Starting phenix.real_space_refine
on Thu Jan 16 03:25:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5q_44221/01_2025/9b5q_44221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5q_44221/01_2025/9b5q_44221.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5q_44221/01_2025/9b5q_44221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5q_44221/01_2025/9b5q_44221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5q_44221/01_2025/9b5q_44221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5q_44221/01_2025/9b5q_44221.cif"
  }
  resolution = 2.95
  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=   0.066
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 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.04, per 1000 atoms: 0.68
  Number of scatterers: 8935
  At special positions: 0
  Unit cell: (85.12, 100.016, 120.232, 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=2.90

  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: 2.41
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      48.3% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.879A  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: 3.817A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.028A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.455A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.576A  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 144
      removed outlier: 3.763A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.368A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 304
      removed outlier: 3.616A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.282A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.554A  pdb=" N   SER A 427 " --> pdb=" O   GLU A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.807A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ARG A 474 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.749A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.963A  pdb=" N   LYS A 528 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.577A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 3.569A  pdb=" N   SER A 582 " --> pdb=" O   TYR A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
      removed outlier: 3.519A  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: 3.561A  pdb=" N   THR A 636 " --> pdb=" O   ASN A 632 " (cutoff:3.500A)
      removed outlier: 3.658A  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
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.597A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.964A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
    Processing helix  chain 'A' and resid 796 through 800
    Processing helix  chain 'A' and resid 818 through 835
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.506A  pdb=" N   THR A 859 " --> pdb=" O   MET A 855 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.661A  pdb=" N   GLU A 882 " --> pdb=" O   LYS A 879 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR A 883 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 879 through 883'
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 145
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.771A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   THR A 129 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   ILE A  43 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.270A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.312A  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: 4.053A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.446A  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: 4.053A  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: 6.435A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.081A  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: 6.331A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ASP A 996 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   VAL A 942 " --> pdb=" O   ASP A 996 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.841A  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: 6.331A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22
      removed outlier: 6.165A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22

    441 hydrogen bonds defined for protein.
    1212 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: 3.22

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1512
        1.27 -     1.40: 2173
        1.40 -     1.54: 5256
        1.54 -     1.67: 137
        1.67 -     1.81: 62
  Bond restraints: 9140
  Sorted by residual:
  bond pdb=" C04 A1AIV D 201 "
       pdb=" C05 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.453  1.525 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.518  0.013 1.20e-02 6.94e+03 1.21e+00
  bond pdb=" C05 A1AIV D 201 "
       pdb=" N06 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.151  1.131  0.020 2.00e-02 2.50e+03 9.60e-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 7.69e-01
  bond pdb=" CA  SER A 789 "
       pdb=" C   SER A 789 "
    ideal  model  delta    sigma   weight residual
    1.524  1.517  0.007 1.27e-02 6.20e+03 2.85e-01
  ... (remaining 9135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 12219
        1.34 -     2.67: 95
        2.67 -     4.01: 67
        4.01 -     5.35: 5
        5.35 -     6.68: 4
  Bond angle restraints: 12390
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  128.38   -6.68 1.80e+00 3.09e-01 1.38e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.01    3.52 1.18e+00 7.24e-01 8.95e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.48    4.71 1.76e+00 3.23e-01 7.16e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  105.15    6.68 2.67e+00 1.40e-01 6.27e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  105.71    6.12 2.67e+00 1.40e-01 5.25e+00
  ... (remaining 12385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 5342
       17.90 -    35.81: 166
       35.81 -    53.71: 37
       53.71 -    71.61: 5
       71.61 -    89.52: 2
  Dihedral angle restraints: 5552
    sinusoidal: 2262
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.05   52.05     1      1.00e+01 1.00e-02 3.70e+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  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" N   CYS C  85 "
           pdb=" CA  CYS C  85 "
           pdb=" CB  CYS C  85 "
           pdb=" SG  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.10   59.10     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1218
       0.058 -    0.115: 130
       0.115 -    0.173: 23
       0.173 -    0.231: 1
       0.231 -    0.288: 2
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.28 2.00e-01 2.50e+01 1.93e+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 1.28e+00
  ... (remaining 1371 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 143 "    0.131 9.50e-02 1.11e+02   5.86e-02 2.11e+00
        pdb=" NE  ARG C 143 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 143 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  94 "    0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO C  95 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  17 "    0.019 5.00e-02 4.00e+02   2.93e-02 1.38e+00
        pdb=" N   PRO C  18 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  18 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  18 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 50
        2.59 -     3.16: 7400
        3.16 -     3.74: 13021
        3.74 -     4.32: 19330
        4.32 -     4.90: 32850
  Nonbonded interactions: 72651
  Sorted by model distance:
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2B ATP A1103 "
     model   vdw
     2.007 2.170
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     2.022 2.170
  nonbonded pdb=" OD2 ASP A 537 "
            pdb="MG    MG A1101 "
     model   vdw
     2.040 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.085 2.170
  nonbonded pdb=" OD2 ASP A 463 "
            pdb=" O3' ATP A1103 "
     model   vdw
     2.175 3.040
  ... (remaining 72646 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:             3.890
  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:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.740
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
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   0.072   9140  Z= 0.203
  Angle     :  0.465   6.685  12390  Z= 0.236
  Chirality :  0.042   0.288   1374
  Planarity :  0.004   0.059   1604
  Dihedral  :  9.514  89.519   3425
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  2.22 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1126
  helix:  1.45 (0.24), residues: 477
  sheet:  0.13 (0.40), residues: 183
  loop :  0.24 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 608 
 HIS   0.003   0.001   HIS C  75 
 PHE   0.010   0.001   PHE A 842 
 TYR   0.008   0.001   TYR A 732 
 ARG   0.003   0.000   ARG A 919 

*********************** 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
  149 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8156 (t70) cc_final: 0.7398 (p0)
REVERT: A  442 MET cc_start: 0.8825 (tpp) cc_final: 0.8500 (mmm)
REVERT: A  582 SER cc_start: 0.8262 (m) cc_final: 0.7927 (p)
REVERT: A  832 MET cc_start: 0.8437 (mtp) cc_final: 0.8216 (mtp)
REVERT: A  911 LYS cc_start: 0.7289 (mtmt) cc_final: 0.7038 (mtpp)
REVERT: A  937 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6877 (mp0)
REVERT: A  983 GLU cc_start: 0.8423 (mp0) cc_final: 0.8045 (mp0)
REVERT: C   42 ASP cc_start: 0.8288 (p0) cc_final: 0.7866 (p0)
REVERT: C   59 ASP cc_start: 0.8211 (m-30) cc_final: 0.7561 (t70)
REVERT: C   72 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8058 (mmm-85)
  outliers start: 13
  outliers final: 4
  residues processed: 145
  average time/residue: 1.4998
  time to fit residues: 231.0357
Evaluate side-chains
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
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:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0070
   chunk 45 optimal weight:    2.9990
   chunk 87 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.5200

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.134974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.099106 restraints weight = 11482.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.92
r_work: 0.2985 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1270

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= 0.205
  Angle     :  0.494   7.996  12390  Z= 0.256
  Chirality :  0.042   0.135   1374
  Planarity :  0.004   0.039   1604
  Dihedral  :  6.019  62.385   1256
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  6.05 %
    Favored  : 91.83 %
  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 (0.25), residues: 1126
  helix:  1.55 (0.24), residues: 486
  sheet:  0.33 (0.41), residues: 174
  loop :  0.19 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 917 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.011   0.001   PHE A 842 
 TYR   0.009   0.001   TYR A 732 
 ARG   0.006   0.000   ARG C 139 

*********************** 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
  109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8161 (t70) cc_final: 0.7402 (p0)
REVERT: A  320 GLU cc_start: 0.7319 (tt0) cc_final: 0.7083 (tt0)
REVERT: A  387 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8408 (p0)
REVERT: A  582 SER cc_start: 0.8052 (m) cc_final: 0.7807 (p)
REVERT: A  596 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7530 (tttt)
REVERT: A  668 MET cc_start: 0.8373 (tpp) cc_final: 0.8116 (mmm)
REVERT: A  879 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8392 (mttp)
REVERT: A  911 LYS cc_start: 0.7230 (mtmt) cc_final: 0.7010 (mtpp)
REVERT: A  983 GLU cc_start: 0.8535 (mp0) cc_final: 0.8123 (mp0)
REVERT: C   59 ASP cc_start: 0.8418 (m-30) cc_final: 0.7633 (t70)
REVERT: C   72 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8187 (mmm-85)
REVERT: C  144 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8498 (tmmt)
  outliers start: 21
  outliers final: 8
  residues processed: 104
  average time/residue: 1.4138
  time to fit residues: 156.6703
Evaluate side-chains
  93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  879 LYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   91 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 61 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 106 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0870
   overall best weight:    0.6160

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.134983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.099012 restraints weight = 11700.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 1.93
r_work: 0.2976 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9140  Z= 0.222
  Angle     :  0.486  10.662  12390  Z= 0.252
  Chirality :  0.042   0.162   1374
  Planarity :  0.004   0.040   1604
  Dihedral  :  5.793  63.993   1250
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  7.16 %
    Favored  : 90.62 %
  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 (0.25), residues: 1126
  helix:  1.56 (0.24), residues: 486
  sheet:  0.29 (0.41), residues: 174
  loop :  0.19 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  93 
 HIS   0.005   0.001   HIS C  32 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.008   0.001   TYR A 736 
 ARG   0.007   0.000   ARG C 139 

*********************** 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
  103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8195 (t70) cc_final: 0.7416 (p0)
REVERT: A  320 GLU cc_start: 0.7341 (tt0) cc_final: 0.7105 (tt0)
REVERT: A  387 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8438 (p0)
REVERT: A  582 SER cc_start: 0.8050 (m) cc_final: 0.7818 (p)
REVERT: A  596 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7472 (tttt)
REVERT: A  668 MET cc_start: 0.8349 (tpp) cc_final: 0.8072 (mmm)
REVERT: A  911 LYS cc_start: 0.7236 (mtmt) cc_final: 0.7034 (mtpp)
REVERT: A  983 GLU cc_start: 0.8603 (mp0) cc_final: 0.8169 (mp0)
REVERT: C   59 ASP cc_start: 0.8321 (m-30) cc_final: 0.7597 (t70)
REVERT: C   72 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8112 (mmm-85)
  outliers start: 22
  outliers final: 16
  residues processed: 94
  average time/residue: 1.3041
  time to fit residues: 131.1360
Evaluate side-chains
  93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  979 LYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   26 VAL
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  143 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0770
   chunk 72 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 105 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.134895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.099384 restraints weight = 11617.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.94
r_work: 0.2984 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1545

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= 0.204
  Angle     :  0.472  10.748  12390  Z= 0.244
  Chirality :  0.041   0.149   1374
  Planarity :  0.004   0.041   1604
  Dihedral  :  5.755  62.240   1250
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  8.17 %
    Favored  : 89.42 %
  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:  1.16 (0.26), residues: 1126
  helix:  1.61 (0.24), residues: 485
  sheet:  0.22 (0.41), residues: 174
  loop :  0.23 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 608 
 HIS   0.002   0.001   HIS A 818 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.012   0.001   TYR C 145 
 ARG   0.007   0.000   ARG C 139 

*********************** 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
  102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8744 (ttp) cc_final: 0.8470 (mtp)
REVERT: A  274 ASP cc_start: 0.8188 (t70) cc_final: 0.7434 (p0)
REVERT: A  387 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8412 (p0)
REVERT: A  465 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8291 (t70)
REVERT: A  582 SER cc_start: 0.8066 (m) cc_final: 0.7842 (p)
REVERT: A  596 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7498 (tttt)
REVERT: A  699 GLN cc_start: 0.8439 (mt0) cc_final: 0.7766 (mp10)
REVERT: A  911 LYS cc_start: 0.7277 (mtmt) cc_final: 0.7064 (mtpp)
REVERT: A  983 GLU cc_start: 0.8559 (mp0) cc_final: 0.8108 (mp0)
REVERT: C   59 ASP cc_start: 0.8343 (m-30) cc_final: 0.7645 (t70)
REVERT: C   72 ARG cc_start: 0.8547 (mmm-85) cc_final: 0.8236 (mmm-85)
  outliers start: 24
  outliers final: 16
  residues processed: 93
  average time/residue: 1.2834
  time to fit residues: 127.8207
Evaluate side-chains
  95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  979 LYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  143 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 110 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.134646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.099384 restraints weight = 11520.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.96
r_work: 0.2989 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9140  Z= 0.208
  Angle     :  0.476  10.222  12390  Z= 0.244
  Chirality :  0.041   0.147   1374
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.732  60.676   1250
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  8.77 %
    Favored  : 89.11 %
  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:  1.66 (0.24), residues: 485
  sheet:  0.17 (0.40), residues: 174
  loop :  0.22 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.007   0.001   TYR A 736 
 ARG   0.008   0.000   ARG C 139 

*********************** 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
  97 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8421 (tp30) cc_final: 0.7971 (tp30)
REVERT: A   35 MET cc_start: 0.8778 (ttp) cc_final: 0.8503 (mtp)
REVERT: A  274 ASP cc_start: 0.8201 (t70) cc_final: 0.7425 (p0)
REVERT: A  387 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (p0)
REVERT: A  465 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8282 (t70)
REVERT: A  582 SER cc_start: 0.8072 (m) cc_final: 0.7847 (p)
REVERT: A  596 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7523 (tttt)
REVERT: A  668 MET cc_start: 0.8364 (tpp) cc_final: 0.8088 (mmm)
REVERT: A  911 LYS cc_start: 0.7260 (mtmt) cc_final: 0.7051 (mtpp)
REVERT: A  983 GLU cc_start: 0.8559 (mp0) cc_final: 0.8096 (mp0)
REVERT: C   59 ASP cc_start: 0.8339 (m-30) cc_final: 0.7639 (t70)
  outliers start: 21
  outliers final: 13
  residues processed: 90
  average time/residue: 1.3711
  time to fit residues: 131.9831
Evaluate side-chains
  89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  979 LYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  143 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0980
   chunk 20 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.134054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.099658 restraints weight = 11596.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.77
r_work: 0.3014 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9140  Z= 0.227
  Angle     :  0.487   9.867  12390  Z= 0.251
  Chirality :  0.042   0.151   1374
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.774  59.961   1250
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  9.17 %
    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:  1.14 (0.26), residues: 1126
  helix:  1.65 (0.24), residues: 484
  sheet:  0.12 (0.40), residues: 174
  loop :  0.19 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 608 
 HIS   0.002   0.001   HIS A 818 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.009   0.001   TYR C 145 
 ARG   0.009   0.000   ARG C 139 

*********************** 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
  97 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8423 (tp30) cc_final: 0.8002 (tp30)
REVERT: A   35 MET cc_start: 0.8794 (ttp) cc_final: 0.8552 (mtp)
REVERT: A  274 ASP cc_start: 0.8161 (t70) cc_final: 0.7497 (p0)
REVERT: A  387 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8372 (p0)
REVERT: A  465 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8332 (t70)
REVERT: A  582 SER cc_start: 0.8148 (m) cc_final: 0.7940 (p)
REVERT: A  596 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7629 (tttt)
REVERT: A  668 MET cc_start: 0.8432 (tpp) cc_final: 0.8147 (mmm)
REVERT: A  699 GLN cc_start: 0.8345 (mp10) cc_final: 0.7600 (mp10)
REVERT: A  983 GLU cc_start: 0.8573 (mp0) cc_final: 0.8151 (mp0)
REVERT: C   59 ASP cc_start: 0.8245 (m-30) cc_final: 0.7670 (t70)
REVERT: C  139 ARG cc_start: 0.7050 (ttm-80) cc_final: 0.6333 (mtm-85)
  outliers start: 22
  outliers final: 11
  residues processed: 89
  average time/residue: 1.3734
  time to fit residues: 130.3651
Evaluate side-chains
  86 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  979 LYS
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   91 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 102 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 91 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.133954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.099955 restraints weight = 11651.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.76
r_work: 0.3014 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9140  Z= 0.233
  Angle     :  0.492   9.900  12390  Z= 0.253
  Chirality :  0.042   0.158   1374
  Planarity :  0.004   0.043   1604
  Dihedral  :  5.790  59.722   1250
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.78 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.26), residues: 1126
  helix:  1.65 (0.24), residues: 484
  sheet:  0.11 (0.40), residues: 174
  loop :  0.20 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 608 
 HIS   0.003   0.001   HIS C  32 
 PHE   0.009   0.001   PHE A 360 
 TYR   0.009   0.001   TYR C 145 
 ARG   0.006   0.000   ARG C   5 

*********************** 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
  93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.8422 (tp30) cc_final: 0.8006 (tp30)
REVERT: A   35 MET cc_start: 0.8795 (ttp) cc_final: 0.8570 (mtp)
REVERT: A  274 ASP cc_start: 0.8130 (t70) cc_final: 0.7494 (p0)
REVERT: A  387 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (p0)
REVERT: A  465 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8346 (t70)
REVERT: A  582 SER cc_start: 0.8162 (m) cc_final: 0.7961 (p)
REVERT: A  596 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7661 (tttt)
REVERT: A  699 GLN cc_start: 0.8334 (mp10) cc_final: 0.7605 (mp10)
REVERT: A  935 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7825 (tm130)
REVERT: A  983 GLU cc_start: 0.8578 (mp0) cc_final: 0.8168 (mp0)
REVERT: A 1005 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8159 (m)
REVERT: C   59 ASP cc_start: 0.8238 (m-30) cc_final: 0.7675 (t70)
REVERT: C  139 ARG cc_start: 0.7073 (ttm-80) cc_final: 0.6360 (mtm-85)
  outliers start: 20
  outliers final: 10
  residues processed: 88
  average time/residue: 1.3496
  time to fit residues: 127.1092
Evaluate side-chains
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain C residue   91 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0010
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.5586

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.134288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.100304 restraints weight = 11812.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.82
r_work: 0.3008 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9140  Z= 0.208
  Angle     :  0.479   9.600  12390  Z= 0.247
  Chirality :  0.042   0.150   1374
  Planarity :  0.004   0.043   1604
  Dihedral  :  5.748  58.215   1250
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.28 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1126
  helix:  1.68 (0.24), residues: 484
  sheet:  0.11 (0.41), residues: 174
  loop :  0.18 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.008   0.001   PHE A 360 
 TYR   0.007   0.001   TYR A 736 
 ARG   0.005   0.000   ARG C 139 

*********************** 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
  89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8423 (tp30) cc_final: 0.8009 (tp30)
REVERT: A   35 MET cc_start: 0.8745 (ttp) cc_final: 0.8532 (mtp)
REVERT: A  274 ASP cc_start: 0.8138 (t70) cc_final: 0.7443 (p0)
REVERT: A  387 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8344 (p0)
REVERT: A  465 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8323 (t70)
REVERT: A  582 SER cc_start: 0.8136 (m) cc_final: 0.7936 (p)
REVERT: A  596 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7600 (tttt)
REVERT: A  699 GLN cc_start: 0.8336 (mp10) cc_final: 0.7568 (mp10)
REVERT: A  935 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7881 (tm-30)
REVERT: A  983 GLU cc_start: 0.8582 (mp0) cc_final: 0.8155 (mp0)
REVERT: A 1005 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8120 (m)
REVERT: C   59 ASP cc_start: 0.8223 (m-30) cc_final: 0.7638 (t70)
  outliers start: 15
  outliers final: 10
  residues processed: 87
  average time/residue: 1.3706
  time to fit residues: 127.4603
Evaluate side-chains
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain C residue   91 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    0.2980
   chunk 68 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 82 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.134598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.100065 restraints weight = 11622.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.78
r_work: 0.3023 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1863

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= 0.182
  Angle     :  0.479   9.553  12390  Z= 0.246
  Chirality :  0.041   0.145   1374
  Planarity :  0.004   0.045   1604
  Dihedral  :  5.692  56.634   1250
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.28 %
    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:  1.21 (0.26), residues: 1126
  helix:  1.71 (0.24), residues: 484
  sheet:  0.16 (0.41), residues: 174
  loop :  0.21 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.008   0.001   PHE A 613 
 TYR   0.010   0.001   TYR C 145 
 ARG   0.013   0.000   ARG C 139 

*********************** 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
  88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8403 (tp30) cc_final: 0.8011 (tp30)
REVERT: A  274 ASP cc_start: 0.8138 (t70) cc_final: 0.7502 (p0)
REVERT: A  387 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8292 (p0)
REVERT: A  465 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8368 (t70)
REVERT: A  596 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7694 (tttt)
REVERT: A  668 MET cc_start: 0.8428 (tpp) cc_final: 0.8164 (mmm)
REVERT: A  699 GLN cc_start: 0.8301 (mp10) cc_final: 0.7590 (mp10)
REVERT: A  983 GLU cc_start: 0.8586 (mp0) cc_final: 0.8190 (mp0)
REVERT: C   59 ASP cc_start: 0.8143 (m-30) cc_final: 0.7650 (t70)
REVERT: C  139 ARG cc_start: 0.6981 (ttm-80) cc_final: 0.6205 (mtm-85)
  outliers start: 16
  outliers final: 9
  residues processed: 83
  average time/residue: 1.3907
  time to fit residues: 123.5589
Evaluate side-chains
  82 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   91 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 10 optimal weight:    0.4980
   chunk 108 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 105 optimal weight:    0.0970
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 75 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.135412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.100974 restraints weight = 11644.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.79
r_work: 0.3033 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9140  Z= 0.166
  Angle     :  0.480   9.125  12390  Z= 0.247
  Chirality :  0.041   0.141   1374
  Planarity :  0.004   0.042   1604
  Dihedral  :  5.627  56.428   1250
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.79 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1126
  helix:  1.78 (0.25), residues: 479
  sheet:  0.25 (0.41), residues: 164
  loop :  0.22 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 917 
 HIS   0.002   0.000   HIS C  32 
 PHE   0.009   0.001   PHE A 613 
 TYR   0.012   0.001   TYR C 145 
 ARG   0.010   0.000   ARG C 139 

********************** 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
  88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.8377 (tp30) cc_final: 0.7961 (tp30)
REVERT: A  274 ASP cc_start: 0.8109 (t70) cc_final: 0.7403 (p0)
REVERT: A  465 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8319 (t70)
REVERT: A  596 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7621 (tttt)
REVERT: A  668 MET cc_start: 0.8386 (tpp) cc_final: 0.8121 (mmm)
REVERT: A  699 GLN cc_start: 0.8310 (mp10) cc_final: 0.7575 (mp10)
REVERT: A  983 GLU cc_start: 0.8575 (mp0) cc_final: 0.8155 (mp0)
REVERT: A 1005 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8103 (m)
REVERT: C   59 ASP cc_start: 0.8164 (m-30) cc_final: 0.7703 (t70)
REVERT: C   72 ARG cc_start: 0.8361 (mtp180) cc_final: 0.8020 (mtp-110)
REVERT: C  139 ARG cc_start: 0.6895 (ttm-80) cc_final: 0.6120 (mtm-85)
  outliers start: 15
  outliers final: 9
  residues processed: 84
  average time/residue: 1.3789
  time to fit residues: 123.9268
Evaluate side-chains
  84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  465 ASP
Chi-restraints excluded: chain A residue  596 LYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain C residue   91 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 106 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 73 optimal weight:    0.2980
   chunk 76 optimal weight:    0.0870
   chunk 29 optimal weight:    0.0770
   chunk 105 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.3516

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.135367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.100160 restraints weight = 11645.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.78
r_work: 0.3024 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9140  Z= 0.159
  Angle     :  0.480   8.711  12390  Z= 0.247
  Chirality :  0.041   0.142   1374
  Planarity :  0.004   0.043   1604
  Dihedral  :  5.581  56.376   1250
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.09 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.26), residues: 1126
  helix:  1.81 (0.25), residues: 479
  sheet:  0.17 (0.40), residues: 174
  loop :  0.26 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C  32 
 PHE   0.009   0.001   PHE A 613 
 TYR   0.011   0.001   TYR C 145 
 ARG   0.009   0.000   ARG C 139 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 6013.50 seconds
wall clock time: 106 minutes 49.89 seconds (6409.89 seconds total)