Starting phenix.real_space_refine
on Thu Mar 13 16:15:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5t_44224/03_2025/9b5t_44224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5t_44224/03_2025/9b5t_44224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5t_44224/03_2025/9b5t_44224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5t_44224/03_2025/9b5t_44224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5t_44224/03_2025/9b5t_44224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5t_44224/03_2025/9b5t_44224.cif"
  }
  resolution = 3.16
  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=   0.072
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 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.50, per 1000 atoms: 0.73
  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=2.81

  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: 2.81
  Conformation dependent library (CDL) restraints added in 2.2 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:
      46 helices and 9 sheets defined
      46.8% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.917A  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: 3.657A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.002A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.088A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.570A  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: 3.671A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LYS A 145 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.232A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 304
      removed outlier: 3.599A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.636A  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 410 through 418
      removed outlier: 4.477A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.913A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.675A  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
      removed outlier: 3.572A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.954A  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
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
      removed outlier: 3.570A  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: 3.552A  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: 3.602A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.761A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 736
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.937A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 4.156A  pdb=" N   GLN A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A 794 " --> pdb=" O   ILE A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 834
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.646A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    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: 6.821A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   THR A 129 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE A  43 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.315A  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: 4.382A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.509A  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: 4.382A  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: 6.507A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 460 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.154A  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: 6.505A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   VAL A 990 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   SER A 947 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   GLU A 992 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   LEU A 945 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   CYS A 994 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.513A  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: 6.505A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.082A  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 24 through 26
      removed outlier: 3.861A  pdb=" N   GLY C  24 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1185 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: 3.89

  Time building geometry restraints manager: 3.27 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 -     1.41: 2183
        1.41 -     1.55: 5376
        1.55 -     1.68: 7
        1.68 -     1.82: 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 1.28e+01
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.519  0.012 1.20e-02 6.94e+03 1.02e+00
  bond pdb=" C05 A1AIV D 201 "
       pdb=" N06 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 8.97e-01
  bond pdb=" C1' ATP A1103 "
       pdb=" O4' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.416  1.405  0.011 1.30e-02 5.92e+03 6.65e-01
  bond pdb=" CB  MET A  35 "
       pdb=" CG  MET A  35 "
    ideal  model  delta    sigma   weight residual
    1.520  1.505  0.015 3.00e-02 1.11e+03 2.56e-01
  ... (remaining 9135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 12227
        1.27 -     2.55: 83
        2.55 -     3.82: 69
        3.82 -     5.09: 7
        5.09 -     6.36: 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  127.63   -5.93 1.80e+00 3.09e-01 1.09e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.08    3.45 1.18e+00 7.24e-01 8.61e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.59    4.60 1.76e+00 3.23e-01 6.83e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  105.47    6.36 2.67e+00 1.40e-01 5.68e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  106.21    5.62 2.67e+00 1.40e-01 4.43e+00
  ... (remaining 12385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 5342
       17.43 -    34.85: 159
       34.85 -    52.28: 42
       52.28 -    69.70: 6
       69.70 -    87.13: 3
  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 -128.05   42.05     1      1.00e+01 1.00e-02 2.47e+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  163.50   16.50     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" N   GLU A 869 "
           pdb=" CA  GLU A 869 "
           pdb=" CB  GLU A 869 "
           pdb=" CG  GLU A 869 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.06  -59.94     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1204
       0.055 -    0.110: 132
       0.110 -    0.164: 35
       0.164 -    0.219: 0
       0.219 -    0.274: 3
  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   -2.95    0.27 2.00e-01 2.50e+01 1.88e+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   -2.90    0.27 2.00e-01 2.50e+01 1.81e+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    0.23 2.00e-01 2.50e+01 1.29e+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   3.10e-02 1.53e+00
        pdb=" N   PRO C  95 "   -0.054 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   VAL A  90 "    0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO A  91 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A  91 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A  91 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 288 "    0.017 5.00e-02 4.00e+02   2.52e-02 1.01e+00
        pdb=" N   PRO A 289 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 59
        2.60 -     3.17: 7537
        3.17 -     3.75: 13113
        3.75 -     4.32: 18989
        4.32 -     4.90: 32186
  Nonbonded interactions: 71884
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     2.024 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.031 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2B ATP A1103 "
     model   vdw
     2.081 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O3G ATP A1103 "
     model   vdw
     2.137 2.170
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2A ATP A1103 "
     model   vdw
     2.160 2.170
  ... (remaining 71879 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:             63.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     29.410
  Find NCS groups from input model:        0.110
  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:3.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   96.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   9140  Z= 0.180
  Angle     :  0.445   6.363  12390  Z= 0.222
  Chirality :  0.041   0.274   1374
  Planarity :  0.003   0.031   1604
  Dihedral  :  9.544  87.130   3425
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  3.93 %
    Favored  : 95.16 %
  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:  1.13 (0.26), residues: 1126
  helix:  1.70 (0.25), residues: 474
  sheet:  0.31 (0.38), residues: 184
  loop :  0.06 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.000   HIS A 818 
 PHE   0.007   0.001   PHE A 842 
 TYR   0.008   0.001   TYR A 732 
 ARG   0.002   0.000   ARG A 409 

*********************** 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
  182 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 173
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.8598 (mm) cc_final: 0.7964 (mp)
REVERT: A   33 LYS cc_start: 0.7988 (tttm) cc_final: 0.7746 (tmmt)
REVERT: A  135 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7544 (mttt)
REVERT: A  188 ILE cc_start: 0.8489 (mt) cc_final: 0.8250 (mt)
REVERT: A  194 VAL cc_start: 0.8255 (t) cc_final: 0.8015 (t)
REVERT: A  218 MET cc_start: 0.7340 (mtt) cc_final: 0.6911 (mmm)
REVERT: A  236 THR cc_start: 0.8258 (p) cc_final: 0.8022 (t)
REVERT: A  274 ASP cc_start: 0.7743 (t70) cc_final: 0.7459 (p0)
REVERT: A  311 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7760 (mtm180)
REVERT: A  441 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7662 (mm-30)
REVERT: A  442 MET cc_start: 0.8601 (tpp) cc_final: 0.8310 (mmm)
REVERT: A  567 ASN cc_start: 0.8691 (p0) cc_final: 0.8490 (p0)
REVERT: A  596 LYS cc_start: 0.8673 (tmtt) cc_final: 0.8296 (tttt)
REVERT: A  675 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8411 (m-30)
REVERT: A  784 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8034 (ptpp)
REVERT: A  806 THR cc_start: 0.8607 (m) cc_final: 0.8190 (p)
REVERT: A  832 MET cc_start: 0.8573 (mtp) cc_final: 0.8297 (mtp)
REVERT: A  841 ARG cc_start: 0.7513 (ttm110) cc_final: 0.7295 (mtp-110)
REVERT: A  869 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7263 (mp0)
REVERT: A  915 LYS cc_start: 0.8119 (mttp) cc_final: 0.7901 (tmtt)
REVERT: A  936 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7494 (mtmt)
REVERT: A  981 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8486 (mmmt)
REVERT: A  997 ASP cc_start: 0.7946 (t0) cc_final: 0.6729 (p0)
REVERT: C   28 ASP cc_start: 0.6894 (m-30) cc_final: 0.6193 (p0)
REVERT: C   29 ASP cc_start: 0.7848 (t0) cc_final: 0.7600 (t0)
REVERT: C   90 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7483 (mmm160)
REVERT: C  116 ASP cc_start: 0.8294 (m-30) cc_final: 0.7934 (m-30)
REVERT: C  144 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7983 (tttt)
  outliers start: 9
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2947
  time to fit residues: 68.2135
Evaluate side-chains
  110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.131494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.102431 restraints weight = 12615.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.21
r_work: 0.3190 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9140  Z= 0.228
  Angle     :  0.507   5.760  12390  Z= 0.268
  Chirality :  0.042   0.133   1374
  Planarity :  0.004   0.040   1604
  Dihedral  :  6.660  77.189   1256
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  6.45 %
    Favored  : 91.33 %
  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:  1.06 (0.26), residues: 1126
  helix:  1.57 (0.25), residues: 483
  sheet:  0.38 (0.39), residues: 182
  loop :  0.02 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A 147 
 PHE   0.009   0.001   PHE A 842 
 TYR   0.011   0.001   TYR A 732 
 ARG   0.006   0.000   ARG A  73 

*********************** 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
  133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8970 (t) cc_final: 0.8721 (m)
REVERT: A  135 LYS cc_start: 0.8464 (mmmt) cc_final: 0.7944 (mttt)
REVERT: A  188 ILE cc_start: 0.8631 (mt) cc_final: 0.8384 (mt)
REVERT: A  311 ARG cc_start: 0.8610 (mtm180) cc_final: 0.8406 (mtm180)
REVERT: A  675 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8451 (m-30)
REVERT: A  710 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7964 (p)
REVERT: A  784 LYS cc_start: 0.8456 (ttpp) cc_final: 0.8089 (ptpp)
REVERT: A  806 THR cc_start: 0.8704 (m) cc_final: 0.8375 (p)
REVERT: A  869 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8123 (mm-30)
REVERT: A  915 LYS cc_start: 0.8168 (mttp) cc_final: 0.7820 (tmtt)
REVERT: A  936 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7671 (mtmt)
REVERT: A  997 ASP cc_start: 0.8119 (t0) cc_final: 0.6915 (p0)
REVERT: C   90 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7722 (mmm160)
REVERT: C  117 ASP cc_start: 0.7518 (t70) cc_final: 0.7225 (t70)
  outliers start: 22
  outliers final: 11
  residues processed: 125
  average time/residue: 0.2728
  time to fit residues: 44.8145
Evaluate side-chains
  112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  137 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 68 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.129211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.099870 restraints weight = 13029.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.39
r_work: 0.3139 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9140  Z= 0.290
  Angle     :  0.511   5.387  12390  Z= 0.269
  Chirality :  0.043   0.139   1374
  Planarity :  0.004   0.044   1604
  Dihedral  :  6.339  66.220   1256
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  :  7.26 %
    Favored  : 90.42 %
  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:  0.86 (0.25), residues: 1126
  helix:  1.41 (0.24), residues: 484
  sheet:  0.28 (0.38), residues: 180
  loop : -0.11 (0.29), residues: 462

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   0.033   0.001   PHE C  62 
 TYR   0.013   0.001   TYR A 732 
 ARG   0.004   0.001   ARG C 143 

*********************** 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
  119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8996 (t) cc_final: 0.8716 (m)
REVERT: A  135 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7849 (mttt)
REVERT: A  218 MET cc_start: 0.7189 (mmm) cc_final: 0.6789 (mmm)
REVERT: A  311 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8335 (mtm180)
REVERT: A  592 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8244 (tp)
REVERT: A  675 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8430 (m-30)
REVERT: A  710 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8032 (p)
REVERT: A  784 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8058 (ptpp)
REVERT: A  869 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7547 (mp0)
REVERT: A  915 LYS cc_start: 0.8249 (mttp) cc_final: 0.7698 (tmtt)
REVERT: A  936 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7682 (mtmt)
REVERT: A  997 ASP cc_start: 0.8095 (t0) cc_final: 0.6841 (p0)
REVERT: C   90 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7752 (mmm160)
REVERT: C  117 ASP cc_start: 0.7421 (t70) cc_final: 0.6990 (t70)
  outliers start: 23
  outliers final: 11
  residues processed: 111
  average time/residue: 0.2608
  time to fit residues: 38.8441
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  136 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0670
   chunk 62 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.130548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.101984 restraints weight = 12865.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.21
r_work: 0.3176 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9140  Z= 0.199
  Angle     :  0.475   5.759  12390  Z= 0.249
  Chirality :  0.041   0.136   1374
  Planarity :  0.004   0.044   1604
  Dihedral  :  6.159  63.529   1256
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.47 %
    Favored  : 89.52 %
  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:  0.96 (0.25), residues: 1126
  helix:  1.51 (0.24), residues: 484
  sheet:  0.21 (0.38), residues: 190
  loop : -0.01 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 917 
 HIS   0.002   0.000   HIS A 202 
 PHE   0.019   0.001   PHE C  62 
 TYR   0.009   0.001   TYR A  81 
 ARG   0.004   0.000   ARG C 143 

*********************** 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
  114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8961 (t) cc_final: 0.8674 (m)
REVERT: A  135 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7754 (mtmt)
REVERT: A  218 MET cc_start: 0.7165 (mmm) cc_final: 0.6909 (mmm)
REVERT: A  406 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7316 (mmt-90)
REVERT: A  592 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8257 (tp)
REVERT: A  675 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8374 (m-30)
REVERT: A  699 GLN cc_start: 0.8633 (mp10) cc_final: 0.8318 (mp10)
REVERT: A  710 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8021 (p)
REVERT: A  784 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8110 (ptpp)
REVERT: A  869 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7535 (mp0)
REVERT: A  915 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7686 (tmtt)
REVERT: A  936 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7704 (mtmt)
REVERT: A  997 ASP cc_start: 0.8096 (t0) cc_final: 0.6875 (p0)
REVERT: C  117 ASP cc_start: 0.7287 (t70) cc_final: 0.6970 (t70)
  outliers start: 20
  outliers final: 12
  residues processed: 104
  average time/residue: 0.2576
  time to fit residues: 36.0264
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  915 LYS
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  136 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0370
   chunk 82 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 110 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 76 optimal weight:    6.9990
   chunk 93 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.130579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.102218 restraints weight = 12744.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.19
r_work: 0.3181 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9140  Z= 0.190
  Angle     :  0.480   9.323  12390  Z= 0.247
  Chirality :  0.041   0.133   1374
  Planarity :  0.004   0.043   1604
  Dihedral  :  5.972  59.710   1256
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  8.37 %
    Favored  : 89.21 %
  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:  1.01 (0.25), residues: 1126
  helix:  1.53 (0.24), residues: 485
  sheet:  0.24 (0.38), residues: 190
  loop :  0.05 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 917 
 HIS   0.002   0.000   HIS A 818 
 PHE   0.041   0.001   PHE C  62 
 TYR   0.008   0.001   TYR A  81 
 ARG   0.006   0.000   ARG C   5 

*********************** 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
  116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8958 (t) cc_final: 0.8663 (m)
REVERT: A  135 LYS cc_start: 0.8410 (mmmt) cc_final: 0.7724 (mtmt)
REVERT: A  218 MET cc_start: 0.7207 (mmm) cc_final: 0.6991 (mmm)
REVERT: A  406 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7303 (mmt-90)
REVERT: A  464 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7905 (pmt)
REVERT: A  592 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8201 (tp)
REVERT: A  675 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8376 (m-30)
REVERT: A  699 GLN cc_start: 0.8610 (mp10) cc_final: 0.8313 (mp10)
REVERT: A  710 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8031 (p)
REVERT: A  784 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8099 (ptpp)
REVERT: A  869 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7501 (mp0)
REVERT: A  915 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7706 (tmtt)
REVERT: A  936 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7673 (mtmt)
REVERT: A  997 ASP cc_start: 0.8086 (t0) cc_final: 0.6869 (p0)
REVERT: C   28 ASP cc_start: 0.7017 (m-30) cc_final: 0.6267 (p0)
REVERT: C   90 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7638 (mmm160)
REVERT: C  117 ASP cc_start: 0.7236 (t70) cc_final: 0.6899 (t70)
  outliers start: 24
  outliers final: 15
  residues processed: 106
  average time/residue: 0.2779
  time to fit residues: 39.7782
Evaluate side-chains
  112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  915 LYS
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  137 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0980
   chunk 20 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.131181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.102999 restraints weight = 12816.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.19
r_work: 0.3188 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9140  Z= 0.168
  Angle     :  0.468   7.381  12390  Z= 0.241
  Chirality :  0.041   0.132   1374
  Planarity :  0.004   0.041   1604
  Dihedral  :  5.874  59.760   1256
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.27 %
    Favored  : 88.61 %
  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:  1.61 (0.24), residues: 485
  sheet:  0.32 (0.39), residues: 178
  loop :  0.07 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 917 
 HIS   0.002   0.000   HIS A 818 
 PHE   0.011   0.001   PHE C  62 
 TYR   0.009   0.001   TYR A  81 
 ARG   0.007   0.000   ARG C   8 

*********************** 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
  119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8947 (t) cc_final: 0.8664 (m)
REVERT: A  135 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7678 (mtmt)
REVERT: A  464 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7863 (pmt)
REVERT: A  675 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8343 (m-30)
REVERT: A  710 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8029 (p)
REVERT: A  784 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8100 (ptpp)
REVERT: A  869 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8115 (mm-30)
REVERT: A  915 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7715 (tmtt)
REVERT: A  936 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7674 (mtmt)
REVERT: A  997 ASP cc_start: 0.8078 (t0) cc_final: 0.6872 (p0)
REVERT: C   90 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7605 (mmm160)
REVERT: C  117 ASP cc_start: 0.7212 (t70) cc_final: 0.6877 (t70)
  outliers start: 21
  outliers final: 14
  residues processed: 107
  average time/residue: 0.2447
  time to fit residues: 35.4056
Evaluate side-chains
  110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  915 LYS
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  137 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0270
   chunk 18 optimal weight:    0.7980
   chunk 95 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0570
   overall best weight:    0.3474

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.132014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.103691 restraints weight = 12866.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.20
r_work: 0.3211 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9140  Z= 0.145
  Angle     :  0.460   7.108  12390  Z= 0.237
  Chirality :  0.040   0.130   1374
  Planarity :  0.004   0.040   1604
  Dihedral  :  5.726  59.295   1256
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.88 %
    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:  1.18 (0.26), residues: 1126
  helix:  1.65 (0.24), residues: 485
  sheet:  0.34 (0.39), residues: 178
  loop :  0.15 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 917 
 HIS   0.002   0.000   HIS A 574 
 PHE   0.024   0.001   PHE C  62 
 TYR   0.006   0.001   TYR A 933 
 ARG   0.006   0.000   ARG C   8 

*********************** 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
  115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8915 (t) cc_final: 0.8645 (m)
REVERT: A  464 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7824 (pmt)
REVERT: A  592 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8188 (tp)
REVERT: A  675 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8339 (m-30)
REVERT: A  699 GLN cc_start: 0.8630 (mp10) cc_final: 0.8414 (mp10)
REVERT: A  710 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8030 (p)
REVERT: A  784 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8067 (ptpp)
REVERT: A  869 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8101 (mm-30)
REVERT: A  915 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7643 (tmtt)
REVERT: A  936 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7656 (mtmt)
REVERT: A  997 ASP cc_start: 0.8083 (t0) cc_final: 0.6911 (p0)
REVERT: C   66 LYS cc_start: 0.8322 (mtpp) cc_final: 0.7745 (tttm)
REVERT: C   90 ARG cc_start: 0.7963 (mmm160) cc_final: 0.7652 (mmm160)
REVERT: C  117 ASP cc_start: 0.7232 (t70) cc_final: 0.6897 (t70)
  outliers start: 20
  outliers final: 11
  residues processed: 104
  average time/residue: 0.2793
  time to fit residues: 39.3739
Evaluate side-chains
  109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  915 LYS
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  137 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0270
   chunk 54 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.131497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.102926 restraints weight = 13050.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.24
r_work: 0.3195 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9140  Z= 0.181
  Angle     :  0.474   8.728  12390  Z= 0.242
  Chirality :  0.041   0.129   1374
  Planarity :  0.004   0.041   1604
  Dihedral  :  5.675  59.111   1256
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 10.08 %
    Favored  : 87.50 %
  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:  1.19 (0.26), residues: 1126
  helix:  1.64 (0.24), residues: 485
  sheet:  0.35 (0.39), residues: 181
  loop :  0.17 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 917 
 HIS   0.002   0.000   HIS A 818 
 PHE   0.009   0.001   PHE C  62 
 TYR   0.008   0.001   TYR A  81 
 ARG   0.007   0.000   ARG C   8 

*********************** 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
  115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8935 (t) cc_final: 0.8689 (m)
REVERT: A  464 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7870 (pmt)
REVERT: A  592 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8289 (tp)
REVERT: A  600 ASN cc_start: 0.8928 (p0) cc_final: 0.8675 (p0)
REVERT: A  675 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8356 (m-30)
REVERT: A  699 GLN cc_start: 0.8609 (mp10) cc_final: 0.8377 (mp10)
REVERT: A  710 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8016 (p)
REVERT: A  784 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8073 (ptpp)
REVERT: A  869 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8118 (mm-30)
REVERT: A  915 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7675 (tmtt)
REVERT: A  936 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7733 (mtmt)
REVERT: A  997 ASP cc_start: 0.8106 (t0) cc_final: 0.7004 (p0)
REVERT: C   90 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7725 (mmm160)
REVERT: C  117 ASP cc_start: 0.7248 (t70) cc_final: 0.6934 (t70)
  outliers start: 24
  outliers final: 17
  residues processed: 103
  average time/residue: 0.2361
  time to fit residues: 33.3466
Evaluate side-chains
  115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  915 LYS
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  137 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 82 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0670
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.132283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.103859 restraints weight = 12867.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.23
r_work: 0.3205 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9140  Z= 0.145
  Angle     :  0.468   8.208  12390  Z= 0.238
  Chirality :  0.040   0.129   1374
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.641  58.716   1256
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.38 %
    Favored  : 87.30 %
  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:  1.25 (0.26), residues: 1126
  helix:  1.72 (0.24), residues: 484
  sheet:  0.37 (0.39), residues: 178
  loop :  0.18 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 917 
 HIS   0.002   0.000   HIS A 818 
 PHE   0.026   0.001   PHE C  62 
 TYR   0.006   0.001   TYR A 933 
 ARG   0.005   0.000   ARG C   8 

*********************** 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
  116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8892 (t) cc_final: 0.8649 (m)
REVERT: A  176 ASP cc_start: 0.7767 (t0) cc_final: 0.6979 (t0)
REVERT: A  464 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7841 (pmt)
REVERT: A  592 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8279 (tp)
REVERT: A  600 ASN cc_start: 0.8885 (p0) cc_final: 0.8663 (p0)
REVERT: A  627 TYR cc_start: 0.8069 (t80) cc_final: 0.7606 (t80)
REVERT: A  675 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8328 (m-30)
REVERT: A  699 GLN cc_start: 0.8632 (mp10) cc_final: 0.8407 (mp10)
REVERT: A  710 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8025 (p)
REVERT: A  784 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8074 (ptpp)
REVERT: A  869 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8152 (mm-30)
REVERT: A  915 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7663 (tmtt)
REVERT: A  936 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7684 (mtmt)
REVERT: A  997 ASP cc_start: 0.8094 (t0) cc_final: 0.6998 (p0)
REVERT: C   66 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7848 (tttm)
REVERT: C   90 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7691 (mmm160)
REVERT: C  117 ASP cc_start: 0.7234 (t70) cc_final: 0.6922 (t70)
  outliers start: 23
  outliers final: 15
  residues processed: 106
  average time/residue: 0.2317
  time to fit residues: 33.7982
Evaluate side-chains
  113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  912 GLU
Chi-restraints excluded: chain A residue  915 LYS
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  136 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    0.2980
   chunk 108 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 57 optimal weight:    0.1980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.131454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103006 restraints weight = 12860.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.22
r_work: 0.3188 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9140  Z= 0.193
  Angle     :  0.477   8.131  12390  Z= 0.244
  Chirality :  0.041   0.130   1374
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.608  58.554   1256
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.38 %
    Favored  : 87.40 %
  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:  1.66 (0.24), residues: 484
  sheet:  0.36 (0.39), residues: 181
  loop :  0.16 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.000   HIS A 818 
 PHE   0.017   0.001   PHE A 985 
 TYR   0.009   0.001   TYR A  81 
 ARG   0.007   0.000   ARG C   8 

********************** 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
  116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 SER cc_start: 0.8945 (t) cc_final: 0.8680 (m)
REVERT: A  464 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7835 (pmt)
REVERT: A  592 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8240 (tp)
REVERT: A  600 ASN cc_start: 0.8945 (p0) cc_final: 0.8693 (p0)
REVERT: A  627 TYR cc_start: 0.8041 (t80) cc_final: 0.7555 (t80)
REVERT: A  675 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8361 (m-30)
REVERT: A  699 GLN cc_start: 0.8633 (mp10) cc_final: 0.8382 (mp10)
REVERT: A  710 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8047 (p)
REVERT: A  784 LYS cc_start: 0.8518 (ttpp) cc_final: 0.7887 (mtmm)
REVERT: A  869 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8116 (mm-30)
REVERT: A  936 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7653 (mtmt)
REVERT: A  997 ASP cc_start: 0.8076 (t0) cc_final: 0.6941 (p0)
REVERT: C   66 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7792 (tttm)
REVERT: C   90 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7668 (mmm160)
  outliers start: 22
  outliers final: 15
  residues processed: 106
  average time/residue: 0.2334
  time to fit residues: 34.0349
Evaluate side-chains
  112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 CYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  675 ASP
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  806 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  912 GLU
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain A residue  993 ILE
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  136 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0000
   chunk 29 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0570
   overall best weight:    0.4702

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.132001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.103491 restraints weight = 12930.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.23
r_work: 0.3193 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9140  Z= 0.164
  Angle     :  0.480   8.262  12390  Z= 0.245
  Chirality :  0.041   0.149   1374
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.590  58.682   1256
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.69 %
    Favored  : 87.20 %
  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:  1.22 (0.26), residues: 1126
  helix:  1.69 (0.24), residues: 486
  sheet:  0.38 (0.39), residues: 181
  loop :  0.16 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 917 
 HIS   0.002   0.000   HIS A 818 
 PHE   0.027   0.001   PHE C  62 
 TYR   0.008   0.001   TYR A  81 
 ARG   0.008   0.000   ARG C   8 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

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Job complete
usr+sys time: 5197.39 seconds
wall clock time: 91 minutes 12.64 seconds (5472.64 seconds total)