight = 9114.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.145427 restraints weight = 5397.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.147338 restraints weight = 3708.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.148485 restraints weight = 2848.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12055  Z= 0.134
  Angle     :  0.607   9.018  16184  Z= 0.313
  Chirality :  0.041   0.207   1726
  Planarity :  0.004   0.048   2127
  Dihedral  :  7.591 170.379   1595
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.91 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.98 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.22), residues: 1441
  helix:  1.42 (0.17), residues: 851
  sheet: -1.57 (0.49), residues: 112
  loop : -0.78 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  87 
 TYR   0.012   0.001   TYR A1082 
 PHE   0.041   0.002   PHE A 853 
 TRP   0.022   0.001   TRP A1253 
 HIS   0.003   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12055)
  covalent geometry    : angle       0.60716 (16184)
  hydrogen bonds       : bond        0.03793 (  670)
  hydrogen bonds       : angle       4.47171 ( 1965)

*********************** 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
  324 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 289
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6594 (pmm) cc_final: 0.6209 (pmm)
REVERT: B   83 GLU cc_start: 0.6943 (tp30) cc_final: 0.6518 (tp30)
REVERT: B  146 MET cc_start: 0.6776 (mmm) cc_final: 0.6534 (mmt)
REVERT: I   50 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7285 (tm-30)
REVERT: I   69 PHE cc_start: 0.7853 (t80) cc_final: 0.7511 (t80)
REVERT: I   70 LEU cc_start: 0.8369 (tt) cc_final: 0.8154 (tt)
REVERT: I   73 MET cc_start: 0.7077 (tpt) cc_final: 0.6122 (tpt)
REVERT: I   77 MET cc_start: 0.7590 (ptp) cc_final: 0.6837 (ptp)
REVERT: I   92 VAL cc_start: 0.8385 (t) cc_final: 0.8160 (t)
REVERT: I  101 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6336 (mm)
REVERT: I  107 ARG cc_start: 0.7391 (ttt-90) cc_final: 0.7107 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7241 (m170) cc_final: 0.7027 (m170)
REVERT: I  110 MET cc_start: 0.7227 (mpp) cc_final: 0.6946 (mpp)
REVERT: I  146 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.5943 (mmm)
REVERT: A   23 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.6874 (t0)
REVERT: A   24 ILE cc_start: 0.7842 (mt) cc_final: 0.7428 (mt)
REVERT: A   56 LYS cc_start: 0.8247 (mppt) cc_final: 0.7916 (mmtm)
REVERT: A   61 ASP cc_start: 0.7105 (t70) cc_final: 0.6711 (t0)
REVERT: A  132 ASP cc_start: 0.6378 (t70) cc_final: 0.6040 (t0)
REVERT: A  196 LYS cc_start: 0.8041 (tttm) cc_final: 0.7836 (ttpp)
REVERT: A  197 THR cc_start: 0.7616 (m) cc_final: 0.7331 (t)
REVERT: A  231 GLU cc_start: 0.6879 (tt0) cc_final: 0.6657 (tt0)
REVERT: A  264 HIS cc_start: 0.7589 (m170) cc_final: 0.7314 (m170)
REVERT: A  415 GLN cc_start: 0.7923 (mt0) cc_final: 0.7143 (mp10)
REVERT: A  448 SER cc_start: 0.8227 (p) cc_final: 0.7992 (m)
REVERT: A  462 TYR cc_start: 0.6538 (p90) cc_final: 0.6292 (p90)
REVERT: A  475 TYR cc_start: 0.7643 (t80) cc_final: 0.7144 (t80)
REVERT: A  479 LYS cc_start: 0.7790 (mttm) cc_final: 0.7296 (mttm)
REVERT: A  580 ARG cc_start: 0.7048 (mpp80) cc_final: 0.6777 (mtt-85)
REVERT: A  596 LYS cc_start: 0.8092 (mptt) cc_final: 0.7519 (mmtp)
REVERT: A  603 MET cc_start: 0.7225 (tpt) cc_final: 0.6765 (tpt)
REVERT: A  732 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7140 (ttp80)
REVERT: A  736 LYS cc_start: 0.7801 (tppt) cc_final: 0.7242 (ttmm)
REVERT: A  765 GLU cc_start: 0.6826 (mp0) cc_final: 0.6364 (mp0)
REVERT: A  848 LYS cc_start: 0.7385 (mmtm) cc_final: 0.7127 (mmtm)
REVERT: A  956 MET cc_start: 0.7683 (tpp) cc_final: 0.7301 (tpp)
REVERT: A  958 LEU cc_start: 0.8507 (mm) cc_final: 0.8079 (mm)
REVERT: A  959 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7309 (tt0)
REVERT: A 1084 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7115 (tp30)
REVERT: A 1089 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7478 (mm)
REVERT: A 1221 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6916 (mttt)
  outliers start: 35
  outliers final: 19
  residues processed: 309
  average time/residue: 0.1316
  time to fit residues: 56.0061
Evaluate side-chains
  295 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 269
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
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    9 GLN
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   23 ASP
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  308 ASP
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
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 1089 ILE
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1221 LYS
Chi-restraints excluded: chain A residue 1227 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 84 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 99 optimal weight:    0.3980
   chunk 107 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 120 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.160586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.136964 restraints weight = 19034.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.141630 restraints weight = 9200.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.144619 restraints weight = 5474.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146588 restraints weight = 3764.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.147686 restraints weight = 2880.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12055  Z= 0.179
  Angle     :  0.643  10.872  16184  Z= 0.332
  Chirality :  0.042   0.159   1726
  Planarity :  0.004   0.049   2127
  Dihedral  :  7.483 160.210   1595
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.40 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.30 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.22), residues: 1441
  helix:  1.32 (0.17), residues: 851
  sheet: -1.56 (0.49), residues: 111
  loop : -0.81 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I  87 
 TYR   0.014   0.002   TYR A 172 
 PHE   0.034   0.003   PHE I  90 
 TRP   0.021   0.002   TRP A1253 
 HIS   0.006   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (12055)
  covalent geometry    : angle       0.64340 (16184)
  hydrogen bonds       : bond        0.04039 (  670)
  hydrogen bonds       : angle       4.56936 ( 1965)

*********************** 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
  308 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 276
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.6611 (pmm) cc_final: 0.6239 (pmm)
REVERT: B   83 GLU cc_start: 0.6939 (tp30) cc_final: 0.6526 (tp30)
REVERT: B  146 MET cc_start: 0.6821 (mmm) cc_final: 0.6472 (mmt)
REVERT: I   38 ARG cc_start: 0.6914 (ttm-80) cc_final: 0.6645 (ttm110)
REVERT: I   70 LEU cc_start: 0.8421 (tt) cc_final: 0.8156 (tt)
REVERT: I   73 MET cc_start: 0.7041 (tpt) cc_final: 0.6157 (tpt)
REVERT: I   77 MET cc_start: 0.7611 (ptp) cc_final: 0.6731 (ptp)
REVERT: I   92 VAL cc_start: 0.8393 (t) cc_final: 0.8162 (t)
REVERT: I  101 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6351 (mm)
REVERT: I  107 ARG cc_start: 0.7293 (ttt-90) cc_final: 0.7036 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7248 (m170) cc_final: 0.7018 (m170)
REVERT: I  146 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6454 (mtm)
REVERT: A   23 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.6854 (t70)
REVERT: A   24 ILE cc_start: 0.7825 (mt) cc_final: 0.7400 (mt)
REVERT: A   61 ASP cc_start: 0.7120 (t70) cc_final: 0.6732 (t0)
REVERT: A  132 ASP cc_start: 0.6371 (t70) cc_final: 0.5995 (t0)
REVERT: A  196 LYS cc_start: 0.8079 (tttm) cc_final: 0.7860 (ttpp)
REVERT: A  197 THR cc_start: 0.7711 (m) cc_final: 0.7434 (t)
REVERT: A  231 GLU cc_start: 0.6902 (tt0) cc_final: 0.6633 (tt0)
REVERT: A  264 HIS cc_start: 0.7615 (m170) cc_final: 0.7330 (m170)
REVERT: A  319 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.6938 (mtm-85)
REVERT: A  383 GLN cc_start: 0.7983 (mt0) cc_final: 0.7725 (mm110)
REVERT: A  387 ARG cc_start: 0.7530 (ptt180) cc_final: 0.7193 (ptt180)
REVERT: A  448 SER cc_start: 0.8210 (p) cc_final: 0.7979 (m)
REVERT: A  475 TYR cc_start: 0.7681 (t80) cc_final: 0.6897 (t80)
REVERT: A  479 LYS cc_start: 0.7804 (mttm) cc_final: 0.7350 (mttp)
REVERT: A  580 ARG cc_start: 0.7111 (mpp80) cc_final: 0.6840 (mtt-85)
REVERT: A  603 MET cc_start: 0.7241 (tpt) cc_final: 0.6898 (tpt)
REVERT: A  732 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7793 (ttp80)
REVERT: A  765 GLU cc_start: 0.6772 (mp0) cc_final: 0.6341 (mp0)
REVERT: A  848 LYS cc_start: 0.7394 (mmtm) cc_final: 0.7155 (mmtm)
REVERT: A  872 LYS cc_start: 0.8603 (mptt) cc_final: 0.8344 (mttp)
REVERT: A  956 MET cc_start: 0.7680 (tpp) cc_final: 0.7352 (tpp)
REVERT: A  958 LEU cc_start: 0.8529 (mm) cc_final: 0.8091 (mm)
REVERT: A  959 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7232 (tt0)
REVERT: A 1084 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7149 (tp30)
REVERT: A 1089 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7526 (mm)
REVERT: A 1104 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6944 (mm-30)
REVERT: A 1221 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6963 (mttt)
  outliers start: 32
  outliers final: 19
  residues processed: 293
  average time/residue: 0.1384
  time to fit residues: 56.0073
Evaluate side-chains
  301 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 275
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
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 I residue    6 THR
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   23 ASP
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  308 ASP
Chi-restraints excluded: chain A residue  313 ASP
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  643 VAL
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 1089 ILE
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1221 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 104 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 131 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 108 optimal weight:    0.0980
   chunk 76 optimal weight:    0.0050
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
A 176 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.161363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137905 restraints weight = 19013.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.142555 restraints weight = 9160.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.145512 restraints weight = 5430.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.147510 restraints weight = 3737.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.148726 restraints weight = 2859.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6690
moved from start:          0.2954

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= 0.146
  Angle     :  0.639  10.653  16184  Z= 0.327
  Chirality :  0.041   0.169   1726
  Planarity :  0.004   0.050   2127
  Dihedral  :  7.202 148.836   1595
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.91 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.84 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.22), residues: 1441
  helix:  1.41 (0.17), residues: 855
  sheet: -1.40 (0.50), residues: 110
  loop : -0.73 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I  87 
 TYR   0.012   0.001   TYR A1082 
 PHE   0.032   0.002   PHE A1105 
 TRP   0.021   0.001   TRP A1253 
 HIS   0.004   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12055)
  covalent geometry    : angle       0.63908 (16184)
  hydrogen bonds       : bond        0.03795 (  670)
  hydrogen bonds       : angle       4.44904 ( 1965)

*********************** 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
  307 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 276
  time to evaluate  : 0.477 
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: 0.6557 (pmm) cc_final: 0.6180 (pmm)
REVERT: B   83 GLU cc_start: 0.6904 (tp30) cc_final: 0.6495 (tp30)
REVERT: B  146 MET cc_start: 0.6645 (mmm) cc_final: 0.6295 (mmt)
REVERT: I   38 ARG cc_start: 0.6860 (ttm-80) cc_final: 0.6640 (ttm110)
REVERT: I   70 LEU cc_start: 0.8367 (tt) cc_final: 0.8100 (tt)
REVERT: I   73 MET cc_start: 0.6992 (tpt) cc_final: 0.6090 (tpt)
REVERT: I   77 MET cc_start: 0.7598 (ptp) cc_final: 0.6678 (ptp)
REVERT: I   92 VAL cc_start: 0.8389 (t) cc_final: 0.8152 (t)
REVERT: I  101 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6447 (mm)
REVERT: I  107 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.7077 (ttt-90)
REVERT: I  108 HIS cc_start: 0.7271 (m170) cc_final: 0.7062 (m170)
REVERT: I  146 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6431 (mtm)
REVERT: A   23 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.6906 (t0)
REVERT: A   24 ILE cc_start: 0.7793 (mt) cc_final: 0.7409 (mt)
REVERT: A   56 LYS cc_start: 0.8288 (mppt) cc_final: 0.7977 (mmtm)
REVERT: A   57 LYS cc_start: 0.7327 (mtmt) cc_final: 0.7081 (mtmm)
REVERT: A   61 ASP cc_start: 0.7168 (t70) cc_final: 0.6793 (t0)
REVERT: A   88 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7751 (t)
REVERT: A  132 ASP cc_start: 0.6326 (t70) cc_final: 0.6090 (t0)
REVERT: A  138 MET cc_start: 0.7254 (tmm) cc_final: 0.7025 (ttp)
REVERT: A  197 THR cc_start: 0.7653 (m) cc_final: 0.7379 (t)
REVERT: A  231 GLU cc_start: 0.6892 (tt0) cc_final: 0.6544 (tt0)
REVERT: A  264 HIS cc_start: 0.7586 (m170) cc_final: 0.7300 (m170)
REVERT: A  383 GLN cc_start: 0.7963 (mt0) cc_final: 0.7684 (mm110)
REVERT: A  415 GLN cc_start: 0.7946 (mt0) cc_final: 0.7182 (pm20)
REVERT: A  596 LYS cc_start: 0.8126 (mptt) cc_final: 0.7876 (mttm)
REVERT: A  603 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6741 (tpt)
REVERT: A  732 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7272 (ttp80)
REVERT: A  736 LYS cc_start: 0.7866 (tppt) cc_final: 0.7467 (ttmm)
REVERT: A  765 GLU cc_start: 0.6759 (mp0) cc_final: 0.6333 (mp0)
REVERT: A  872 LYS cc_start: 0.8628 (mptt) cc_final: 0.8373 (mttp)
REVERT: A  956 MET cc_start: 0.7676 (tpp) cc_final: 0.7376 (tpp)
REVERT: A  958 LEU cc_start: 0.8526 (mm) cc_final: 0.8084 (mm)
REVERT: A  959 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7317 (tt0)
REVERT: A 1084 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7131 (tp30)
REVERT: A 1089 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7553 (mm)
REVERT: A 1104 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6894 (mm-30)
REVERT: A 1207 GLU cc_start: 0.7452 (pm20) cc_final: 0.6927 (mp0)
REVERT: A 1221 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6942 (mttt)
  outliers start: 31
  outliers final: 17
  residues processed: 294
  average time/residue: 0.1353
  time to fit residues: 54.7620
Evaluate side-chains
  296 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 270
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain I residue    6 THR
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   23 ASP
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  308 ASP
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  603 MET
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  643 VAL
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 1089 ILE
Chi-restraints excluded: chain A residue 1132 LYS
Chi-restraints excluded: chain A residue 1221 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 134 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   chunk 142 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0370
   chunk 115 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 GLN
A 290 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.162125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.138312 restraints weight = 19233.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.143046 restraints weight = 9146.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.146134 restraints weight = 5404.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.148040 restraints weight = 3716.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.149436 restraints weight = 2861.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12055  Z= 0.160
  Angle     :  0.668  11.174  16184  Z= 0.341
  Chirality :  0.042   0.169   1726
  Planarity :  0.004   0.051   2127
  Dihedral  :  7.154 140.328   1595
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.05 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.00 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.22), residues: 1441
  helix:  1.38 (0.17), residues: 855
  sheet: -1.45 (0.50), residues: 111
  loop : -0.72 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I  87 
 TYR   0.012   0.001   TYR A1082 
 PHE   0.031   0.002   PHE A1105 
 TRP   0.021   0.001   TRP A1253 
 HIS   0.004   0.001   HIS A 833 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (12055)
  covalent geometry    : angle       0.66810 (16184)
  hydrogen bonds       : bond        0.03878 (  670)
  hydrogen bonds       : angle       4.48315 ( 1965)

********************** 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
  302 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 273
  time to evaluate  : 0.489 
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: 0.6577 (pmm) cc_final: 0.6176 (pmm)
REVERT: B   83 GLU cc_start: 0.6936 (tp30) cc_final: 0.6523 (tp30)
REVERT: B  146 MET cc_start: 0.6670 (mmm) cc_final: 0.6310 (mmt)
REVERT: I   38 ARG cc_start: 0.6925 (ttm-80) cc_final: 0.6700 (ttm110)
REVERT: I   70 LEU cc_start: 0.8407 (tt) cc_final: 0.8126 (tt)
REVERT: I   73 MET cc_start: 0.6942 (tpt) cc_final: 0.6084 (tpt)
REVERT: I   77 MET cc_start: 0.7606 (ptp) cc_final: 0.6674 (ptp)
REVERT: I   92 VAL cc_start: 0.8366 (t) cc_final: 0.8134 (t)
REVERT: I  101 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6426 (mm)
REVERT: I  146 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6467 (mtm)
REVERT: A   23 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.6841 (t70)
REVERT: A   24 ILE cc_start: 0.7802 (mt) cc_final: 0.7413 (mt)
REVERT: A   56 LYS cc_start: 0.8288 (mppt) cc_final: 0.7973 (mmtm)
REVERT: A   61 ASP cc_start: 0.7118 (t70) cc_final: 0.6769 (t0)
REVERT: A   88 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7732 (t)
REVERT: A  132 ASP cc_start: 0.6407 (t70) cc_final: 0.5971 (t0)
REVERT: A  197 THR cc_start: 0.7705 (m) cc_final: 0.7484 (t)
REVERT: A  237 VAL cc_start: 0.8121 (t) cc_final: 0.7752 (p)
REVERT: A  264 HIS cc_start: 0.7590 (m170) cc_final: 0.7276 (m170)
REVERT: A  316 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.5837 (m-30)
REVERT: A  383 GLN cc_start: 0.7991 (mt0) cc_final: 0.7741 (mm110)
REVERT: A  387 ARG cc_start: 0.7662 (ptt180) cc_final: 0.7364 (ptt180)
REVERT: A  415 GLN cc_start: 0.7941 (mt0) cc_final: 0.7200 (pm20)
REVERT: A  580 ARG cc_start: 0.7106 (mtt-85) cc_final: 0.6817 (mtt180)
REVERT: A  596 LYS cc_start: 0.8104 (mptt) cc_final: 0.7868 (mttm)
REVERT: A  603 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6771 (tpt)
REVERT: A  714 LEU cc_start: 0.8264 (mt) cc_final: 0.8026 (mt)
REVERT: A  732 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7801 (ttp80)
REVERT: A  765 GLU cc_start: 0.6760 (mp0) cc_final: 0.6340 (mp0)
REVERT: A  872 LYS cc_start: 0.8619 (mptt) cc_final: 0.8357 (mttp)
REVERT: A  956 MET cc_start: 0.7658 (tpp) cc_final: 0.7414 (tpp)
REVERT: A  958 LEU cc_start: 0.8525 (mm) cc_final: 0.8058 (mm)
REVERT: A  959 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7372 (tt0)
REVERT: A 1084 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7137 (tp30)
REVERT: A 1104 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6986 (mm-30)
REVERT: A 1202 ILE cc_start: 0.8047 (tp) cc_final: 0.7620 (tt)
REVERT: A 1207 GLU cc_start: 0.7468 (pm20) cc_final: 0.6923 (mp0)
REVERT: A 1221 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6934 (mtmt)
  outliers start: 29
  outliers final: 17
  residues processed: 292
  average time/residue: 0.1414
  time to fit residues: 56.8432
Evaluate side-chains
  296 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 270
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain I residue    6 THR
Chi-restraints excluded: chain I residue   45 THR
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   23 ASP
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  308 ASP
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  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 1221 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 18 optimal weight:    0.0770
   chunk 9 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 106 optimal weight:    0.1980
   chunk 5 optimal weight:    0.5980
   chunk 122 optimal weight:    3.9990
   chunk 139 optimal weight:    0.0010
   chunk 129 optimal weight:    0.5980
   chunk 95 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.2944

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

Flipped N/Q/H residues before XYZ refinement:
I 108 HIS
A 176 GLN
A 290 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.161758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.138594 restraints weight = 18870.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.143145 restraints weight = 9035.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.146135 restraints weight = 5388.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.148087 restraints weight = 3704.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.149156 restraints weight = 2827.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6668
moved from start:          0.3209

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= 0.133
  Angle     :  0.660  10.752  16184  Z= 0.337
  Chirality :  0.042   0.188   1726
  Planarity :  0.004   0.051   2127
  Dihedral  :  6.918 133.798   1595
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.71 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 20.16 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.22), residues: 1441
  helix:  1.51 (0.17), residues: 855
  sheet: -1.34 (0.50), residues: 110
  loop : -0.68 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I  87 
 TYR   0.012   0.001   TYR A1082 
 PHE   0.030   0.002   PHE A1105 
 TRP   0.021   0.001   TRP A1253 
 HIS   0.021   0.001   HIS I 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12055)
  covalent geometry    : angle       0.66049 (16184)
  hydrogen bonds       : bond        0.03661 (  670)
  hydrogen bonds       : angle       4.40553 ( 1965)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2313.39 seconds
wall clock time: 40 minutes 56.54 seconds (2456.54 seconds total)