Starting phenix.real_space_refine
on Sat Aug 23 04:56:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c6q_45254/08_2025/9c6q_45254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c6q_45254/08_2025/9c6q_45254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2025/9c6q_45254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2025/9c6q_45254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2025/9c6q_45254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2025/9c6q_45254.cif"
  }
  resolution = 3.18
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      24      5.16       5
     C    6189      2.51       5
     N    1721      2.21       5
     O    1895      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 9841
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 241
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "C"
      Number of atoms: 9600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1190, 9600
          Classifications: {'peptide': 1190}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1155}
  Time building chain proxies: 2.60, per 1000 atoms: 0.26
  Number of scatterers: 9841
  At special positions: 0
  Unit cell: (90.3495, 106.531, 133.951, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      12     15.00
     O    1895      8.00
     N    1721      7.00
     C    6189      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: 1.15
  Conformation dependent library (CDL) restraints added in 396.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 10 sheets defined
      49.7% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 10
      removed outlier: 3.564A  pdb=" N   PHE C   8 " --> pdb=" O   ILE C   5 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR C   9 " --> pdb=" O   GLU C   6 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   HIS C  10 " --> pdb=" O   GLU C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 37
      removed outlier: 3.558A  pdb=" N   THR C  27 " --> pdb=" O   ASP C  23 " (cutoff:3.500A)
      Proline residue:  C  29  - end of helix
    Processing helix  chain 'C' and resid 55 through 78
      removed outlier: 3.565A  pdb=" N   ALA C  59 " --> pdb=" O   LYS C  55 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU C  75 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LYS C  76 " --> pdb=" O   ARG C  72 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   GLU C  77 " --> pdb=" O   SER C  73 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU C  78 " --> pdb=" O   GLU C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 111
    Processing helix  chain 'C' and resid 121 through 130
    Processing helix  chain 'C' and resid 137 through 143
      removed outlier: 3.777A  pdb=" N   LEU C 143 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 157
    Processing helix  chain 'C' and resid 162 through 178
      removed outlier: 3.827A  pdb=" N   GLN C 166 " --> pdb=" O   GLU C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 208
      removed outlier: 3.518A  pdb=" N   ASN C 198 " --> pdb=" O   TYR C 194 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE C 200 " --> pdb=" O   TYR C 196 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP C 201 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 227
      removed outlier: 3.691A  pdb=" N   ALA C 221 " --> pdb=" O   GLY C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 234
      removed outlier: 4.085A  pdb=" N   LYS C 231 " --> pdb=" O   LEU C 227 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ILE C 232 " --> pdb=" O   PRO C 228 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG C 233 " --> pdb=" O   GLY C 229 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASN C 234 " --> pdb=" O   GLU C 230 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 227 through 234'
    Processing helix  chain 'C' and resid 244 through 248
    Processing helix  chain 'C' and resid 259 through 263
    Processing helix  chain 'C' and resid 276 through 287
      removed outlier: 3.798A  pdb=" N   VAL C 280 " --> pdb=" O   LYS C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 304
      removed outlier: 3.508A  pdb=" N   PHE C 304 " --> pdb=" O   LEU C 300 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 321
    Processing helix  chain 'C' and resid 322 through 337
      removed outlier: 3.799A  pdb=" N   ASN C 335 " --> pdb=" O   GLU C 331 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   TRP C 336 " --> pdb=" O   PHE C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 401 through 433
      removed outlier: 3.508A  pdb=" N   PHE C 405 " --> pdb=" O   LEU C 401 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   MET C 420 " --> pdb=" O   PHE C 416 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ARG C 421 " --> pdb=" O   LEU C 417 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LYS C 422 " --> pdb=" O   GLY C 418 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY C 433 " --> pdb=" O   GLU C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 459
    Processing helix  chain 'C' and resid 461 through 463
      No H-bonds generated for 'chain 'C' and resid 461 through 463'
    Processing helix  chain 'C' and resid 464 through 471
      removed outlier: 3.840A  pdb=" N   GLU C 470 " --> pdb=" O   SER C 466 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   SER C 471 " --> pdb=" O   ALA C 467 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 524 through 536
      removed outlier: 3.863A  pdb=" N   GLY C 536 " --> pdb=" O   MET C 532 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 556 through 564
      removed outlier: 3.640A  pdb=" N   GLU C 562 " --> pdb=" O   LYS C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 572 through 587
    Processing helix  chain 'C' and resid 605 through 616
    Processing helix  chain 'C' and resid 621 through 629
    Processing helix  chain 'C' and resid 637 through 657
      removed outlier: 3.523A  pdb=" N   SER C 657 " --> pdb=" O   ALA C 653 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 672 through 674
      No H-bonds generated for 'chain 'C' and resid 672 through 674'
    Processing helix  chain 'C' and resid 675 through 693
    Processing helix  chain 'C' and resid 704 through 711
    Processing helix  chain 'C' and resid 713 through 723
      removed outlier: 3.698A  pdb=" N   SER C 717 " --> pdb=" O   TYR C 713 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU C 723 " --> pdb=" O   HIS C 719 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 734 through 738
      removed outlier: 3.532A  pdb=" N   ALA C 738 " --> pdb=" O   SER C 735 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 789 through 808
      removed outlier: 4.359A  pdb=" N   ASN C 793 " --> pdb=" O   SER C 789 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLN C 794 " --> pdb=" O   HIS C 790 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY C 808 " --> pdb=" O   LEU C 804 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 811 through 824
      removed outlier: 3.554A  pdb=" N   MET C 824 " --> pdb=" O   ARG C 820 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 827 through 836
    Processing helix  chain 'C' and resid 839 through 855
      removed outlier: 3.807A  pdb=" N   SER C 843 " --> pdb=" O   SER C 839 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 874 through 879
    Processing helix  chain 'C' and resid 891 through 901
      removed outlier: 3.619A  pdb=" N   SER C 901 " --> pdb=" O   ASN C 897 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 909 through 938
      removed outlier: 4.409A  pdb=" N   ARG C 913 " --> pdb=" O   ASP C 909 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   HIS C 938 " --> pdb=" O   VAL C 934 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 943 through 960
      removed outlier: 3.531A  pdb=" N   ILE C 947 " --> pdb=" O   SER C 943 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1000 through 1002
      No H-bonds generated for 'chain 'C' and resid 1000 through 1002'
    Processing helix  chain 'C' and resid 1009 through 1014
      removed outlier: 3.972A  pdb=" N   CYS C1013 " --> pdb=" O   SER C1009 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER C1014 " --> pdb=" O   GLU C1010 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1009 through 1014'
    Processing helix  chain 'C' and resid 1014 through 1020
      removed outlier: 3.900A  pdb=" N   LEU C1018 " --> pdb=" O   SER C1014 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1024 through 1032
    Processing helix  chain 'C' and resid 1045 through 1052
      removed outlier: 3.799A  pdb=" N   THR C1050 " --> pdb=" O   PRO C1046 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ASN C1051 " --> pdb=" O   ILE C1047 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE C1052 " --> pdb=" O   MET C1048 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1052 through 1067
      removed outlier: 3.584A  pdb=" N   ALA C1061 " --> pdb=" O   LEU C1057 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1112 through 1127
      removed outlier: 4.536A  pdb=" N   SER C1116 " --> pdb=" O   SER C1112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1176 through 1187
      removed outlier: 3.649A  pdb=" N   VAL C1180 " --> pdb=" O   ASN C1176 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 48
      removed outlier: 3.723A  pdb=" N   ALA C  43 " --> pdb=" O   ALA C 537 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE C 539 " --> pdb=" O   ALA C  43 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA C 267 " --> pdb=" O   VAL C 538 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   LEU C 540 " --> pdb=" O   ALA C 267 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU C 269 " --> pdb=" O   LEU C 540 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   ILE C 542 " --> pdb=" O   LEU C 269 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE C 271 " --> pdb=" O   ILE C 542 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LEU C  87 " --> pdb=" O   VAL C 268 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   ILE C 270 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 91 through 92
      removed outlier: 3.833A  pdb=" N   THR C  92 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 251 through 252
    Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292
      removed outlier: 3.720A  pdb=" N   LEU C 521 " --> pdb=" O   LEU C 499 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL C 354 " --> pdb=" O   VAL C 504 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 342 through 344
      removed outlier: 3.844A  pdb=" N   LYS C 382 " --> pdb=" O   ASP C 377 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASP C 377 " --> pdb=" O   LYS C 382 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU C 384 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 595 through 601
      removed outlier: 6.811A  pdb=" N   VAL C 595 " --> pdb=" O   ILE C 866 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   LEU C 868 " --> pdb=" O   VAL C 595 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR C 597 " --> pdb=" O   LEU C 868 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   VAL C 870 " --> pdb=" O   THR C 597 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   LYS C 599 " --> pdb=" O   VAL C 870 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   SER C 773 " --> pdb=" O   TYR C 662 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER C 731 " --> pdb=" O   SER C 665 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 744 through 745
      removed outlier: 3.628A  pdb=" N   TYR C 744 " --> pdb=" O   SER C 769 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 974 through 975
    Processing sheet with id=AA9, first strand: chain 'C' and resid 997 through 998
    Processing sheet with id=AB1, first strand: chain 'C' and resid 1072 through 1074
      removed outlier: 3.797A  pdb=" N   THR C1072 " --> pdb=" O   ILE C1089 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE C1089 " --> pdb=" O   THR C1072 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASN C1086 " --> pdb=" O   LEU C1099 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU C1099 " --> pdb=" O   ASN C1086 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   PHE C1131 " --> pdb=" O   ILE C1162 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   ILE C1164 " --> pdb=" O   PHE C1131 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   TYR C1133 " --> pdb=" O   ILE C1164 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLU C1163 " --> pdb=" O   ARG C1145 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ARG C1145 " --> pdb=" O   GLU C1163 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1182 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: 1.80

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2047
        1.33 -     1.45: 2395
        1.45 -     1.57: 5558
        1.57 -     1.69: 23
        1.69 -     1.81: 39
  Bond restraints: 10062
  Sorted by residual:
  bond pdb=" C   GLU C 465 "
       pdb=" N   SER C 466 "
    ideal  model  delta    sigma   weight residual
    1.335  1.697 -0.362 1.38e-02 5.25e+03 6.88e+02
  bond pdb=" C   LEU C 456 "
       pdb=" N   THR C 457 "
    ideal  model  delta    sigma   weight residual
    1.334  1.525 -0.191 1.41e-02 5.03e+03 1.84e+02
  bond pdb=" N   GLU C 463 "
       pdb=" CA  GLU C 463 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.23e+00
  bond pdb=" N   PHE C 459 "
       pdb=" CA  PHE C 459 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.26e-02 6.30e+03 6.10e+00
  bond pdb=" N   HIS C 458 "
       pdb=" CA  HIS C 458 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.20e-02 6.94e+03 5.28e+00
  ... (remaining 10057 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.41: 13621
        4.41 -     8.82: 24
        8.82 -    13.22: 1
       13.22 -    17.63: 2
       17.63 -    22.04: 1
  Bond angle restraints: 13649
  Sorted by residual:
  angle pdb=" CA  LEU C 456 "
        pdb=" C   LEU C 456 "
        pdb=" N   THR C 457 "
      ideal   model   delta    sigma   weight residual
     118.14   96.10   22.04 1.31e+00 5.83e-01 2.83e+02
  angle pdb=" O   LEU C 456 "
        pdb=" C   LEU C 456 "
        pdb=" N   THR C 457 "
      ideal   model   delta    sigma   weight residual
     122.43  138.64  -16.21 1.34e+00 5.57e-01 1.46e+02
  angle pdb=" C   LEU C 456 "
        pdb=" N   THR C 457 "
        pdb=" CA  THR C 457 "
      ideal   model   delta    sigma   weight residual
     120.71  103.17   17.54 1.67e+00 3.59e-01 1.10e+02
  angle pdb=" C   PHE C 999 "
        pdb=" CA  PHE C 999 "
        pdb=" CB  PHE C 999 "
      ideal   model   delta    sigma   weight residual
     116.63  110.70    5.93 1.16e+00 7.43e-01 2.61e+01
  angle pdb=" C   LYS C 590 "
        pdb=" N   ASP C 591 "
        pdb=" CA  ASP C 591 "
      ideal   model   delta    sigma   weight residual
     122.09  129.84   -7.75 1.86e+00 2.89e-01 1.73e+01
  ... (remaining 13644 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 5277
       16.85 -    33.71: 577
       33.71 -    50.56: 139
       50.56 -    67.42: 38
       67.42 -    84.27: 16
  Dihedral angle restraints: 6047
    sinusoidal: 2551
      harmonic: 3496
  Sorted by residual:
  dihedral pdb=" CA  ILE C 294 "
           pdb=" C   ILE C 294 "
           pdb=" N   TRP C 295 "
           pdb=" CA  TRP C 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.35   29.65     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  THR C 780 "
           pdb=" C   THR C 780 "
           pdb=" N   GLN C 781 "
           pdb=" CA  GLN C 781 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.04  -28.96     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  PHE C 459 "
           pdb=" C   PHE C 459 "
           pdb=" N   ASN C 460 "
           pdb=" CA  ASN C 460 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.69   25.31     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 6044 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1164
       0.044 -    0.089: 257
       0.089 -    0.133: 74
       0.133 -    0.178: 6
       0.178 -    0.222: 1
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" CA  VAL C 354 "
            pdb=" N   VAL C 354 "
            pdb=" C   VAL C 354 "
            pdb=" CB  VAL C 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  THR C  80 "
            pdb=" CA  THR C  80 "
            pdb=" OG1 THR C  80 "
            pdb=" CG2 THR C  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CA  LEU C 356 "
            pdb=" N   LEU C 356 "
            pdb=" C   LEU C 356 "
            pdb=" CB  LEU C 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.82e-01
  ... (remaining 1499 not shown)

  Planarity restraints: 1736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 456 "    0.029 2.00e-02 2.50e+03   7.35e-02 5.41e+01
        pdb=" C   LEU C 456 "   -0.126 2.00e-02 2.50e+03
        pdb=" O   LEU C 456 "    0.057 2.00e-02 2.50e+03
        pdb=" N   THR C 457 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 473 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.82e+00
        pdb=" CG  ASP C 473 "    0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 473 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 473 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 181 "    0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO C 182 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C 182 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 182 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1733 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 175
        2.69 -     3.24: 9101
        3.24 -     3.80: 13587
        3.80 -     4.35: 17694
        4.35 -     4.90: 30147
  Nonbonded interactions: 70704
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C 465 "
            pdb=" OH  TYR C 469 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OH  TYR C 733 "
            pdb=" O   GLU C 777 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" O   CYS C1013 "
            pdb=" OH  TYR C1103 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" N   LEU C 456 "
            pdb=" N   THR C 457 "
     model   vdw
     2.265 2.560
  nonbonded pdb=" O   TYR C 662 "
            pdb=" OG  SER C 773 "
     model   vdw
     2.269 3.040
  ... (remaining 70699 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             18.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.570
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
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      :  0.005   0.362  10062  Z= 0.325
  Angle     :  0.637  22.041  13649  Z= 0.369
  Chirality :  0.040   0.222   1502
  Planarity :  0.004   0.074   1736
  Dihedral  : 15.428  84.274   3783
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.57 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.00 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -0.07 (0.25), residues: 1188
  helix:  1.92 (0.24), residues: 524
  sheet: -0.03 (0.49), residues: 120
  loop : -2.18 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1145 
 TYR   0.027   0.001   TYR C 469 
 PHE   0.019   0.001   PHE C   8 
 TRP   0.021   0.002   TRP C 428 
 HIS   0.005   0.001   HIS C 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (10062)
  covalent geometry    : angle       0.63723 (13649)
  hydrogen bonds       : bond        0.18526 (  410)
  hydrogen bonds       : angle       5.83313 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 177
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
REVERT: C  119 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6978 (ttt-90)
REVERT: C  422 LYS cc_start: 0.5476 (mtmm) cc_final: 0.4753 (mmtt)
REVERT: C  517 LYS cc_start: 0.7411 (mmmt) cc_final: 0.6812 (mmtm)
REVERT: C  599 LYS cc_start: 0.7392 (ttmm) cc_final: 0.7076 (tptt)
REVERT: C  948 GLN cc_start: 0.7513 (tp40) cc_final: 0.7221 (mm-40)
REVERT: C  952 ASP cc_start: 0.7998 (m-30) cc_final: 0.7730 (m-30)
REVERT: C 1022 GLN cc_start: 0.5712 (pt0) cc_final: 0.5332 (pm20)
  outliers start: 2
  outliers final: 1
  residues processed: 179
  average time/residue: 0.1304
  time to fit residues: 31.1399
Evaluate side-chains
  94 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C  37 ASN
C  70 GLN
C 335 ASN
C 364 HIS
C 383 ASN
C 462 GLN
C 575 GLN
C 668 ASN
C 951 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.216261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.173271 restraints weight = 10951.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.93
r_work: 0.3550 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10062  Z= 0.129
  Angle     :  0.560   8.008  13649  Z= 0.297
  Chirality :  0.041   0.137   1502
  Planarity :  0.004   0.068   1736
  Dihedral  :  9.402  77.453   1437
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  :  5.41 %
    Favored  : 92.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.03 (0.25), residues: 1188
  helix:  1.89 (0.23), residues: 536
  sheet:  0.32 (0.49), residues: 114
  loop : -2.24 (0.24), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 587 
 TYR   0.017   0.002   TYR C 127 
 PHE   0.019   0.002   PHE C  62 
 TRP   0.018   0.002   TRP C 643 
 HIS   0.007   0.001   HIS C 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10062)
  covalent geometry    : angle       0.56019 (13649)
  hydrogen bonds       : bond        0.04312 (  410)
  hydrogen bonds       : angle       3.91660 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: C   51 THR cc_start: 0.7216 (p) cc_final: 0.6913 (p)
REVERT: C  517 LYS cc_start: 0.7452 (mmmt) cc_final: 0.6735 (mmtm)
REVERT: C  540 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7895 (mp)
REVERT: C  599 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7639 (tttp)
REVERT: C  661 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6553 (mmm-85)
REVERT: C  708 MET cc_start: 0.8102 (mtt) cc_final: 0.7514 (mtt)
REVERT: C  882 SER cc_start: 0.7489 (p) cc_final: 0.7004 (t)
REVERT: C  931 LYS cc_start: 0.7434 (tppt) cc_final: 0.6867 (ttpt)
REVERT: C  952 ASP cc_start: 0.8401 (m-30) cc_final: 0.8150 (m-30)
REVERT: C  954 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6973 (mtt180)
REVERT: C 1022 GLN cc_start: 0.5935 (pt0) cc_final: 0.5341 (pm20)
  outliers start: 22
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1224
  time to fit residues: 17.8715
Evaluate side-chains
  99 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  222 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  597 THR
Chi-restraints excluded: chain C residue  628 HIS
Chi-restraints excluded: chain C residue  774 ILE
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue 1080 ILE
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1180 VAL
Chi-restraints excluded: chain C residue 1183 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 89 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
C 370 HIS
C 836 HIS
C 951 GLN
C1042 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.207614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.165398 restraints weight = 11111.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.90
r_work: 0.3438 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10062  Z= 0.145
  Angle     :  0.569   8.509  13649  Z= 0.301
  Chirality :  0.040   0.140   1502
  Planarity :  0.004   0.039   1736
  Dihedral  :  9.304  75.640   1434
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.45 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -0.16 (0.24), residues: 1188
  helix:  1.76 (0.23), residues: 536
  sheet:  0.33 (0.48), residues: 114
  loop : -2.29 (0.24), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C1001 
 TYR   0.014   0.002   TYR C 127 
 PHE   0.029   0.002   PHE C 916 
 TRP   0.021   0.001   TRP C1027 
 HIS   0.005   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10062)
  covalent geometry    : angle       0.56893 (13649)
  hydrogen bonds       : bond        0.06154 (  410)
  hydrogen bonds       : angle       4.08487 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.393 
Fit side-chains
REVERT: C   51 THR cc_start: 0.7500 (p) cc_final: 0.7219 (p)
REVERT: C  230 GLU cc_start: 0.7830 (tp30) cc_final: 0.7316 (tm-30)
REVERT: C  517 LYS cc_start: 0.7355 (mmmt) cc_final: 0.6397 (tmtt)
REVERT: C  521 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7762 (mp)
REVERT: C  540 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: C  599 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7928 (tttm)
REVERT: C  708 MET cc_start: 0.8115 (mtt) cc_final: 0.7749 (mtt)
REVERT: C  931 LYS cc_start: 0.7775 (tppt) cc_final: 0.7195 (ttpt)
REVERT: C  952 ASP cc_start: 0.8455 (m-30) cc_final: 0.8129 (m-30)
REVERT: C  954 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7386 (mtt90)
REVERT: C 1022 GLN cc_start: 0.6593 (pt0) cc_final: 0.5663 (pm20)
REVERT: C 1029 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7871 (mp0)
  outliers start: 20
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1143
  time to fit residues: 16.9051
Evaluate side-chains
  88 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue  521 LEU
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  597 THR
Chi-restraints excluded: chain C residue  628 HIS
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  893 VAL
Chi-restraints excluded: chain C residue 1029 GLU
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1161 VAL
Chi-restraints excluded: chain C residue 1180 VAL
Chi-restraints excluded: chain C residue 1183 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   chunk 93 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 98 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
C 668 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.209342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.170035 restraints weight = 11056.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 2.89
r_work: 0.3436 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10062  Z= 0.109
  Angle     :  0.495   9.790  13649  Z= 0.260
  Chirality :  0.038   0.134   1502
  Planarity :  0.003   0.038   1736
  Dihedral  :  9.019  75.314   1434
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.02 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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:  0.08 (0.25), residues: 1188
  helix:  2.06 (0.23), residues: 534
  sheet:  0.36 (0.47), residues: 114
  loop : -2.24 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 587 
 TYR   0.010   0.001   TYR C 892 
 PHE   0.012   0.001   PHE C 607 
 TRP   0.020   0.001   TRP C 643 
 HIS   0.004   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10062)
  covalent geometry    : angle       0.49501 (13649)
  hydrogen bonds       : bond        0.04304 (  410)
  hydrogen bonds       : angle       3.75482 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.381 
Fit side-chains
REVERT: C   51 THR cc_start: 0.7563 (p) cc_final: 0.7266 (p)
REVERT: C  230 GLU cc_start: 0.7847 (tp30) cc_final: 0.7484 (tm-30)
REVERT: C  599 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7984 (tttm)
REVERT: C  697 THR cc_start: 0.8260 (p) cc_final: 0.7734 (m)
REVERT: C  708 MET cc_start: 0.8085 (mtt) cc_final: 0.7678 (mtt)
REVERT: C  931 LYS cc_start: 0.7797 (tppt) cc_final: 0.7244 (tttt)
REVERT: C  952 ASP cc_start: 0.8537 (m-30) cc_final: 0.8228 (m-30)
REVERT: C 1022 GLN cc_start: 0.6739 (pt0) cc_final: 0.5683 (pm20)
REVERT: C 1029 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7877 (mp0)
  outliers start: 14
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1028
  time to fit residues: 12.9383
Evaluate side-chains
  79 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  597 THR
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue 1029 GLU
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1183 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 111 optimal weight:    0.4980
   chunk 73 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 85 optimal weight:    0.4980
   chunk 75 optimal weight:    5.9990
   chunk 118 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
C 623 HIS
C 951 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.203679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.158514 restraints weight = 11128.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 3.34
r_work: 0.3328 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.5379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10062  Z= 0.161
  Angle     :  0.579   8.972  13649  Z= 0.304
  Chirality :  0.041   0.201   1502
  Planarity :  0.004   0.043   1736
  Dihedral  :  9.410  72.647   1434
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.54 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.25), residues: 1188
  helix:  1.85 (0.23), residues: 533
  sheet:  0.32 (0.46), residues: 123
  loop : -2.37 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C1145 
 TYR   0.015   0.002   TYR C 892 
 PHE   0.022   0.002   PHE C 607 
 TRP   0.021   0.002   TRP C 428 
 HIS   0.005   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10062)
  covalent geometry    : angle       0.57867 (13649)
  hydrogen bonds       : bond        0.06217 (  410)
  hydrogen bonds       : angle       4.05510 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.256 
Fit side-chains
REVERT: C    1 MET cc_start: 0.1590 (ppp) cc_final: 0.0984 (ppp)
REVERT: C   51 THR cc_start: 0.7652 (p) cc_final: 0.7363 (p)
REVERT: C  517 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6330 (tmtt)
REVERT: C  521 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7717 (mp)
REVERT: C  540 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8049 (mp)
REVERT: C  599 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8179 (tttm)
REVERT: C  683 GLN cc_start: 0.7236 (mt0) cc_final: 0.6911 (tp-100)
REVERT: C  697 THR cc_start: 0.8438 (p) cc_final: 0.8148 (m)
REVERT: C  931 LYS cc_start: 0.7901 (tppt) cc_final: 0.7238 (ttpt)
REVERT: C  952 ASP cc_start: 0.8525 (m-30) cc_final: 0.8145 (m-30)
REVERT: C 1029 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7847 (mp0)
  outliers start: 19
  outliers final: 12
  residues processed: 97
  average time/residue: 0.0870
  time to fit residues: 12.3091
Evaluate side-chains
  93 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  403 THR
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  521 LEU
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  562 GLU
Chi-restraints excluded: chain C residue  597 THR
Chi-restraints excluded: chain C residue  724 LEU
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue 1029 GLU
Chi-restraints excluded: chain C residue 1042 ASN
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1175 THR
Chi-restraints excluded: chain C residue 1180 VAL
Chi-restraints excluded: chain C residue 1183 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 116 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0970
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
C 668 ASN
C 951 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.206674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.162712 restraints weight = 11223.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 3.21
r_work: 0.3401 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.5552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10062  Z= 0.108
  Angle     :  0.488   9.651  13649  Z= 0.258
  Chirality :  0.038   0.135   1502
  Planarity :  0.004   0.072   1736
  Dihedral  :  9.022  72.282   1434
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.58 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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:  0.11 (0.25), residues: 1188
  helix:  2.11 (0.23), residues: 535
  sheet:  0.33 (0.48), residues: 116
  loop : -2.27 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 587 
 TYR   0.010   0.001   TYR C 744 
 PHE   0.012   0.001   PHE C 416 
 TRP   0.021   0.001   TRP C 428 
 HIS   0.004   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (10062)
  covalent geometry    : angle       0.48818 (13649)
  hydrogen bonds       : bond        0.04324 (  410)
  hydrogen bonds       : angle       3.73015 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.354 
Fit side-chains
REVERT: C    1 MET cc_start: 0.1525 (ppp) cc_final: 0.1215 (ppp)
REVERT: C   51 THR cc_start: 0.7642 (p) cc_final: 0.7303 (p)
REVERT: C  123 GLU cc_start: 0.6768 (tp30) cc_final: 0.6188 (mp0)
REVERT: C  230 GLU cc_start: 0.7794 (tp30) cc_final: 0.7503 (tm-30)
REVERT: C  599 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8131 (tttm)
REVERT: C  697 THR cc_start: 0.8375 (p) cc_final: 0.8053 (m)
REVERT: C  931 LYS cc_start: 0.7843 (tppt) cc_final: 0.7228 (ttpt)
REVERT: C  952 ASP cc_start: 0.8499 (m-30) cc_final: 0.8117 (m-30)
REVERT: C 1029 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7777 (mp0)
REVERT: C 1145 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.6493 (mtt180)
  outliers start: 19
  outliers final: 10
  residues processed: 98
  average time/residue: 0.0892
  time to fit residues: 12.5855
Evaluate side-chains
  84 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  403 THR
Chi-restraints excluded: chain C residue  424 VAL
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  597 THR
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue 1029 GLU
Chi-restraints excluded: chain C residue 1129 SER
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1161 VAL
Chi-restraints excluded: chain C residue 1183 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0270
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    2.0044

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

Flipped N/Q/H residues before XYZ refinement:
C 951 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.202515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.157580 restraints weight = 11185.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 3.21
r_work: 0.3353 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.5940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10062  Z= 0.172
  Angle     :  0.587  11.616  13649  Z= 0.306
  Chirality :  0.041   0.143   1502
  Planarity :  0.004   0.058   1736
  Dihedral  :  9.351  72.305   1434
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.34 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.11 (0.24), residues: 1188
  helix:  1.94 (0.23), residues: 533
  sheet:  0.28 (0.48), residues: 114
  loop : -2.39 (0.23), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C1001 
 TYR   0.015   0.002   TYR C 258 
 PHE   0.017   0.002   PHE C 607 
 TRP   0.024   0.002   TRP C 428 
 HIS   0.005   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (10062)
  covalent geometry    : angle       0.58733 (13649)
  hydrogen bonds       : bond        0.06227 (  410)
  hydrogen bonds       : angle       4.02243 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.369 
Fit side-chains
REVERT: C    1 MET cc_start: 0.1591 (ppp) cc_final: 0.0877 (ppp)
REVERT: C   51 THR cc_start: 0.7681 (p) cc_final: 0.7352 (p)
REVERT: C  517 LYS cc_start: 0.7328 (mmmt) cc_final: 0.6450 (tmtt)
REVERT: C  521 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7647 (mp)
REVERT: C  599 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8211 (tttm)
REVERT: C  697 THR cc_start: 0.8458 (p) cc_final: 0.8247 (m)
REVERT: C  754 SER cc_start: 0.7208 (p) cc_final: 0.6757 (p)
REVERT: C  931 LYS cc_start: 0.7953 (tppt) cc_final: 0.7326 (tttt)
REVERT: C  952 ASP cc_start: 0.8545 (m-30) cc_final: 0.8164 (m-30)
REVERT: C  989 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7866 (mt)
REVERT: C 1145 ARG cc_start: 0.7019 (mtm-85) cc_final: 0.6798 (mtt180)
REVERT: C 1182 GLU cc_start: 0.6818 (tp30) cc_final: 0.6606 (tp30)
  outliers start: 21
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0997
  time to fit residues: 13.9447
Evaluate side-chains
  92 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue  403 THR
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  521 LEU
Chi-restraints excluded: chain C residue  562 GLU
Chi-restraints excluded: chain C residue  597 THR
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  896 VAL
Chi-restraints excluded: chain C residue  989 LEU
Chi-restraints excluded: chain C residue 1129 SER
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1161 VAL
Chi-restraints excluded: chain C residue 1175 THR
Chi-restraints excluded: chain C residue 1176 ASN
Chi-restraints excluded: chain C residue 1183 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 119 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0870
   chunk 43 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.3962

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

Flipped N/Q/H residues before XYZ refinement:
C 951 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.203383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.158652 restraints weight = 11139.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 3.02
r_work: 0.3390 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.6138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10062  Z= 0.132
  Angle     :  0.533  11.496  13649  Z= 0.277
  Chirality :  0.039   0.171   1502
  Planarity :  0.004   0.050   1736
  Dihedral  :  9.103  70.183   1434
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.91 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.01 (0.25), residues: 1188
  helix:  2.08 (0.23), residues: 532
  sheet:  0.71 (0.52), residues: 96
  loop : -2.37 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 669 
 TYR   0.012   0.001   TYR C 258 
 PHE   0.014   0.001   PHE C 607 
 TRP   0.027   0.002   TRP C 428 
 HIS   0.005   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10062)
  covalent geometry    : angle       0.53310 (13649)
  hydrogen bonds       : bond        0.05071 (  410)
  hydrogen bonds       : angle       3.82685 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.417 
Fit side-chains
REVERT: C    1 MET cc_start: 0.1436 (ppp) cc_final: 0.0679 (ppp)
REVERT: C   51 THR cc_start: 0.7666 (p) cc_final: 0.7345 (p)
REVERT: C  123 GLU cc_start: 0.6695 (tp30) cc_final: 0.6143 (mp0)
REVERT: C  517 LYS cc_start: 0.7290 (mmmt) cc_final: 0.6419 (tmtt)
REVERT: C  521 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7503 (mp)
REVERT: C  540 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7976 (mp)
REVERT: C  599 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8169 (tttm)
REVERT: C  697 THR cc_start: 0.8422 (p) cc_final: 0.8204 (m)
REVERT: C  931 LYS cc_start: 0.7915 (tppt) cc_final: 0.7297 (ttpt)
REVERT: C  952 ASP cc_start: 0.8495 (m-30) cc_final: 0.8112 (m-30)
REVERT: C  989 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7829 (mt)
REVERT: C 1145 ARG cc_start: 0.6987 (mtm-85) cc_final: 0.6779 (mtt180)
REVERT: C 1182 GLU cc_start: 0.6800 (tp30) cc_final: 0.6586 (tp30)
  outliers start: 16
  outliers final: 11
  residues processed: 93
  average time/residue: 0.1005
  time to fit residues: 13.7077
Evaluate side-chains
  86 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  403 THR
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  521 LEU
Chi-restraints excluded: chain C residue  540 LEU
Chi-restraints excluded: chain C residue  562 GLU
Chi-restraints excluded: chain C residue  597 THR
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  989 LEU
Chi-restraints excluded: chain C residue 1129 SER
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1161 VAL
Chi-restraints excluded: chain C residue 1176 ASN
Chi-restraints excluded: chain C residue 1183 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0670
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.7318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.205513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.163794 restraints weight = 11118.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 3.13
r_work: 0.3376 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.6232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.057  10062  Z= 0.105
  Angle     :  0.498  11.982  13649  Z= 0.259
  Chirality :  0.038   0.141   1502
  Planarity :  0.003   0.045   1736
  Dihedral  :  8.781  69.301   1434
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.19 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.19 (0.25), residues: 1188
  helix:  2.26 (0.23), residues: 535
  sheet:  0.63 (0.51), residues: 104
  loop : -2.34 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 587 
 TYR   0.009   0.001   TYR C1133 
 PHE   0.010   0.001   PHE C 362 
 TRP   0.022   0.001   TRP C 643 
 HIS   0.003   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10062)
  covalent geometry    : angle       0.49768 (13649)
  hydrogen bonds       : bond        0.04114 (  410)
  hydrogen bonds       : angle       3.60427 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.412 
Fit side-chains
REVERT: C    1 MET cc_start: 0.1464 (ppp) cc_final: 0.0758 (ppp)
REVERT: C   51 THR cc_start: 0.7657 (p) cc_final: 0.7357 (p)
REVERT: C  123 GLU cc_start: 0.6616 (tp30) cc_final: 0.6089 (mp0)
REVERT: C  230 GLU cc_start: 0.7711 (tp30) cc_final: 0.7470 (tm-30)
REVERT: C  521 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7346 (mp)
REVERT: C  599 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8196 (tttm)
REVERT: C  697 THR cc_start: 0.8386 (p) cc_final: 0.8139 (m)
REVERT: C  931 LYS cc_start: 0.7873 (tppt) cc_final: 0.7236 (ttpt)
REVERT: C  952 ASP cc_start: 0.8455 (m-30) cc_final: 0.8068 (m-30)
REVERT: C 1145 ARG cc_start: 0.6869 (mtm-85) cc_final: 0.6664 (mtt180)
REVERT: C 1182 GLU cc_start: 0.6771 (tp30) cc_final: 0.6566 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0953
  time to fit residues: 12.1829
Evaluate side-chains
  80 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  403 THR
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  521 LEU
Chi-restraints excluded: chain C residue  562 GLU
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1161 VAL
Chi-restraints excluded: chain C residue 1176 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 111 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.200317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.155866 restraints weight = 11062.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 3.15
r_work: 0.3290 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.6419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10062  Z= 0.165
  Angle     :  0.586  13.290  13649  Z= 0.303
  Chirality :  0.041   0.135   1502
  Planarity :  0.004   0.043   1736
  Dihedral  :  9.066  71.173   1434
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.10 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.03 (0.25), residues: 1188
  helix:  2.04 (0.23), residues: 534
  sheet:  0.56 (0.50), residues: 102
  loop : -2.40 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 669 
 TYR   0.014   0.002   TYR C 258 
 PHE   0.015   0.002   PHE C 869 
 TRP   0.030   0.002   TRP C 428 
 HIS   0.006   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10062)
  covalent geometry    : angle       0.58552 (13649)
  hydrogen bonds       : bond        0.06004 (  410)
  hydrogen bonds       : angle       3.92981 ( 1182)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.425 
Fit side-chains
REVERT: C    1 MET cc_start: 0.1293 (ppp) cc_final: 0.0541 (ppp)
REVERT: C   51 THR cc_start: 0.7730 (p) cc_final: 0.7432 (p)
REVERT: C  123 GLU cc_start: 0.6632 (tp30) cc_final: 0.6063 (mp0)
REVERT: C  225 THR cc_start: 0.6804 (m) cc_final: 0.6594 (p)
REVERT: C  517 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6444 (tmtt)
REVERT: C  521 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7624 (mp)
REVERT: C  599 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8226 (tttm)
REVERT: C  697 THR cc_start: 0.8484 (p) cc_final: 0.8268 (m)
REVERT: C  931 LYS cc_start: 0.7972 (tppt) cc_final: 0.7285 (ttpt)
REVERT: C  952 ASP cc_start: 0.8536 (m-30) cc_final: 0.8156 (m-30)
REVERT: C 1131 PHE cc_start: 0.8251 (m-80) cc_final: 0.7842 (m-80)
REVERT: C 1182 GLU cc_start: 0.6795 (tp30) cc_final: 0.6575 (tp30)
  outliers start: 13
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0979
  time to fit residues: 13.0134
Evaluate side-chains
  88 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  403 THR
Chi-restraints excluded: chain C residue  424 VAL
Chi-restraints excluded: chain C residue  490 SER
Chi-restraints excluded: chain C residue  521 LEU
Chi-restraints excluded: chain C residue  562 GLU
Chi-restraints excluded: chain C residue  785 SER
Chi-restraints excluded: chain C residue  878 LEU
Chi-restraints excluded: chain C residue  896 VAL
Chi-restraints excluded: chain C residue 1129 SER
Chi-restraints excluded: chain C residue 1144 ILE
Chi-restraints excluded: chain C residue 1161 VAL
Chi-restraints excluded: chain C residue 1175 THR
Chi-restraints excluded: chain C residue 1176 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0010
   chunk 108 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 112 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 102 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.205114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.158326 restraints weight = 11180.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 3.53
r_work: 0.3383 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.6442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10062  Z= 0.100
  Angle     :  0.497  12.256  13649  Z= 0.259
  Chirality :  0.038   0.140   1502
  Planarity :  0.003   0.041   1736
  Dihedral  :  8.758  68.325   1434
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.38 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.24 (0.25), residues: 1188
  helix:  2.31 (0.23), residues: 533
  sheet:  0.64 (0.50), residues: 104
  loop : -2.31 (0.23), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 587 
 TYR   0.009   0.001   TYR C1133 
 PHE   0.009   0.001   PHE C 362 
 TRP   0.032   0.001   TRP C 428 
 HIS   0.003   0.001   HIS C 496 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (10062)
  covalent geometry    : angle       0.49667 (13649)
  hydrogen bonds       : bond        0.04046 (  410)
  hydrogen bonds       : angle       3.60886 ( 1182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3072.24 seconds
wall clock time: 53 minutes 16.17 seconds (3196.17 seconds total)