Starting phenix.real_space_refine
on Wed Sep 17 14:19:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kk6_62383/09_2025/9kk6_62383.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kk6_62383/09_2025/9kk6_62383.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kk6_62383/09_2025/9kk6_62383.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kk6_62383/09_2025/9kk6_62383.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kk6_62383/09_2025/9kk6_62383.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kk6_62383/09_2025/9kk6_62383.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     V       2      8.30       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      37      5.16       5
     C    5792      2.51       5
     N    1533      2.21       5
     O    1696      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9066
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1170, 9000
          Classifications: {'peptide': 1170}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 1140}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 66
          Unusual residues: {' MG': 2, 'ADP': 2, 'VO4': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 2.11, per 1000 atoms: 0.23
  Number of scatterers: 9066
  At special positions: 0
  Unit cell: (78.66, 80.37, 141.075, 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)
     V       2     22.97
     S      37     16.00
     P       4     15.00
     Mg      2     11.99
     O    1696      8.00
     N    1533      7.00
     C    5792      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: 0.86
  Conformation dependent library (CDL) restraints added in 366.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      70.6% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 30
    Processing helix  chain 'A' and resid 34 through 67
      removed outlier: 4.568A  pdb=" N   MET A  55 " --> pdb=" O   HIS A  51 " (cutoff:3.500A)
      Proline residue:  A  56  - end of helix
      removed outlier: 4.305A  pdb=" N   GLN A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   MET A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.905A  pdb=" N   ASN A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 128
      removed outlier: 3.758A  pdb=" N   MET A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   HIS A  81 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 103 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 138
      removed outlier: 3.804A  pdb=" N   PHE A 135 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR A 137 " --> pdb=" O   GLY A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 159
      removed outlier: 3.518A  pdb=" N   ASP A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   THR A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU A 153 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 184
      removed outlier: 4.174A  pdb=" N   GLY A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 194
      removed outlier: 3.967A  pdb=" N   ALA A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 233
      removed outlier: 4.213A  pdb=" N   ILE A 198 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN A 233 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 242 through 254
      removed outlier: 3.570A  pdb=" N   ILE A 254 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 297
      removed outlier: 4.400A  pdb=" N   LYS A 259 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 344
      removed outlier: 4.700A  pdb=" N   SER A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ASN A 324 " --> pdb=" O   GLN A 320 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE A 341 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN A 344 " --> pdb=" O   GLU A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 414
      removed outlier: 4.078A  pdb=" N   VAL A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 442
    Processing helix  chain 'A' and resid 456 through 463
    Processing helix  chain 'A' and resid 469 through 480
    Processing helix  chain 'A' and resid 482 through 488
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 3.641A  pdb=" N   GLY A 501 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 521
      removed outlier: 3.615A  pdb=" N   LYS A 520 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 550
    Processing helix  chain 'A' and resid 584 through 592
      removed outlier: 3.761A  pdb=" N   LYS A 591 " --> pdb=" O   GLU A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 607
      removed outlier: 3.531A  pdb=" N   LEU A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 679
    Processing helix  chain 'A' and resid 683 through 718
      removed outlier: 3.658A  pdb=" N   SER A 687 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 700 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLY A 701 " --> pdb=" O   SER A 697 " (cutoff:3.500A)
      Proline residue:  A 702  - end of helix
      removed outlier: 4.225A  pdb=" N   ALA A 705 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 774
    Processing helix  chain 'A' and resid 775 through 780
      removed outlier: 3.933A  pdb=" N   PHE A 779 " --> pdb=" O   GLU A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 829
      removed outlier: 3.653A  pdb=" N   ALA A 797 " --> pdb=" O   LEU A 793 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 798 " --> pdb=" O   ALA A 794 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER A 809 " --> pdb=" O   ALA A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 838
    Processing helix  chain 'A' and resid 839 through 878
      removed outlier: 3.658A  pdb=" N   LEU A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS A 855 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLY A 856 " --> pdb=" O   LEU A 852 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   PHE A 857 " --> pdb=" O   SER A 853 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A 859 " --> pdb=" O   LYS A 855 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ASP A 860 " --> pdb=" O   GLY A 856 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR A 861 " --> pdb=" O   PHE A 857 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS A 863 " --> pdb=" O   GLY A 859 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASN A 878 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 885
    Processing helix  chain 'A' and resid 887 through 942
      removed outlier: 4.701A  pdb=" N   VAL A 901 " --> pdb=" O   HIS A 897 " (cutoff:3.500A)
      Proline residue:  A 902  - end of helix
      removed outlier: 3.698A  pdb=" N   TYR A 908 " --> pdb=" O   LYS A 904 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLU A 928 " --> pdb=" O   LEU A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 964
      removed outlier: 3.580A  pdb=" N   VAL A 949 " --> pdb=" O   THR A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 975
      Proline residue:  A 971  - end of helix
    Processing helix  chain 'A' and resid 976 through 989
    Processing helix  chain 'A' and resid 1052 through 1059
      removed outlier: 3.552A  pdb=" N   ALA A1056 " --> pdb=" O   SER A1052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1087
      removed outlier: 3.661A  pdb=" N   LEU A1084 " --> pdb=" O   ASN A1080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1107
    Processing helix  chain 'A' and resid 1114 through 1125
    Processing helix  chain 'A' and resid 1127 through 1134
    Processing helix  chain 'A' and resid 1136 through 1140
      removed outlier: 4.251A  pdb=" N   THR A1140 " --> pdb=" O   GLY A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1166
    Processing helix  chain 'A' and resid 1183 through 1195
    Processing helix  chain 'A' and resid 1196 through 1198
      No H-bonds generated for 'chain 'A' and resid 1196 through 1198'
    Processing helix  chain 'A' and resid 1229 through 1236
    Processing helix  chain 'A' and resid 1239 through 1252
    Processing sheet with id=AA1, first strand: chain 'A' and resid 383 through 390
      removed outlier: 6.888A  pdb=" N   ARG A 384 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR A 371 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   PHE A 386 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A 368 " --> pdb=" O   GLN A 423 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLN A 423 " --> pdb=" O   LYS A 368 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   VAL A 370 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   SER A 421 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 446
      removed outlier: 6.326A  pdb=" N   LEU A 525 " --> pdb=" O   VAL A 556 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   VAL A 558 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU A 527 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   THR A 395 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   ALA A 572 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ALA A 397 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE A 574 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   GLY A 583 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLU A 581 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1028 through 1031
      removed outlier: 3.800A  pdb=" N   PHE A1017 " --> pdb=" O   PHE A1028 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   ASP A1030 " --> pdb=" O   VAL A1015 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL A1015 " --> pdb=" O   ASP A1030 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1028 through 1031
      removed outlier: 3.800A  pdb=" N   PHE A1017 " --> pdb=" O   PHE A1028 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   ASP A1030 " --> pdb=" O   VAL A1015 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL A1015 " --> pdb=" O   ASP A1030 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   VAL A1015 " --> pdb=" O   ALA A1066 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ALA A1066 " --> pdb=" O   VAL A1015 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1088 through 1090
      removed outlier: 6.994A  pdb=" N   GLY A1089 " --> pdb=" O   LEU A1171 " (cutoff:3.500A)

    603 hydrogen bonds defined for protein.
    1782 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: 1.50

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.36: 2978
        1.36 -     1.50: 2377
        1.50 -     1.64: 3807
        1.64 -     1.77: 0
        1.77 -     1.91: 73
  Bond restraints: 9235
  Sorted by residual:
  bond pdb=" C   PHE A 840 "
       pdb=" N   PRO A 841 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.021 1.51e-02 4.39e+03 2.02e+00
  bond pdb=" C   ASP A 351 "
       pdb=" N   PRO A 352 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.50e+00
  bond pdb=" CB  ASP A 418 "
       pdb=" CG  ASP A 418 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.38e+00
  bond pdb=" CA  GLY A 363 "
       pdb=" C   GLY A 363 "
    ideal  model  delta    sigma   weight residual
    1.514  1.531 -0.016 1.41e-02 5.03e+03 1.34e+00
  bond pdb=" C4  ADP A1304 "
       pdb=" C5  ADP A1304 "
    ideal  model  delta    sigma   weight residual
    1.490  1.468  0.022 2.00e-02 2.50e+03 1.20e+00
  ... (remaining 9230 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12197
        1.64 -     3.28: 233
        3.28 -     4.93: 59
        4.93 -     6.57: 17
        6.57 -     8.21: 3
  Bond angle restraints: 12509
  Sorted by residual:
  angle pdb=" C   THR A 945 "
        pdb=" N   PHE A 946 "
        pdb=" CA  PHE A 946 "
      ideal   model   delta    sigma   weight residual
     120.54  124.84   -4.30 1.35e+00 5.49e-01 1.01e+01
  angle pdb=" N   ILE A1216 "
        pdb=" CA  ILE A1216 "
        pdb=" C   ILE A1216 "
      ideal   model   delta    sigma   weight residual
     109.34  115.80   -6.46 2.08e+00 2.31e-01 9.63e+00
  angle pdb=" N   ASP A 351 "
        pdb=" CA  ASP A 351 "
        pdb=" C   ASP A 351 "
      ideal   model   delta    sigma   weight residual
     109.81  116.42   -6.61 2.21e+00 2.05e-01 8.95e+00
  angle pdb=" C   TYR A 717 "
        pdb=" N   THR A 718 "
        pdb=" CA  THR A 718 "
      ideal   model   delta    sigma   weight residual
     121.54  126.97   -5.43 1.91e+00 2.74e-01 8.07e+00
  angle pdb=" CB  MET A 711 "
        pdb=" CG  MET A 711 "
        pdb=" SD  MET A 711 "
      ideal   model   delta    sigma   weight residual
     112.70  120.91   -8.21 3.00e+00 1.11e-01 7.49e+00
  ... (remaining 12504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.27: 5226
       28.27 -    56.54: 204
       56.54 -    84.81: 23
       84.81 -   113.08: 3
      113.08 -   141.35: 2
  Dihedral angle restraints: 5458
    sinusoidal: 2109
      harmonic: 3349
  Sorted by residual:
  dihedral pdb=" O2A ADP A1304 "
           pdb=" O3A ADP A1304 "
           pdb=" PA  ADP A1304 "
           pdb=" PB  ADP A1304 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   81.36 -141.35     1      2.00e+01 2.50e-03 4.27e+01
  dihedral pdb=" O2A ADP A1302 "
           pdb=" O3A ADP A1302 "
           pdb=" PA  ADP A1302 "
           pdb=" PB  ADP A1302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   81.30 -141.30     1      2.00e+01 2.50e-03 4.27e+01
  dihedral pdb=" CA  ASP A 547 "
           pdb=" C   ASP A 547 "
           pdb=" N   ARG A 548 "
           pdb=" CA  ARG A 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.91   26.09     0      5.00e+00 4.00e-02 2.72e+01
  ... (remaining 5455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1340
       0.074 -    0.149: 95
       0.149 -    0.223: 0
       0.223 -    0.297: 2
       0.297 -    0.371: 1
  Chirality restraints: 1438
  Sorted by residual:
  chirality pdb=" CG  LEU A 696 "
            pdb=" CB  LEU A 696 "
            pdb=" CD1 LEU A 696 "
            pdb=" CD2 LEU A 696 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.22   -0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CG  LEU A 187 "
            pdb=" CB  LEU A 187 "
            pdb=" CD1 LEU A 187 "
            pdb=" CD2 LEU A 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ASP A 351 "
            pdb=" N   ASP A 351 "
            pdb=" C   ASP A 351 "
            pdb=" CB  ASP A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.25 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1435 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 351 "   -0.026 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO A 352 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 352 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 352 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 901 "    0.023 5.00e-02 4.00e+02   3.45e-02 1.90e+00
        pdb=" N   PRO A 902 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 902 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 902 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1236 "    0.021 5.00e-02 4.00e+02   3.21e-02 1.64e+00
        pdb=" N   PRO A1237 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A1237 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1237 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 75
        2.60 -     3.18: 8299
        3.18 -     3.75: 14018
        3.75 -     4.33: 18330
        4.33 -     4.90: 30584
  Nonbonded interactions: 71306
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 407 "
            pdb="MG    MG A1305 "
     model   vdw
     2.031 2.170
  nonbonded pdb=" O3  VO4 A1301 "
            pdb="MG    MG A1305 "
     model   vdw
     2.098 2.170
  nonbonded pdb=" O3  VO4 A1303 "
            pdb="MG    MG A1306 "
     model   vdw
     2.111 2.170
  nonbonded pdb=" OE1 GLN A 448 "
            pdb="MG    MG A1305 "
     model   vdw
     2.169 2.170
  nonbonded pdb=" OG1 THR A 469 "
            pdb=" OE1 GLU A 472 "
     model   vdw
     2.207 3.040
  ... (remaining 71301 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.770
  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:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
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      :  0.003   0.038   9235  Z= 0.133
  Angle     :  0.620   8.211  12509  Z= 0.333
  Chirality :  0.041   0.371   1438
  Planarity :  0.003   0.038   1584
  Dihedral  : 15.108 141.354   3320
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.23 (0.26), residues: 1166
  helix:  2.28 (0.19), residues: 754
  sheet: -0.88 (0.82), residues: 45
  loop : -2.28 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  85 
 TYR   0.010   0.001   TYR A 205 
 PHE   0.014   0.001   PHE A 752 
 TRP   0.003   0.001   TRP A 684 
 HIS   0.002   0.000   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9235)
  covalent geometry    : angle       0.61961 (12509)
  hydrogen bonds       : bond        0.17983 (  602)
  hydrogen bonds       : angle       5.10926 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.323 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0829
  time to fit residues: 19.8468
Evaluate side-chains
  136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.3980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1148 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.169101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141013 restraints weight = 12870.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.144188 restraints weight = 7999.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.145908 restraints weight = 5887.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.147618 restraints weight = 4922.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.148114 restraints weight = 4336.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9235  Z= 0.136
  Angle     :  0.607   8.214  12509  Z= 0.314
  Chirality :  0.039   0.226   1438
  Planarity :  0.004   0.041   1584
  Dihedral  :  7.229 140.710   1293
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.85 %
    Favored  : 89.10 %
  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:  1.42 (0.26), residues: 1166
  helix:  2.44 (0.19), residues: 781
  sheet: -1.28 (0.75), residues: 46
  loop : -2.55 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 762 
 TYR   0.021   0.001   TYR A 740 
 PHE   0.029   0.001   PHE A 946 
 TRP   0.012   0.001   TRP A 185 
 HIS   0.007   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9235)
  covalent geometry    : angle       0.60712 (12509)
  hydrogen bonds       : bond        0.05640 (  602)
  hydrogen bonds       : angle       3.97796 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  688 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.8027 (mp)
  outliers start: 10
  outliers final: 5
  residues processed: 145
  average time/residue: 0.0836
  time to fit residues: 17.4835
Evaluate side-chains
  131 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  931 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 91 optimal weight:    0.1980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
A 560 HIS
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.165749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.137390 restraints weight = 12984.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.140588 restraints weight = 7712.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.142870 restraints weight = 5566.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.144326 restraints weight = 4533.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145209 restraints weight = 3989.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9235  Z= 0.134
  Angle     :  0.581   6.388  12509  Z= 0.301
  Chirality :  0.039   0.184   1438
  Planarity :  0.003   0.037   1584
  Dihedral  :  7.220 144.512   1293
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.26 %
    Favored  : 85.95 %
  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:  1.40 (0.26), residues: 1166
  helix:  2.44 (0.19), residues: 780
  sheet: -1.13 (0.78), residues: 40
  loop : -2.60 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.014   0.001   TYR A 205 
 PHE   0.024   0.001   PHE A 946 
 TRP   0.011   0.001   TRP A 185 
 HIS   0.004   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9235)
  covalent geometry    : angle       0.58118 (12509)
  hydrogen bonds       : bond        0.05607 (  602)
  hydrogen bonds       : angle       3.88394 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  684 TRP cc_start: 0.7633 (p90) cc_final: 0.7056 (p-90)
REVERT: A  688 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8089 (mp)
REVERT: A  827 ILE cc_start: 0.7970 (mm) cc_final: 0.7761 (mm)
REVERT: A 1192 GLU cc_start: 0.7544 (tp30) cc_final: 0.7158 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 138
  average time/residue: 0.0840
  time to fit residues: 16.5749
Evaluate side-chains
  134 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1171 LEU
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 69 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
A 748 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.163956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.135300 restraints weight = 13014.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.138646 restraints weight = 7810.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.140838 restraints weight = 5622.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.142311 restraints weight = 4606.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.143040 restraints weight = 4041.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9235  Z= 0.142
  Angle     :  0.592   6.773  12509  Z= 0.306
  Chirality :  0.039   0.246   1438
  Planarity :  0.004   0.039   1584
  Dihedral  :  7.215 144.567   1293
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.15 %
    Favored  : 83.75 %
  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:  1.35 (0.26), residues: 1166
  helix:  2.41 (0.19), residues: 779
  sheet: -1.52 (0.72), residues: 46
  loop : -2.59 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 762 
 TYR   0.011   0.001   TYR A  86 
 PHE   0.024   0.001   PHE A 946 
 TRP   0.009   0.001   TRP A 684 
 HIS   0.003   0.001   HIS A 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9235)
  covalent geometry    : angle       0.59201 (12509)
  hydrogen bonds       : bond        0.05703 (  602)
  hydrogen bonds       : angle       3.87946 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  688 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8043 (mp)
REVERT: A 1147 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8071 (m)
REVERT: A 1192 GLU cc_start: 0.7682 (tp30) cc_final: 0.7333 (tp30)
  outliers start: 20
  outliers final: 10
  residues processed: 147
  average time/residue: 0.0810
  time to fit residues: 17.0215
Evaluate side-chains
  133 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1147 VAL
Chi-restraints excluded: chain A residue 1216 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 94 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.161283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.132623 restraints weight = 13095.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.135901 restraints weight = 7964.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.138041 restraints weight = 5774.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139501 restraints weight = 4741.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.140147 restraints weight = 4171.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9235  Z= 0.152
  Angle     :  0.611   8.028  12509  Z= 0.316
  Chirality :  0.039   0.185   1438
  Planarity :  0.004   0.045   1584
  Dihedral  :  7.240 144.793   1293
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.62 %
    Favored  : 81.87 %
  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:  1.28 (0.26), residues: 1166
  helix:  2.39 (0.19), residues: 778
  sheet: -1.60 (0.72), residues: 46
  loop : -2.66 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  85 
 TYR   0.011   0.001   TYR A  86 
 PHE   0.025   0.002   PHE A  58 
 TRP   0.009   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A1230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9235)
  covalent geometry    : angle       0.61113 (12509)
  hydrogen bonds       : bond        0.05895 (  602)
  hydrogen bonds       : angle       3.91063 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 PHE cc_start: 0.5749 (t80) cc_final: 0.5547 (t80)
REVERT: A  684 TRP cc_start: 0.7585 (p90) cc_final: 0.7145 (p-90)
REVERT: A 1147 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8062 (m)
REVERT: A 1192 GLU cc_start: 0.7720 (tp30) cc_final: 0.7366 (tp30)
REVERT: A 1218 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6646 (t)
  outliers start: 24
  outliers final: 15
  residues processed: 143
  average time/residue: 0.0721
  time to fit residues: 14.9499
Evaluate side-chains
  138 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1147 VAL
Chi-restraints excluded: chain A residue 1202 VAL
Chi-restraints excluded: chain A residue 1216 ILE
Chi-restraints excluded: chain A residue 1218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 89 optimal weight:    9.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.162364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.133786 restraints weight = 13157.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137080 restraints weight = 8027.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139292 restraints weight = 5830.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.140391 restraints weight = 4768.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.141575 restraints weight = 4254.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9235  Z= 0.137
  Angle     :  0.603  10.090  12509  Z= 0.309
  Chirality :  0.038   0.158   1438
  Planarity :  0.003   0.042   1584
  Dihedral  :  7.255 145.559   1293
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.98 %
    Favored  : 80.82 %
  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:  1.32 (0.26), residues: 1166
  helix:  2.43 (0.19), residues: 776
  sheet: -1.60 (0.72), residues: 46
  loop : -2.65 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  85 
 TYR   0.013   0.001   TYR A  86 
 PHE   0.024   0.001   PHE A 946 
 TRP   0.009   0.001   TRP A 684 
 HIS   0.003   0.001   HIS A1230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9235)
  covalent geometry    : angle       0.60276 (12509)
  hydrogen bonds       : bond        0.05605 (  602)
  hydrogen bonds       : angle       3.85131 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 ASP cc_start: 0.7876 (p0) cc_final: 0.7654 (p0)
REVERT: A  684 TRP cc_start: 0.7651 (p90) cc_final: 0.7347 (p-90)
REVERT: A  688 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7967 (mp)
REVERT: A 1147 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8042 (m)
REVERT: A 1192 GLU cc_start: 0.7688 (tp30) cc_final: 0.7300 (tp30)
REVERT: A 1218 VAL cc_start: 0.6946 (OUTLIER) cc_final: 0.6659 (t)
  outliers start: 21
  outliers final: 12
  residues processed: 142
  average time/residue: 0.0749
  time to fit residues: 15.4134
Evaluate side-chains
  136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1147 VAL
Chi-restraints excluded: chain A residue 1218 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 112 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 96 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 15 optimal weight:   10.0000
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.162877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.134485 restraints weight = 13051.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.137740 restraints weight = 7832.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.140036 restraints weight = 5664.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141470 restraints weight = 4594.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.142171 restraints weight = 4039.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9235  Z= 0.132
  Angle     :  0.589   7.306  12509  Z= 0.304
  Chirality :  0.038   0.156   1438
  Planarity :  0.003   0.040   1584
  Dihedral  :  7.252 147.335   1293
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.67 %
    Favored  : 80.50 %
  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:  1.30 (0.26), residues: 1166
  helix:  2.41 (0.19), residues: 778
  sheet: -1.59 (0.72), residues: 46
  loop : -2.66 (0.30), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  85 
 TYR   0.012   0.001   TYR A  86 
 PHE   0.024   0.001   PHE A  27 
 TRP   0.009   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A1230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9235)
  covalent geometry    : angle       0.58938 (12509)
  hydrogen bonds       : bond        0.05451 (  602)
  hydrogen bonds       : angle       3.83620 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 MET cc_start: 0.5211 (tpt) cc_final: 0.5002 (tpt)
REVERT: A  270 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7738 (mp)
REVERT: A  418 ASP cc_start: 0.7859 (p0) cc_final: 0.7647 (p0)
REVERT: A  684 TRP cc_start: 0.7600 (p90) cc_final: 0.7378 (p-90)
REVERT: A  688 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8017 (mp)
REVERT: A 1192 GLU cc_start: 0.7662 (tp30) cc_final: 0.7307 (tp30)
REVERT: A 1218 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6664 (t)
  outliers start: 27
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0831
  time to fit residues: 18.0999
Evaluate side-chains
  148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1218 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.163971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135564 restraints weight = 12963.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.138881 restraints weight = 7848.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.141115 restraints weight = 5680.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142532 restraints weight = 4608.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143190 restraints weight = 4054.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9235  Z= 0.129
  Angle     :  0.600   8.016  12509  Z= 0.307
  Chirality :  0.039   0.194   1438
  Planarity :  0.003   0.041   1584
  Dihedral  :  7.191 148.652   1293
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.82 %
    Favored  : 79.77 %
  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:  1.37 (0.26), residues: 1166
  helix:  2.46 (0.19), residues: 777
  sheet: -1.54 (0.73), residues: 46
  loop : -2.63 (0.30), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  85 
 TYR   0.014   0.001   TYR A  86 
 PHE   0.024   0.001   PHE A  27 
 TRP   0.009   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A1230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9235)
  covalent geometry    : angle       0.59985 (12509)
  hydrogen bonds       : bond        0.05302 (  602)
  hydrogen bonds       : angle       3.80996 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7709 (mp)
REVERT: A  684 TRP cc_start: 0.7577 (p90) cc_final: 0.7176 (p-90)
REVERT: A  688 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7840 (mp)
REVERT: A  689 MET cc_start: 0.7568 (ttt) cc_final: 0.7111 (ttm)
REVERT: A  851 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7361 (tm-30)
REVERT: A 1188 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7998 (mt0)
REVERT: A 1192 GLU cc_start: 0.7651 (tp30) cc_final: 0.7273 (tp30)
REVERT: A 1218 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6566 (t)
  outliers start: 23
  outliers final: 14
  residues processed: 146
  average time/residue: 0.0828
  time to fit residues: 17.1355
Evaluate side-chains
  144 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1218 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0980
   chunk 81 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0060
   chunk 12 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0060
   chunk 105 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    1.0216

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

Flipped N/Q/H residues before XYZ refinement:
A 483 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.164412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.137792 restraints weight = 12891.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138972 restraints weight = 8540.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.140342 restraints weight = 6991.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.140777 restraints weight = 5502.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141040 restraints weight = 5474.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9235  Z= 0.135
  Angle     :  0.618  10.647  12509  Z= 0.313
  Chirality :  0.039   0.180   1438
  Planarity :  0.003   0.036   1584
  Dihedral  :  7.240 149.623   1293
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.66 %
    Favored  : 79.14 %
  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:  1.34 (0.26), residues: 1166
  helix:  2.42 (0.19), residues: 779
  sheet: -1.51 (0.74), residues: 46
  loop : -2.63 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  85 
 TYR   0.013   0.001   TYR A  86 
 PHE   0.025   0.001   PHE A  27 
 TRP   0.011   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A1230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9235)
  covalent geometry    : angle       0.61757 (12509)
  hydrogen bonds       : bond        0.05362 (  602)
  hydrogen bonds       : angle       3.83329 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7666 (mp)
REVERT: A  684 TRP cc_start: 0.7599 (p90) cc_final: 0.7196 (p-90)
REVERT: A  688 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7793 (mp)
REVERT: A  689 MET cc_start: 0.7550 (ttt) cc_final: 0.7081 (ttm)
REVERT: A  851 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7335 (tm-30)
REVERT: A 1188 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8060 (mt0)
REVERT: A 1192 GLU cc_start: 0.7817 (tp30) cc_final: 0.7438 (tp30)
REVERT: A 1218 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6654 (t)
  outliers start: 21
  outliers final: 14
  residues processed: 143
  average time/residue: 0.0906
  time to fit residues: 18.3015
Evaluate side-chains
  149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1218 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 65 optimal weight:    0.8980
   chunk 106 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0170
   chunk 103 optimal weight:    0.5980
   overall best weight:    1.5022

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
A 483 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.160723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.131923 restraints weight = 12980.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.135036 restraints weight = 7981.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137198 restraints weight = 5839.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.138570 restraints weight = 4792.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.139283 restraints weight = 4240.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9235  Z= 0.152
  Angle     :  0.631   9.525  12509  Z= 0.321
  Chirality :  0.040   0.159   1438
  Planarity :  0.004   0.038   1584
  Dihedral  :  7.258 148.330   1293
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.76 %
    Favored  : 79.14 %
  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:  1.23 (0.26), residues: 1166
  helix:  2.35 (0.19), residues: 776
  sheet: -1.55 (0.73), residues: 46
  loop : -2.66 (0.30), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  85 
 TYR   0.014   0.001   TYR A  86 
 PHE   0.028   0.002   PHE A  27 
 TRP   0.009   0.001   TRP A 684 
 HIS   0.003   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9235)
  covalent geometry    : angle       0.63147 (12509)
  hydrogen bonds       : bond        0.05843 (  602)
  hydrogen bonds       : angle       3.93820 ( 1782)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 PHE cc_start: 0.8258 (t80) cc_final: 0.7941 (t80)
REVERT: A  270 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7685 (mp)
REVERT: A  684 TRP cc_start: 0.7672 (p90) cc_final: 0.7435 (p-90)
REVERT: A  688 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7844 (mp)
REVERT: A  851 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7354 (tm-30)
REVERT: A 1074 LYS cc_start: 0.7123 (pttt) cc_final: 0.6875 (pttt)
REVERT: A 1188 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8113 (mt0)
REVERT: A 1192 GLU cc_start: 0.7693 (tp30) cc_final: 0.7352 (tp30)
  outliers start: 20
  outliers final: 16
  residues processed: 148
  average time/residue: 0.0835
  time to fit residues: 17.4038
Evaluate side-chains
  151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain A residue  823 ILE
Chi-restraints excluded: chain A residue  991 THR
Chi-restraints excluded: chain A residue 1069 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 37 optimal weight:    0.0000
   chunk 19 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 112 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 114 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 483 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.161288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.132373 restraints weight = 12995.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135601 restraints weight = 8018.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137737 restraints weight = 5872.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.139114 restraints weight = 4833.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139853 restraints weight = 4286.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9235  Z= 0.148
  Angle     :  0.636   9.698  12509  Z= 0.325
  Chirality :  0.040   0.270   1438
  Planarity :  0.004   0.038   1584
  Dihedral  :  7.263 147.498   1293
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 19.08 %
    Favored  : 78.83 %
  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:  1.23 (0.26), residues: 1166
  helix:  2.32 (0.19), residues: 780
  sheet: -1.09 (0.77), residues: 45
  loop : -2.71 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  85 
 TYR   0.014   0.001   TYR A  86 
 PHE   0.029   0.001   PHE A  27 
 TRP   0.011   0.001   TRP A 830 
 HIS   0.004   0.001   HIS A1230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9235)
  covalent geometry    : angle       0.63635 (12509)
  hydrogen bonds       : bond        0.05757 (  602)
  hydrogen bonds       : angle       3.94182 ( 1782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1356.94 seconds
wall clock time: 24 minutes 14.92 seconds (1454.92 seconds total)