Starting phenix.real_space_refine
on Sun Jul 27 02:44:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5s_44223/07_2025/9b5s_44223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5s_44223/07_2025/9b5s_44223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5s_44223/07_2025/9b5s_44223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5s_44223/07_2025/9b5s_44223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5s_44223/07_2025/9b5s_44223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5s_44223/07_2025/9b5s_44223.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.064
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      41      5.16       5
     C    5703      2.51       5
     N    1470      2.21       5
     O    1716      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8935
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Classifications: {'peptide': 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.32, per 1000 atoms: 0.82
  Number of scatterers: 8935
  At special positions: 0
  Unit cell: (85.12, 98.952, 119.168, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      41     16.00
     P       3     15.00
     Mg      2     11.99
     O    1716      8.00
     N    1470      7.00
     C    5703      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.89

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.33
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      48.5% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.868A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.708A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.005A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.429A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 132 through 146
      removed outlier: 3.759A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LYS A 145 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 224
      removed outlier: 4.101A  pdb=" N   GLY A 224 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.259A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 304
      removed outlier: 3.647A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.365A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.546A  pdb=" N   SER A 427 " --> pdb=" O   GLU A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.856A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ARG A 474 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.720A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 538 through 553
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 3.675A  pdb=" N   SER A 581 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER A 582 " --> pdb=" O   TYR A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 578 through 582'
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
      removed outlier: 3.536A  pdb=" N   THR A 605 " --> pdb=" O   ARG A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 630
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.534A  pdb=" N   LYS A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 3.548A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.596A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.988A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 3.766A  pdb=" N   GLN A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 794 " --> pdb=" O   ILE A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 800
    Processing helix  chain 'A' and resid 818 through 835
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.504A  pdb=" N   THR A 859 " --> pdb=" O   MET A 855 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.523A  pdb=" N   GLU A 882 " --> pdb=" O   LYS A 879 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TYR A 883 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 879 through 883'
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 145
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.850A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   THR A 129 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE A  43 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.099A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.099A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.500A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER A 460 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.400A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   VAL A 990 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   SER A 947 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   GLU A 992 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LEU A 945 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   CYS A 994 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.400A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22
      removed outlier: 6.260A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22

    438 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.29

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1512
        1.27 -     1.40: 2173
        1.40 -     1.54: 5261
        1.54 -     1.67: 132
        1.67 -     1.81: 62
  Bond restraints: 9140
  Sorted by residual:
  bond pdb=" C04 A1AIV D 201 "
       pdb=" C05 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.453  1.524 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C1' ATP A1103 "
       pdb=" O4' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.416  1.402  0.014 1.30e-02 5.92e+03 1.16e+00
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.518  0.013 1.20e-02 6.94e+03 1.13e+00
  bond pdb=" C05 A1AIV D 201 "
       pdb=" N06 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.151  1.131  0.020 2.00e-02 2.50e+03 9.51e-01
  bond pdb=" CG  PRO A 312 "
       pdb=" CD  PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.503  1.484  0.019 3.40e-02 8.65e+02 3.26e-01
  ... (remaining 9135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 12250
        1.39 -     2.79: 68
        2.79 -     4.18: 64
        4.18 -     5.58: 4
        5.58 -     6.97: 4
  Bond angle restraints: 12390
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  128.15   -6.45 1.80e+00 3.09e-01 1.28e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.12    3.41 1.18e+00 7.24e-01 8.44e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.53    4.66 1.76e+00 3.23e-01 7.02e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  104.86    6.97 2.67e+00 1.40e-01 6.82e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  104.91    6.92 2.67e+00 1.40e-01 6.72e+00
  ... (remaining 12385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 5337
       17.53 -    35.07: 157
       35.07 -    52.60: 47
       52.60 -    70.14: 9
       70.14 -    87.67: 2
  Dihedral angle restraints: 5552
    sinusoidal: 2262
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.34   57.34     1      1.00e+01 1.00e-02 4.42e+01
  dihedral pdb=" CA  LYS A 884 "
           pdb=" C   LYS A 884 "
           pdb=" N   ASN A 885 "
           pdb=" CA  ASN A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.74   17.26     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" N   GLN A  80 "
           pdb=" CA  GLN A  80 "
           pdb=" CB  GLN A  80 "
           pdb=" CG  GLN A  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.00   57.00     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 5549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1222
       0.060 -    0.119: 137
       0.119 -    0.179: 12
       0.179 -    0.239: 1
       0.239 -    0.298: 2
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.98    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" C4' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" C5' ATP A1103 "
            pdb=" O4' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.72    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1371 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  94 "    0.020 5.00e-02 4.00e+02   3.07e-02 1.51e+00
        pdb=" N   PRO C  95 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 499 "    0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO A 500 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 120 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.43e-01
        pdb=" N   PRO C 121 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO C 121 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 121 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 53
        2.57 -     3.15: 7217
        3.15 -     3.73: 13100
        3.73 -     4.32: 19171
        4.32 -     4.90: 33011
  Nonbonded interactions: 72552
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     1.986 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2B ATP A1103 "
     model   vdw
     2.015 2.170
  nonbonded pdb=" OD2 ASP A 537 "
            pdb="MG    MG A1101 "
     model   vdw
     2.093 2.170
  nonbonded pdb=" N   GLU A 489 "
            pdb=" OE1 GLU A 489 "
     model   vdw
     2.198 3.120
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.218 2.170
  ... (remaining 72547 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.260
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
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      :  0.010   0.855   9143  Z= 0.482
  Angle     :  0.628  45.318  12392  Z= 0.308
  Chirality :  0.042   0.298   1374
  Planarity :  0.003   0.031   1604
  Dihedral  :  9.815  87.672   3425
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  3.02 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1126
  helix:  1.63 (0.25), residues: 476
  sheet:  0.44 (0.38), residues: 185
  loop :  0.19 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A 818 
 PHE   0.009   0.001   PHE A 842 
 TYR   0.011   0.001   TYR A 732 
 ARG   0.003   0.000   ARG A 919 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14729 (  423)
  hydrogen bonds       : angle       5.75825 ( 1203)
  SS BOND              : bond        0.85468 (    1)
  SS BOND              : angle      33.93977 (    2)
  covalent geometry    : bond        0.00338 ( 9140)
  covalent geometry    : angle       0.45658 (12390)
  Misc. bond           : bond        0.07816 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 2.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.8034 (mtp) cc_final: 0.7424 (mtm)
REVERT: A  196 MET cc_start: 0.8349 (mmp) cc_final: 0.7858 (mmp)
REVERT: A  255 THR cc_start: 0.8923 (m) cc_final: 0.8662 (p)
REVERT: A  527 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7638 (mt-10)
REVERT: A  543 MET cc_start: 0.8576 (mmt) cc_final: 0.8165 (mmt)
REVERT: A  668 MET cc_start: 0.7762 (mmm) cc_final: 0.7397 (mmm)
REVERT: A  879 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8130 (mmmt)
REVERT: A  935 GLN cc_start: 0.8233 (tp40) cc_final: 0.7707 (tt0)
REVERT: C   32 HIS cc_start: 0.7573 (t-170) cc_final: 0.6995 (t70)
REVERT: C   49 VAL cc_start: 0.8406 (t) cc_final: 0.8159 (m)
REVERT: C   59 ASP cc_start: 0.7925 (m-30) cc_final: 0.7201 (t70)
REVERT: C   66 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7717 (mttp)
REVERT: C   72 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.8040 (mmm-85)
REVERT: C   80 SER cc_start: 0.8827 (m) cc_final: 0.8617 (p)
  outliers start: 12
  outliers final: 4
  residues processed: 143
  average time/residue: 1.5242
  time to fit residues: 232.4091
Evaluate side-chains
  91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  110 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.127432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.094594 restraints weight = 11457.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 2.02
r_work: 0.2989 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9143  Z= 0.180
  Angle     :  0.538   7.391  12392  Z= 0.280
  Chirality :  0.043   0.144   1374
  Planarity :  0.004   0.042   1604
  Dihedral  :  7.064  75.366   1253
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  9.27 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.25), residues: 1126
  helix:  1.42 (0.24), residues: 492
  sheet:  0.52 (0.39), residues: 169
  loop :  0.09 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.012   0.001   PHE A 321 
 TYR   0.011   0.001   TYR A 732 
 ARG   0.003   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04543 (  423)
  hydrogen bonds       : angle       4.61104 ( 1203)
  SS BOND              : bond        0.01327 (    1)
  SS BOND              : angle       5.43086 (    2)
  covalent geometry    : bond        0.00447 ( 9140)
  covalent geometry    : angle       0.53392 (12390)
  Misc. bond           : bond        0.00136 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.7970 (mtp) cc_final: 0.7539 (mtp)
REVERT: A  196 MET cc_start: 0.8285 (mmp) cc_final: 0.7845 (mmp)
REVERT: A  206 ASN cc_start: 0.8330 (m110) cc_final: 0.8009 (t0)
REVERT: A  401 GLU cc_start: 0.8362 (tp30) cc_final: 0.8042 (mp0)
REVERT: A  527 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7195 (mt-10)
REVERT: A  543 MET cc_start: 0.8468 (mmt) cc_final: 0.8111 (mmt)
REVERT: A  879 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8008 (mmmt)
REVERT: C   32 HIS cc_start: 0.7722 (t-170) cc_final: 0.7236 (t70)
REVERT: C   38 MET cc_start: 0.8920 (mtm) cc_final: 0.8610 (mtm)
REVERT: C   59 ASP cc_start: 0.8004 (m-30) cc_final: 0.7419 (t0)
REVERT: C   66 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7923 (mttp)
REVERT: C   72 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8272 (mmm-85)
REVERT: C   80 SER cc_start: 0.8911 (m) cc_final: 0.8650 (p)
REVERT: C  140 GLU cc_start: 0.7947 (tp30) cc_final: 0.7364 (tm-30)
  outliers start: 18
  outliers final: 12
  residues processed: 96
  average time/residue: 1.6806
  time to fit residues: 173.3382
Evaluate side-chains
  99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  110 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.126752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.094065 restraints weight = 11695.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.04
r_work: 0.2985 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9143  Z= 0.169
  Angle     :  0.514   6.877  12392  Z= 0.267
  Chirality :  0.043   0.142   1374
  Planarity :  0.004   0.046   1604
  Dihedral  :  6.721  77.763   1253
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  9.68 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1126
  helix:  1.37 (0.24), residues: 492
  sheet:  0.41 (0.39), residues: 169
  loop :  0.07 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.011   0.001   PHE A 321 
 TYR   0.009   0.001   TYR A  81 
 ARG   0.004   0.000   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 (  423)
  hydrogen bonds       : angle       4.43633 ( 1203)
  SS BOND              : bond        0.00658 (    1)
  SS BOND              : angle       5.16548 (    2)
  covalent geometry    : bond        0.00424 ( 9140)
  covalent geometry    : angle       0.51004 (12390)
  Misc. bond           : bond        0.00264 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8166 (mmm)
REVERT: A  184 MET cc_start: 0.7922 (mtp) cc_final: 0.7328 (mtm)
REVERT: A  196 MET cc_start: 0.8307 (mmp) cc_final: 0.7875 (mmp)
REVERT: A  206 ASN cc_start: 0.8341 (m110) cc_final: 0.8028 (t0)
REVERT: A  401 GLU cc_start: 0.8343 (tp30) cc_final: 0.8035 (mp0)
REVERT: A  527 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7896 (tm-30)
REVERT: A  543 MET cc_start: 0.8395 (mmt) cc_final: 0.8049 (mmt)
REVERT: A  879 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8025 (mmmt)
REVERT: C   32 HIS cc_start: 0.7710 (t-170) cc_final: 0.7246 (t70)
REVERT: C   34 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8382 (tp-100)
REVERT: C   38 MET cc_start: 0.8927 (mtm) cc_final: 0.8560 (mtm)
REVERT: C   59 ASP cc_start: 0.7957 (m-30) cc_final: 0.7358 (t0)
REVERT: C   66 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7905 (mttp)
REVERT: C   72 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8312 (mmm-85)
REVERT: C   80 SER cc_start: 0.8884 (m) cc_final: 0.8620 (p)
REVERT: C  135 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6227 (mp0)
REVERT: C  140 GLU cc_start: 0.7944 (tp30) cc_final: 0.7375 (tm-30)
  outliers start: 22
  outliers final: 12
  residues processed: 97
  average time/residue: 1.3068
  time to fit residues: 135.7600
Evaluate side-chains
  92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  944 MET
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0070
   chunk 105 optimal weight:    0.1980
   chunk 81 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.4398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.095454 restraints weight = 11555.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.06
r_work: 0.3003 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9143  Z= 0.116
  Angle     :  0.475   6.569  12392  Z= 0.246
  Chirality :  0.041   0.140   1374
  Planarity :  0.004   0.047   1604
  Dihedral  :  6.543  77.181   1253
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  9.58 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1126
  helix:  1.52 (0.24), residues: 491
  sheet:  0.28 (0.40), residues: 177
  loop :  0.17 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C 125 
 PHE   0.008   0.001   PHE A 321 
 TYR   0.008   0.001   TYR A 834 
 ARG   0.002   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03586 (  423)
  hydrogen bonds       : angle       4.26594 ( 1203)
  SS BOND              : bond        0.00710 (    1)
  SS BOND              : angle       4.52512 (    2)
  covalent geometry    : bond        0.00278 ( 9140)
  covalent geometry    : angle       0.47122 (12390)
  Misc. bond           : bond        0.00025 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8163 (mmm)
REVERT: A  184 MET cc_start: 0.7891 (mtp) cc_final: 0.7302 (mtm)
REVERT: A  196 MET cc_start: 0.8277 (mmp) cc_final: 0.7853 (mmp)
REVERT: A  206 ASN cc_start: 0.8330 (m110) cc_final: 0.8018 (t0)
REVERT: A  401 GLU cc_start: 0.8324 (tp30) cc_final: 0.8039 (mp0)
REVERT: A  527 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7950 (tm-30)
REVERT: A  543 MET cc_start: 0.8360 (mmt) cc_final: 0.8012 (mmt)
REVERT: A  699 GLN cc_start: 0.7780 (mp10) cc_final: 0.7573 (mp10)
REVERT: A  879 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8001 (mmmt)
REVERT: C   32 HIS cc_start: 0.7702 (t-170) cc_final: 0.7197 (t70)
REVERT: C   34 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8379 (tp-100)
REVERT: C   38 MET cc_start: 0.8934 (mtm) cc_final: 0.8649 (mtm)
REVERT: C   59 ASP cc_start: 0.8002 (m-30) cc_final: 0.7403 (t0)
REVERT: C   66 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7898 (mttp)
REVERT: C   72 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8114 (mmm-85)
REVERT: C   80 SER cc_start: 0.8865 (m) cc_final: 0.8580 (p)
REVERT: C  111 THR cc_start: 0.7421 (m) cc_final: 0.7178 (p)
REVERT: C  135 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6156 (mp0)
REVERT: C  140 GLU cc_start: 0.7932 (tp30) cc_final: 0.7382 (tm-30)
  outliers start: 22
  outliers final: 10
  residues processed: 94
  average time/residue: 1.3965
  time to fit residues: 139.8809
Evaluate side-chains
  88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  944 MET
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 19 optimal weight:    0.2980
   chunk 110 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0980
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.095286 restraints weight = 11459.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.06
r_work: 0.3006 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9143  Z= 0.123
  Angle     :  0.477   6.268  12392  Z= 0.245
  Chirality :  0.041   0.135   1374
  Planarity :  0.004   0.047   1604
  Dihedral  :  6.493  77.760   1253
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.98 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1126
  helix:  1.54 (0.24), residues: 491
  sheet:  0.27 (0.39), residues: 177
  loop :  0.19 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C 125 
 PHE   0.009   0.001   PHE A 321 
 TYR   0.008   0.001   TYR A 834 
 ARG   0.002   0.000   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  423)
  hydrogen bonds       : angle       4.21371 ( 1203)
  SS BOND              : bond        0.00489 (    1)
  SS BOND              : angle       4.28154 (    2)
  covalent geometry    : bond        0.00299 ( 9140)
  covalent geometry    : angle       0.47348 (12390)
  Misc. bond           : bond        0.00068 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8154 (mmm)
REVERT: A  184 MET cc_start: 0.7919 (mtp) cc_final: 0.7327 (mtm)
REVERT: A  196 MET cc_start: 0.8282 (mmp) cc_final: 0.7885 (mmp)
REVERT: A  206 ASN cc_start: 0.8331 (m110) cc_final: 0.8011 (t0)
REVERT: A  333 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: A  401 GLU cc_start: 0.8329 (tp30) cc_final: 0.8033 (mp0)
REVERT: A  527 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7947 (tm-30)
REVERT: A  543 MET cc_start: 0.8336 (mmt) cc_final: 0.7988 (mmt)
REVERT: A  699 GLN cc_start: 0.7789 (mp10) cc_final: 0.7543 (mp10)
REVERT: A  879 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8000 (mmmt)
REVERT: C   32 HIS cc_start: 0.7661 (t-170) cc_final: 0.7144 (t70)
REVERT: C   34 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8385 (tp-100)
REVERT: C   38 MET cc_start: 0.8902 (mtm) cc_final: 0.8612 (mtm)
REVERT: C   59 ASP cc_start: 0.8093 (m-30) cc_final: 0.7484 (t0)
REVERT: C   66 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7915 (mttp)
REVERT: C   72 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8126 (mmm-85)
REVERT: C   80 SER cc_start: 0.8857 (m) cc_final: 0.8574 (p)
REVERT: C  111 THR cc_start: 0.7416 (m) cc_final: 0.7189 (p)
REVERT: C  135 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6181 (mp0)
REVERT: C  140 GLU cc_start: 0.7982 (tp30) cc_final: 0.7441 (tm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 93
  average time/residue: 1.3037
  time to fit residues: 129.6112
Evaluate side-chains
  92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 106 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.126628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.094282 restraints weight = 11613.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.02
r_work: 0.2990 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9143  Z= 0.168
  Angle     :  0.498   7.680  12392  Z= 0.256
  Chirality :  0.042   0.139   1374
  Planarity :  0.004   0.048   1604
  Dihedral  :  6.551  74.558   1253
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  :  9.68 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.26), residues: 1126
  helix:  1.48 (0.24), residues: 491
  sheet:  0.19 (0.39), residues: 177
  loop :  0.18 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.011   0.001   PHE A 321 
 TYR   0.010   0.001   TYR A  81 
 ARG   0.002   0.000   ARG A 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  423)
  hydrogen bonds       : angle       4.26315 ( 1203)
  SS BOND              : bond        0.00812 (    1)
  SS BOND              : angle       4.41888 (    2)
  covalent geometry    : bond        0.00422 ( 9140)
  covalent geometry    : angle       0.49494 (12390)
  Misc. bond           : bond        0.00054 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8130 (mmm)
REVERT: A  184 MET cc_start: 0.7919 (mtp) cc_final: 0.7344 (mtm)
REVERT: A  196 MET cc_start: 0.8298 (mmp) cc_final: 0.7900 (mmp)
REVERT: A  206 ASN cc_start: 0.8339 (m110) cc_final: 0.8043 (t0)
REVERT: A  333 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: A  401 GLU cc_start: 0.8347 (tp30) cc_final: 0.8055 (mp0)
REVERT: A  527 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7978 (tm-30)
REVERT: A  543 MET cc_start: 0.8425 (mmt) cc_final: 0.8052 (mmt)
REVERT: A  699 GLN cc_start: 0.7843 (mp10) cc_final: 0.7594 (mp10)
REVERT: A  879 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8230 (mttp)
REVERT: C   32 HIS cc_start: 0.7693 (t-170) cc_final: 0.7212 (t70)
REVERT: C   34 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8405 (tp-100)
REVERT: C   38 MET cc_start: 0.8861 (mtm) cc_final: 0.8577 (mtm)
REVERT: C   59 ASP cc_start: 0.8191 (m-30) cc_final: 0.7674 (t0)
REVERT: C   66 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7960 (mttp)
REVERT: C   72 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8137 (mmm-85)
REVERT: C   80 SER cc_start: 0.8856 (m) cc_final: 0.8577 (p)
REVERT: C  111 THR cc_start: 0.7437 (m) cc_final: 0.7221 (p)
REVERT: C  135 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6168 (mp0)
REVERT: C  140 GLU cc_start: 0.8001 (tp30) cc_final: 0.7453 (tm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 93
  average time/residue: 1.3940
  time to fit residues: 138.7687
Evaluate side-chains
  96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  856 CYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 102 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.126687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.094242 restraints weight = 11655.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.04
r_work: 0.2990 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9143  Z= 0.156
  Angle     :  0.489   9.527  12392  Z= 0.251
  Chirality :  0.042   0.139   1374
  Planarity :  0.004   0.048   1604
  Dihedral  :  6.525  73.276   1253
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.78 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1126
  helix:  1.49 (0.24), residues: 491
  sheet:  0.06 (0.40), residues: 172
  loop :  0.16 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.010   0.001   PHE A 321 
 TYR   0.010   0.001   TYR A  81 
 ARG   0.002   0.000   ARG A 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03843 (  423)
  hydrogen bonds       : angle       4.24138 ( 1203)
  SS BOND              : bond        0.00658 (    1)
  SS BOND              : angle       4.37401 (    2)
  covalent geometry    : bond        0.00391 ( 9140)
  covalent geometry    : angle       0.48627 (12390)
  Misc. bond           : bond        0.00026 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8319 (mmm)
REVERT: A  184 MET cc_start: 0.7924 (mtp) cc_final: 0.7340 (mtm)
REVERT: A  196 MET cc_start: 0.8189 (mmp) cc_final: 0.7676 (mmp)
REVERT: A  206 ASN cc_start: 0.8341 (m110) cc_final: 0.8039 (t0)
REVERT: A  333 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7653 (tm-30)
REVERT: A  401 GLU cc_start: 0.8337 (tp30) cc_final: 0.8056 (mp0)
REVERT: A  527 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7980 (tm-30)
REVERT: A  543 MET cc_start: 0.8418 (mmt) cc_final: 0.8051 (mmt)
REVERT: A  601 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7815 (ttm-80)
REVERT: A  879 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8226 (mttp)
REVERT: C   32 HIS cc_start: 0.7700 (t-170) cc_final: 0.7233 (t70)
REVERT: C   34 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8398 (tp-100)
REVERT: C   38 MET cc_start: 0.8859 (mtm) cc_final: 0.8569 (mtm)
REVERT: C   59 ASP cc_start: 0.8114 (m-30) cc_final: 0.7726 (t0)
REVERT: C   66 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7953 (mttp)
REVERT: C   72 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8149 (mmm-85)
REVERT: C   80 SER cc_start: 0.8848 (m) cc_final: 0.8569 (p)
REVERT: C  111 THR cc_start: 0.7452 (m) cc_final: 0.7249 (p)
REVERT: C  135 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6160 (mp0)
REVERT: C  140 GLU cc_start: 0.8004 (tp30) cc_final: 0.7460 (tm-30)
  outliers start: 25
  outliers final: 16
  residues processed: 94
  average time/residue: 1.9622
  time to fit residues: 198.7291
Evaluate side-chains
  92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 2.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  856 CYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 99 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 64 optimal weight:    0.4980
   chunk 54 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0670
   overall best weight:    0.4918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.095591 restraints weight = 11781.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.04
r_work: 0.3005 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9143  Z= 0.122
  Angle     :  0.480   9.035  12392  Z= 0.247
  Chirality :  0.041   0.134   1374
  Planarity :  0.004   0.048   1604
  Dihedral  :  6.416  73.402   1253
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.79 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.26), residues: 1126
  helix:  1.55 (0.24), residues: 491
  sheet:  0.05 (0.40), residues: 172
  loop :  0.18 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C 125 
 PHE   0.008   0.001   PHE A 321 
 TYR   0.008   0.001   TYR C 127 
 ARG   0.001   0.000   ARG A 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03481 (  423)
  hydrogen bonds       : angle       4.16158 ( 1203)
  SS BOND              : bond        0.00547 (    1)
  SS BOND              : angle       4.02593 (    2)
  covalent geometry    : bond        0.00301 ( 9140)
  covalent geometry    : angle       0.47744 (12390)
  Misc. bond           : bond        0.00086 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8268 (mmm)
REVERT: A  184 MET cc_start: 0.7904 (mtp) cc_final: 0.7358 (mtm)
REVERT: A  196 MET cc_start: 0.8152 (mmp) cc_final: 0.7631 (mmp)
REVERT: A  206 ASN cc_start: 0.8337 (m110) cc_final: 0.8037 (t0)
REVERT: A  401 GLU cc_start: 0.8322 (tp30) cc_final: 0.8061 (mp0)
REVERT: A  527 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8000 (tm-30)
REVERT: A  543 MET cc_start: 0.8411 (mmt) cc_final: 0.8041 (mmt)
REVERT: A  746 ILE cc_start: 0.7875 (tt) cc_final: 0.7657 (pt)
REVERT: A  879 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8110 (mmmt)
REVERT: C   32 HIS cc_start: 0.7684 (t-170) cc_final: 0.7187 (t70)
REVERT: C   34 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8408 (tp-100)
REVERT: C   38 MET cc_start: 0.8865 (mtm) cc_final: 0.8571 (mtm)
REVERT: C   59 ASP cc_start: 0.8108 (m-30) cc_final: 0.7738 (t0)
REVERT: C   66 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7947 (mttp)
REVERT: C   72 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8132 (mmm-85)
REVERT: C   80 SER cc_start: 0.8854 (m) cc_final: 0.8605 (p)
REVERT: C  135 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6166 (mp0)
REVERT: C  140 GLU cc_start: 0.8018 (tp30) cc_final: 0.7458 (tm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 97
  average time/residue: 1.2503
  time to fit residues: 129.8913
Evaluate side-chains
  95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    0.0870
   chunk 68 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.127094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.094735 restraints weight = 11650.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.04
r_work: 0.2997 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9143  Z= 0.148
  Angle     :  0.500   8.847  12392  Z= 0.258
  Chirality :  0.042   0.160   1374
  Planarity :  0.004   0.044   1604
  Dihedral  :  6.420  70.950   1253
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.09 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1126
  helix:  1.50 (0.24), residues: 491
  sheet:  0.02 (0.39), residues: 175
  loop :  0.18 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A 818 
 PHE   0.010   0.001   PHE A 321 
 TYR   0.009   0.001   TYR A  81 
 ARG   0.002   0.000   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  423)
  hydrogen bonds       : angle       4.20068 ( 1203)
  SS BOND              : bond        0.00490 (    1)
  SS BOND              : angle       4.18700 (    2)
  covalent geometry    : bond        0.00371 ( 9140)
  covalent geometry    : angle       0.49670 (12390)
  Misc. bond           : bond        0.00054 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8234 (mmm)
REVERT: A  184 MET cc_start: 0.7914 (mtp) cc_final: 0.7324 (mtm)
REVERT: A  196 MET cc_start: 0.8185 (mmp) cc_final: 0.7650 (mmp)
REVERT: A  206 ASN cc_start: 0.8342 (m110) cc_final: 0.8071 (t160)
REVERT: A  401 GLU cc_start: 0.8341 (tp30) cc_final: 0.8063 (mp0)
REVERT: A  527 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7993 (tm-30)
REVERT: A  543 MET cc_start: 0.8397 (mmt) cc_final: 0.8030 (mmt)
REVERT: A  601 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7819 (ttm-80)
REVERT: A  746 ILE cc_start: 0.7876 (tt) cc_final: 0.7658 (pt)
REVERT: A  879 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8115 (mmmt)
REVERT: C   32 HIS cc_start: 0.7675 (t-170) cc_final: 0.7164 (t70)
REVERT: C   34 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8402 (tp-100)
REVERT: C   38 MET cc_start: 0.8881 (mtm) cc_final: 0.8574 (mtm)
REVERT: C   59 ASP cc_start: 0.8077 (m-30) cc_final: 0.7596 (t0)
REVERT: C   66 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7918 (mttp)
REVERT: C   72 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8136 (mmm-85)
REVERT: C   80 SER cc_start: 0.8857 (m) cc_final: 0.8589 (p)
REVERT: C  135 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6158 (mp0)
REVERT: C  140 GLU cc_start: 0.7986 (tp30) cc_final: 0.7445 (tm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 95
  average time/residue: 1.3799
  time to fit residues: 139.9187
Evaluate side-chains
  93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  856 CYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 10 optimal weight:    0.3980
   chunk 108 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0870
   chunk 57 optimal weight:    0.0010
   overall best weight:    0.2964

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.128604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.096099 restraints weight = 11598.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.07
r_work: 0.3016 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9143  Z= 0.104
  Angle     :  0.482   8.746  12392  Z= 0.249
  Chirality :  0.041   0.152   1374
  Planarity :  0.004   0.053   1604
  Dihedral  :  6.314  72.203   1253
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.30 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1126
  helix:  1.67 (0.24), residues: 484
  sheet: -0.00 (0.39), residues: 175
  loop :  0.14 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.000   HIS A  29 
 PHE   0.008   0.001   PHE A 842 
 TYR   0.007   0.001   TYR C 127 
 ARG   0.002   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03282 (  423)
  hydrogen bonds       : angle       4.10327 ( 1203)
  SS BOND              : bond        0.00497 (    1)
  SS BOND              : angle       3.84626 (    2)
  covalent geometry    : bond        0.00250 ( 9140)
  covalent geometry    : angle       0.47995 (12390)
  Misc. bond           : bond        0.00015 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A   32 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8221 (mmm)
REVERT: A  184 MET cc_start: 0.7882 (mtp) cc_final: 0.7288 (mtm)
REVERT: A  196 MET cc_start: 0.8158 (mmp) cc_final: 0.7612 (mmp)
REVERT: A  206 ASN cc_start: 0.8329 (m110) cc_final: 0.8012 (t0)
REVERT: A  401 GLU cc_start: 0.8312 (tp30) cc_final: 0.8044 (mp0)
REVERT: A  527 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7972 (tm-30)
REVERT: A  543 MET cc_start: 0.8342 (mmt) cc_final: 0.8001 (mmt)
REVERT: A  668 MET cc_start: 0.7656 (mtp) cc_final: 0.7280 (mtp)
REVERT: A  746 ILE cc_start: 0.7907 (tt) cc_final: 0.7704 (pt)
REVERT: A  879 LYS cc_start: 0.8575 (mmmm) cc_final: 0.8076 (mmmt)
REVERT: C   32 HIS cc_start: 0.7657 (t-170) cc_final: 0.7135 (t70)
REVERT: C   34 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8178 (tp40)
REVERT: C   38 MET cc_start: 0.8892 (mtm) cc_final: 0.8587 (mtm)
REVERT: C   59 ASP cc_start: 0.8049 (m-30) cc_final: 0.7593 (t0)
REVERT: C   66 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7898 (mttp)
REVERT: C   72 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8112 (mmm-85)
REVERT: C   80 SER cc_start: 0.8843 (m) cc_final: 0.8577 (p)
REVERT: C  135 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6157 (mp0)
REVERT: C  140 GLU cc_start: 0.7964 (tp30) cc_final: 0.7435 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 91
  average time/residue: 1.2823
  time to fit residues: 124.8639
Evaluate side-chains
  88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  201 ARG
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  856 CYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   34 GLN
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    0.0010
   chunk 106 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0470
   chunk 96 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.3684

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.128753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.096585 restraints weight = 11698.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.03
r_work: 0.3020 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9143  Z= 0.111
  Angle     :  0.504  11.192  12392  Z= 0.258
  Chirality :  0.042   0.181   1374
  Planarity :  0.004   0.052   1604
  Dihedral  :  6.135  69.004   1252
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.20 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1126
  helix:  1.72 (0.24), residues: 484
  sheet:  0.04 (0.39), residues: 175
  loop :  0.25 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.001   0.000   HIS C 125 
 PHE   0.010   0.001   PHE C  62 
 TYR   0.008   0.001   TYR C 127 
 ARG   0.004   0.000   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  423)
  hydrogen bonds       : angle       4.06861 ( 1203)
  SS BOND              : bond        0.01435 (    1)
  SS BOND              : angle       2.31783 (    2)
  covalent geometry    : bond        0.00268 ( 9140)
  covalent geometry    : angle       0.50326 (12390)
  Misc. bond           : bond        0.00094 (    2)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 6607.73 seconds
wall clock time: 116 minutes 59.74 seconds (7019.74 seconds total)