Starting phenix.real_space_refine
on Mon Apr 28 08:37:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mg8_9111/04_2025/6mg8_9111.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mg8_9111/04_2025/6mg8_9111.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mg8_9111/04_2025/6mg8_9111.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mg8_9111/04_2025/6mg8_9111.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mg8_9111/04_2025/6mg8_9111.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mg8_9111/04_2025/6mg8_9111.cif"
  }
  resolution = 3.6
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    4653      2.51       5
     N    1165      2.21       5
     O    1187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7034
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 6922
          Classifications: {'peptide': 985}
          Incomplete info: {'truncation_to_alanine': 266}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 940}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 881
          Unresolved non-hydrogen angles: 1088
          Unresolved non-hydrogen dihedrals: 717
          Unresolved non-hydrogen chiralities: 62
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 32, 'PHE:plan': 7, 'GLU:plan': 33, 'ARG:plan': 19}
          Unresolved non-hydrogen planarities: 483
    Chain: "A"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 112
          Unusual residues: {'CLR': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.31, per 1000 atoms: 0.75
  Number of scatterers: 7034
  At special positions: 0
  Unit cell: (83.84, 110.04, 121.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1187      8.00
     N    1165      7.00
     C    4653      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 313 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 290 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.99
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1846

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      60.8% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 84
      removed outlier: 3.753A  pdb=" N   LEU A  63 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TRP A  64 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LEU A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLY A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS A  82 " --> pdb=" O   CYS A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 100
      removed outlier: 3.903A  pdb=" N   PHE A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA A  99 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A 100 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 104
    Processing helix  chain 'A' and resid 120 through 133
      removed outlier: 3.694A  pdb=" N   THR A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLN A 131 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 161 through 166
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 184 through 188
      removed outlier: 3.548A  pdb=" N   HIS A 187 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 209
    Processing helix  chain 'A' and resid 221 through 225
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 4.093A  pdb=" N   GLU A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 266
    Processing helix  chain 'A' and resid 304 through 309
      removed outlier: 3.740A  pdb=" N   VAL A 308 " --> pdb=" O   ASP A 304 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 309 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 309'
    Processing helix  chain 'A' and resid 354 through 362
      removed outlier: 3.642A  pdb=" N   GLU A 360 " --> pdb=" O   LYS A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 395
      removed outlier: 3.813A  pdb=" N   ALA A 380 " --> pdb=" O   ASP A 376 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ILE A 381 " --> pdb=" O   ARG A 377 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 382 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 391 " --> pdb=" O   ARG A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 422
      removed outlier: 3.609A  pdb=" N   LEU A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 445
      removed outlier: 3.674A  pdb=" N   GLY A 431 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TYR A 432 " --> pdb=" O   VAL A 428 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ARG A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 478
      removed outlier: 3.949A  pdb=" N   ALA A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 496
      removed outlier: 3.605A  pdb=" N   LEU A 494 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 514
      removed outlier: 3.552A  pdb=" N   VAL A 501 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 530
      removed outlier: 4.097A  pdb=" N   CYS A 526 " --> pdb=" O   ARG A 522 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU A 527 " --> pdb=" O   THR A 523 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 529 " --> pdb=" O   GLU A 525 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR A 530 " --> pdb=" O   CYS A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 546
      removed outlier: 3.562A  pdb=" N   SER A 538 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASN A 541 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 549
      No H-bonds generated for 'chain 'A' and resid 547 through 549'
    Processing helix  chain 'A' and resid 553 through 589
      removed outlier: 4.338A  pdb=" N   PHE A 578 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
      Proline residue:  A 579  - end of helix
      removed outlier: 3.636A  pdb=" N   ASP A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 730
      removed outlier: 3.726A  pdb=" N   PHE A 721 " --> pdb=" O   THR A 717 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ALA A 727 " --> pdb=" O   GLU A 723 " (cutoff:3.500A)
      Proline residue:  A 728  - end of helix
    Processing helix  chain 'A' and resid 732 through 755
      removed outlier: 3.648A  pdb=" N   ILE A 740 " --> pdb=" O   LYS A 736 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 745 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A 755 " --> pdb=" O   LEU A 751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 784
      removed outlier: 3.908A  pdb=" N   PHE A 776 " --> pdb=" O   ARG A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 811
    Processing helix  chain 'A' and resid 830 through 851
      removed outlier: 4.152A  pdb=" N   ASP A 836 " --> pdb=" O   HIS A 832 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLN A 839 " --> pdb=" O   ARG A 835 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLY A 840 " --> pdb=" O   ASP A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 874
    Processing helix  chain 'A' and resid 884 through 889
      removed outlier: 4.125A  pdb=" N   THR A 889 " --> pdb=" O   SER A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 905 through 910
    Processing helix  chain 'A' and resid 917 through 922
    Processing helix  chain 'A' and resid 969 through 989
      removed outlier: 3.807A  pdb=" N   ILE A 983 " --> pdb=" O   LYS A 979 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   SER A 989 " --> pdb=" O   ASN A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1004
      removed outlier: 3.698A  pdb=" N   TRP A1004 " --> pdb=" O   PRO A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1034
      removed outlier: 4.448A  pdb=" N   SER A1009 " --> pdb=" O   GLU A1005 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ARG A1011 " --> pdb=" O   TYR A1007 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   HIS A1012 " --> pdb=" O   ILE A1008 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   SER A1019 " --> pdb=" O   LEU A1015 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1035 through 1061
      removed outlier: 3.505A  pdb=" N   GLY A1061 " --> pdb=" O   MET A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1093
      removed outlier: 3.750A  pdb=" N   GLY A1077 " --> pdb=" O   ILE A1073 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   VAL A1080 " --> pdb=" O   VAL A1076 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLU A1081 " --> pdb=" O   GLY A1077 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   PHE A1082 " --> pdb=" O   ILE A1078 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   HIS A1085 " --> pdb=" O   GLU A1081 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   VAL A1086 " --> pdb=" O   PHE A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1109
      removed outlier: 4.257A  pdb=" N   ALA A1101 " --> pdb=" O   LYS A1097 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   MET A1102 " --> pdb=" O   ASN A1098 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1123
    Processing helix  chain 'A' and resid 1124 through 1129
    Processing helix  chain 'A' and resid 1131 through 1138
      removed outlier: 3.618A  pdb=" N   VAL A1135 " --> pdb=" O   PHE A1131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1155
    Processing helix  chain 'A' and resid 1155 through 1164
      removed outlier: 3.864A  pdb=" N   VAL A1159 " --> pdb=" O   VAL A1155 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 352
    Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 178
      removed outlier: 3.630A  pdb=" N   VAL A 176 " --> pdb=" O   TRP A 183 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET A 178 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG A 181 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232
    Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 334
    Processing sheet with id=AA5, first strand: chain 'A' and resid 959 through 964

    389 hydrogen bonds defined for protein.
    1122 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: 2.20

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2223
        1.34 -     1.46: 1789
        1.46 -     1.58: 3161
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 7221
  Sorted by residual:
  bond pdb=" C10 CLR A1401 "
       pdb=" C5  CLR A1401 "
    ideal  model  delta    sigma   weight residual
    1.519  1.402  0.117 2.00e-02 2.50e+03 3.45e+01
  bond pdb=" C10 CLR A1403 "
       pdb=" C5  CLR A1403 "
    ideal  model  delta    sigma   weight residual
    1.519  1.404  0.115 2.00e-02 2.50e+03 3.32e+01
  bond pdb=" C10 CLR A1402 "
       pdb=" C5  CLR A1402 "
    ideal  model  delta    sigma   weight residual
    1.519  1.405  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" C10 CLR A1404 "
       pdb=" C5  CLR A1404 "
    ideal  model  delta    sigma   weight residual
    1.519  1.405  0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C4  CLR A1401 "
       pdb=" C5  CLR A1401 "
    ideal  model  delta    sigma   weight residual
    1.506  1.397  0.109 2.00e-02 2.50e+03 3.00e+01
  ... (remaining 7216 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 9732
        2.16 -     4.31: 173
        4.31 -     6.47: 46
        6.47 -     8.62: 5
        8.62 -    10.78: 1
  Bond angle restraints: 9957
  Sorted by residual:
  angle pdb=" C   HIS A 930 "
        pdb=" N   ARG A 931 "
        pdb=" CA  ARG A 931 "
      ideal   model   delta    sigma   weight residual
     120.97  131.75  -10.78 2.84e+00 1.24e-01 1.44e+01
  angle pdb=" C   GLU A 108 "
        pdb=" N   THR A 109 "
        pdb=" CA  THR A 109 "
      ideal   model   delta    sigma   weight residual
     121.54  126.56   -5.02 1.91e+00 2.74e-01 6.90e+00
  angle pdb=" N   GLY A 862 "
        pdb=" CA  GLY A 862 "
        pdb=" C   GLY A 862 "
      ideal   model   delta    sigma   weight residual
     111.78  116.20   -4.42 1.69e+00 3.50e-01 6.83e+00
  angle pdb=" C   ASP A 895 "
        pdb=" N   ALA A 896 "
        pdb=" CA  ALA A 896 "
      ideal   model   delta    sigma   weight residual
     122.15  115.01    7.14 2.83e+00 1.25e-01 6.37e+00
  angle pdb=" N   ASP A 895 "
        pdb=" CA  ASP A 895 "
        pdb=" C   ASP A 895 "
      ideal   model   delta    sigma   weight residual
     110.80  116.17   -5.37 2.13e+00 2.20e-01 6.37e+00
  ... (remaining 9952 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 3945
       16.65 -    33.29: 303
       33.29 -    49.94: 74
       49.94 -    66.58: 4
       66.58 -    83.23: 5
  Dihedral angle restraints: 4331
    sinusoidal: 1463
      harmonic: 2868
  Sorted by residual:
  dihedral pdb=" CB  CYS A 220 "
           pdb=" SG  CYS A 220 "
           pdb=" SG  CYS A 313 "
           pdb=" CB  CYS A 313 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.74  -75.74     1      1.00e+01 1.00e-02 7.24e+01
  dihedral pdb=" CA  VAL A 894 "
           pdb=" C   VAL A 894 "
           pdb=" N   ASP A 895 "
           pdb=" CA  ASP A 895 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.90  -21.10     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  LYS A 191 "
           pdb=" C   LYS A 191 "
           pdb=" N   SER A 192 "
           pdb=" CA  SER A 192 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.12  -19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 4328 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1168
       0.106 -    0.211: 26
       0.211 -    0.317: 6
       0.317 -    0.423: 3
       0.423 -    0.529: 7
  Chirality restraints: 1210
  Sorted by residual:
  chirality pdb=" C10 CLR A1401 "
            pdb=" C1  CLR A1401 "
            pdb=" C5  CLR A1401 "
            pdb=" C9  CLR A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.32   -0.53 2.00e-01 2.50e+01 6.99e+00
  chirality pdb=" C10 CLR A1404 "
            pdb=" C1  CLR A1404 "
            pdb=" C5  CLR A1404 "
            pdb=" C9  CLR A1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.39   -0.46 2.00e-01 2.50e+01 5.37e+00
  chirality pdb=" C10 CLR A1402 "
            pdb=" C1  CLR A1402 "
            pdb=" C5  CLR A1402 "
            pdb=" C9  CLR A1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.39   -0.46 2.00e-01 2.50e+01 5.20e+00
  ... (remaining 1207 not shown)

  Planarity restraints: 1242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1067 "    0.027 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO A1068 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A1068 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A1068 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 931 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A 932 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 932 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 932 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 354 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO A 355 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 355 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 355 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1239 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 148
        2.71 -     3.25: 7542
        3.25 -     3.80: 11010
        3.80 -     4.35: 13506
        4.35 -     4.90: 22463
  Nonbonded interactions: 54669
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 280 "
            pdb=" O   GLY A 315 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" O   PRO A 856 "
            pdb=" OH  TYR A 870 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   TRP A1013 "
            pdb=" OG  SER A1017 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG1 THR A 485 "
            pdb=" OE1 GLN A 562 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OH  TYR A 806 "
            pdb=" NE  ARG A 835 "
     model   vdw
     2.310 3.120
  ... (remaining 54664 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.910
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.620
  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:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
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      :  0.006   0.117   7224  Z= 0.299
  Angle     :  0.748  10.778   9963  Z= 0.362
  Chirality :  0.061   0.529   1210
  Planarity :  0.004   0.040   1242
  Dihedral  : 12.860  83.230   2476
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -3.49 (0.23), residues: 981
  helix: -1.83 (0.18), residues: 562
  sheet: -4.46 (0.49), residues: 47
  loop : -2.59 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A 175 
 PHE   0.015   0.001   PHE A 502 
 TYR   0.015   0.001   TYR A 999 
 ARG   0.002   0.000   ARG A 931 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16786 (  389)
  hydrogen bonds       : angle       6.29175 ( 1122)
  SS BOND              : bond        0.00357 (    3)
  SS BOND              : angle       1.75972 (    6)
  covalent geometry    : bond        0.00612 ( 7221)
  covalent geometry    : angle       0.74684 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.9230 (mp) cc_final: 0.8790 (tt)
REVERT: A  358 MET cc_start: 0.9062 (tpt) cc_final: 0.8782 (tpp)
REVERT: A  489 LEU cc_start: 0.8479 (tp) cc_final: 0.8277 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1218
  time to fit residues: 21.7894
Evaluate side-chains
  84 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0270
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0980
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN
A 163 GLN
A 182 GLN
A 228 GLN
A 314 GLN
A 506 HIS
A 809 HIS
A 875 GLN
A 915 ASN
A 926 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.114094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090992 restraints weight = 14388.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.093666 restraints weight = 7308.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.095374 restraints weight = 4719.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7224  Z= 0.138
  Angle     :  0.609   8.175   9963  Z= 0.302
  Chirality :  0.041   0.148   1210
  Planarity :  0.004   0.041   1242
  Dihedral  :  6.439  44.688   1302
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.94 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -1.96 (0.26), residues: 981
  helix: -0.54 (0.21), residues: 566
  sheet: -3.88 (0.59), residues: 46
  loop : -2.04 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 849 
 HIS   0.003   0.001   HIS A 275 
 PHE   0.020   0.002   PHE A 781 
 TYR   0.016   0.001   TYR A 870 
 ARG   0.002   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  389)
  hydrogen bonds       : angle       4.39660 ( 1122)
  SS BOND              : bond        0.00375 (    3)
  SS BOND              : angle       1.59684 (    6)
  covalent geometry    : bond        0.00313 ( 7221)
  covalent geometry    : angle       0.60756 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A  204 GLN cc_start: 0.7803 (tt0) cc_final: 0.7568 (tt0)
REVERT: A  248 LEU cc_start: 0.9112 (mp) cc_final: 0.8713 (tt)
REVERT: A  358 MET cc_start: 0.8979 (tpt) cc_final: 0.8680 (tpp)
REVERT: A  489 LEU cc_start: 0.8500 (tp) cc_final: 0.8266 (tp)
REVERT: A  819 MET cc_start: 0.8272 (ttm) cc_final: 0.7954 (ttp)
REVERT: A 1002 LEU cc_start: 0.9053 (mt) cc_final: 0.8715 (mt)
REVERT: A 1091 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8506 (pt)
  outliers start: 8
  outliers final: 4
  residues processed: 111
  average time/residue: 0.1655
  time to fit residues: 27.8560
Evaluate side-chains
  95 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1091 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 80 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0170
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN
** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.113650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.093311 restraints weight = 14374.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.094169 restraints weight = 7151.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.095419 restraints weight = 5165.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7224  Z= 0.151
  Angle     :  0.622  10.344   9963  Z= 0.303
  Chirality :  0.041   0.169   1210
  Planarity :  0.004   0.042   1242
  Dihedral  :  6.203  55.792   1302
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.99 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -1.23 (0.27), residues: 981
  helix:  0.10 (0.22), residues: 568
  sheet: -3.87 (0.56), residues: 46
  loop : -1.77 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A 344 
 PHE   0.015   0.001   PHE A 569 
 TYR   0.017   0.001   TYR A 438 
 ARG   0.008   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 (  389)
  hydrogen bonds       : angle       4.19316 ( 1122)
  SS BOND              : bond        0.00332 (    3)
  SS BOND              : angle       1.64949 (    6)
  covalent geometry    : bond        0.00346 ( 7221)
  covalent geometry    : angle       0.62124 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.8980 (tpt) cc_final: 0.8515 (tpp)
REVERT: A  489 LEU cc_start: 0.8512 (tp) cc_final: 0.8302 (tp)
REVERT: A  569 PHE cc_start: 0.8902 (m-80) cc_final: 0.8546 (m-10)
REVERT: A  819 MET cc_start: 0.8278 (ttm) cc_final: 0.7947 (ttp)
REVERT: A 1002 LEU cc_start: 0.9068 (mt) cc_final: 0.8695 (mt)
REVERT: A 1056 MET cc_start: 0.9076 (mmm) cc_final: 0.8839 (mmm)
REVERT: A 1091 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8594 (pt)
  outliers start: 18
  outliers final: 14
  residues processed: 117
  average time/residue: 0.1526
  time to fit residues: 28.5883
Evaluate side-chains
  107 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0270
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 64 optimal weight:    0.1980
   overall best weight:    0.2416

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

Flipped N/Q/H residues before XYZ refinement:
** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.116399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.096471 restraints weight = 14318.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.097772 restraints weight = 6837.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098570 restraints weight = 4935.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
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   0.033   7224  Z= 0.111
  Angle     :  0.584   9.204   9963  Z= 0.283
  Chirality :  0.040   0.201   1210
  Planarity :  0.003   0.040   1242
  Dihedral  :  5.912  58.586   1302
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.69 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -0.69 (0.28), residues: 981
  helix:  0.55 (0.22), residues: 568
  sheet: -3.62 (0.59), residues: 45
  loop : -1.57 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 830 
 HIS   0.002   0.001   HIS A1085 
 PHE   0.022   0.001   PHE A 781 
 TYR   0.032   0.001   TYR A 999 
 ARG   0.004   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02914 (  389)
  hydrogen bonds       : angle       4.01253 ( 1122)
  SS BOND              : bond        0.00541 (    3)
  SS BOND              : angle       1.40535 (    6)
  covalent geometry    : bond        0.00247 ( 7221)
  covalent geometry    : angle       0.58294 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 1.642 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.8943 (tpt) cc_final: 0.8478 (tpp)
REVERT: A  411 THR cc_start: 0.8770 (p) cc_final: 0.8381 (p)
REVERT: A  489 LEU cc_start: 0.8457 (tp) cc_final: 0.8253 (tp)
REVERT: A  556 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8451 (mm)
REVERT: A  561 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8956 (mm)
REVERT: A  569 PHE cc_start: 0.8786 (m-80) cc_final: 0.8446 (m-10)
REVERT: A  806 TYR cc_start: 0.7978 (m-80) cc_final: 0.7740 (m-80)
REVERT: A  906 TYR cc_start: 0.8465 (m-10) cc_final: 0.8171 (m-10)
REVERT: A 1002 LEU cc_start: 0.9112 (mt) cc_final: 0.8713 (mt)
REVERT: A 1056 MET cc_start: 0.8947 (mmm) cc_final: 0.8725 (mmm)
REVERT: A 1091 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8580 (pt)
  outliers start: 21
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1660
  time to fit residues: 32.0628
Evaluate side-chains
  112 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 71 optimal weight:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0980
   chunk 9 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.114502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.093611 restraints weight = 14075.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.094620 restraints weight = 7013.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.095599 restraints weight = 5255.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7224  Z= 0.149
  Angle     :  0.621  10.410   9963  Z= 0.299
  Chirality :  0.042   0.335   1210
  Planarity :  0.003   0.040   1242
  Dihedral  :  5.756  58.093   1302
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.96 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -0.51 (0.28), residues: 981
  helix:  0.71 (0.22), residues: 569
  sheet: -3.61 (0.57), residues: 45
  loop : -1.52 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 344 
 PHE   0.014   0.001   PHE A1090 
 TYR   0.029   0.001   TYR A 999 
 ARG   0.001   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02987 (  389)
  hydrogen bonds       : angle       4.02199 ( 1122)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       1.04976 (    6)
  covalent geometry    : bond        0.00345 ( 7221)
  covalent geometry    : angle       0.62020 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: A  561 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8949 (mm)
REVERT: A  906 TYR cc_start: 0.8570 (m-10) cc_final: 0.8276 (m-10)
REVERT: A 1002 LEU cc_start: 0.9028 (mt) cc_final: 0.8653 (mt)
REVERT: A 1056 MET cc_start: 0.8906 (mmm) cc_final: 0.8686 (mmm)
  outliers start: 23
  outliers final: 16
  residues processed: 120
  average time/residue: 0.1573
  time to fit residues: 30.7410
Evaluate side-chains
  115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 54 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 69 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    0.2980
   chunk 88 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.113999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.093112 restraints weight = 14235.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.094516 restraints weight = 6960.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.095219 restraints weight = 5171.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7224  Z= 0.146
  Angle     :  0.617  10.386   9963  Z= 0.297
  Chirality :  0.041   0.191   1210
  Planarity :  0.003   0.039   1242
  Dihedral  :  5.715  53.081   1302
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 21.19 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -0.28 (0.28), residues: 981
  helix:  0.91 (0.23), residues: 564
  sheet: -3.62 (0.57), residues: 45
  loop : -1.41 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 275 
 PHE   0.017   0.002   PHE A1090 
 TYR   0.028   0.001   TYR A 999 
 ARG   0.001   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02984 (  389)
  hydrogen bonds       : angle       4.01182 ( 1122)
  SS BOND              : bond        0.00152 (    3)
  SS BOND              : angle       0.77140 (    6)
  covalent geometry    : bond        0.00340 ( 7221)
  covalent geometry    : angle       0.61714 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A  561 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: A  819 MET cc_start: 0.8231 (ttm) cc_final: 0.7914 (ttp)
REVERT: A  906 TYR cc_start: 0.8599 (m-10) cc_final: 0.8389 (m-10)
REVERT: A 1002 LEU cc_start: 0.9052 (mt) cc_final: 0.8673 (mt)
REVERT: A 1019 SER cc_start: 0.9519 (t) cc_final: 0.9264 (m)
REVERT: A 1056 MET cc_start: 0.8955 (mmm) cc_final: 0.8715 (mmm)
REVERT: A 1091 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8568 (pt)
  outliers start: 23
  outliers final: 16
  residues processed: 117
  average time/residue: 0.1257
  time to fit residues: 23.3620
Evaluate side-chains
  115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0020
   chunk 45 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 15 optimal weight:    0.1980
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0870
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.2966

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

Flipped N/Q/H residues before XYZ refinement:
A1152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.115968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.095386 restraints weight = 14257.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.096115 restraints weight = 7123.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.097382 restraints weight = 5252.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7224  Z= 0.116
  Angle     :  0.605  12.470   9963  Z= 0.287
  Chirality :  0.040   0.180   1210
  Planarity :  0.003   0.038   1242
  Dihedral  :  5.602  57.986   1302
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.72 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -0.07 (0.28), residues: 981
  helix:  1.04 (0.23), residues: 566
  sheet: -3.37 (0.62), residues: 45
  loop : -1.29 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 837 
 HIS   0.002   0.000   HIS A 275 
 PHE   0.016   0.001   PHE A1131 
 TYR   0.026   0.001   TYR A 999 
 ARG   0.001   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02801 (  389)
  hydrogen bonds       : angle       3.94002 ( 1122)
  SS BOND              : bond        0.00548 (    3)
  SS BOND              : angle       1.16186 (    6)
  covalent geometry    : bond        0.00266 ( 7221)
  covalent geometry    : angle       0.60471 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 1.727 
Fit side-chains
   revert: symmetry clash
REVERT: A  556 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8411 (mm)
REVERT: A  561 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8965 (mm)
REVERT: A  819 MET cc_start: 0.8286 (ttm) cc_final: 0.8005 (ttp)
REVERT: A  906 TYR cc_start: 0.8553 (m-10) cc_final: 0.8271 (m-10)
REVERT: A 1002 LEU cc_start: 0.9044 (mt) cc_final: 0.8663 (mt)
REVERT: A 1019 SER cc_start: 0.9500 (t) cc_final: 0.9259 (m)
REVERT: A 1056 MET cc_start: 0.8930 (mmm) cc_final: 0.8542 (mmm)
  outliers start: 21
  outliers final: 16
  residues processed: 112
  average time/residue: 0.1475
  time to fit residues: 26.7941
Evaluate side-chains
  109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  767 VAL
Chi-restraints excluded: chain A residue  771 THR
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.112277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.090743 restraints weight = 14497.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.090763 restraints weight = 7462.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.092313 restraints weight = 5846.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7224  Z= 0.213
  Angle     :  0.686  12.967   9963  Z= 0.329
  Chirality :  0.044   0.333   1210
  Planarity :  0.004   0.039   1242
  Dihedral  :  5.781  52.121   1302
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 21.02 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -0.21 (0.28), residues: 981
  helix:  0.96 (0.23), residues: 566
  sheet: -3.42 (0.62), residues: 46
  loop : -1.38 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 837 
 HIS   0.004   0.001   HIS A 275 
 PHE   0.015   0.002   PHE A 743 
 TYR   0.023   0.002   TYR A 999 
 ARG   0.002   0.000   ARG A 835 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03174 (  389)
  hydrogen bonds       : angle       4.17217 ( 1122)
  SS BOND              : bond        0.00556 (    3)
  SS BOND              : angle       1.44482 (    6)
  covalent geometry    : bond        0.00495 ( 7221)
  covalent geometry    : angle       0.68497 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 1.421 
Fit side-chains
REVERT: A  561 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9010 (mm)
REVERT: A  569 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8574 (m-10)
REVERT: A 1002 LEU cc_start: 0.9098 (mt) cc_final: 0.8700 (mt)
REVERT: A 1019 SER cc_start: 0.9513 (t) cc_final: 0.9249 (m)
REVERT: A 1056 MET cc_start: 0.8972 (mmm) cc_final: 0.8594 (mmm)
  outliers start: 28
  outliers final: 24
  residues processed: 110
  average time/residue: 0.1802
  time to fit residues: 32.5210
Evaluate side-chains
  112 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  569 PHE
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  767 VAL
Chi-restraints excluded: chain A residue  771 THR
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1046 LEU
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1059 LEU
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.1980
   chunk 97 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0270
   chunk 84 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.113631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.092697 restraints weight = 14259.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.093749 restraints weight = 7056.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.094748 restraints weight = 5191.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7224  Z= 0.157
  Angle     :  0.656  14.208   9963  Z= 0.309
  Chirality :  0.043   0.381   1210
  Planarity :  0.003   0.037   1242
  Dihedral  :  5.746  54.435   1302
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 21.54 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    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: -0.07 (0.28), residues: 981
  helix:  1.06 (0.23), residues: 564
  sheet: -3.32 (0.65), residues: 46
  loop : -1.32 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 837 
 HIS   0.004   0.001   HIS A 275 
 PHE   0.014   0.001   PHE A1131 
 TYR   0.024   0.001   TYR A 999 
 ARG   0.001   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02991 (  389)
  hydrogen bonds       : angle       4.09772 ( 1122)
  SS BOND              : bond        0.00513 (    3)
  SS BOND              : angle       1.35418 (    6)
  covalent geometry    : bond        0.00366 ( 7221)
  covalent geometry    : angle       0.65508 ( 9957)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A  819 MET cc_start: 0.8393 (ttm) cc_final: 0.8123 (ttp)
REVERT: A 1002 LEU cc_start: 0.9071 (mt) cc_final: 0.8681 (mt)
REVERT: A 1019 SER cc_start: 0.9500 (t) cc_final: 0.9269 (m)
REVERT: A 1056 MET cc_start: 0.8906 (mmm) cc_final: 0.8537 (mmm)
  outliers start: 26
  outliers final: 23
  residues processed: 108
  average time/residue: 0.1730
  time to fit residues: 29.8781
Evaluate side-chains
  108 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  767 VAL
Chi-restraints excluded: chain A residue  771 THR
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1037 TRP
Chi-restraints excluded: chain A residue 1046 LEU
Chi-restraints excluded: chain A residue 1053 LEU
Chi-restraints excluded: chain A residue 1059 LEU
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1717 > 50:
  distance: 51 - 56:  35.528
  distance: 57 - 58:   5.731
  distance: 58 - 59:  39.811
  distance: 58 - 61:  22.964
  distance: 61 - 62:  13.105
  distance: 61 - 67:  14.258
  distance: 62 - 63:  12.748
  distance: 62 - 65:  48.676
  distance: 63 - 64:  55.915
  distance: 63 - 68:  39.801
  distance: 66 - 67:  39.814
  distance: 68 - 69:  56.297
  distance: 69 - 70:  47.168
  distance: 69 - 72:  27.071
  distance: 70 - 71:  15.032
  distance: 70 - 73:  42.508
  distance: 73 - 74:  61.971
  distance: 74 - 75:  25.397
  distance: 74 - 77:  24.252
  distance: 75 - 76:  40.841
  distance: 79 - 80:  39.057
  distance: 82 - 83:  57.024
  distance: 84 - 85:  16.141
  distance: 85 - 86:  16.660
  distance: 86 - 87:  37.303
  distance: 86 - 88:  13.676
  distance: 89 - 90:  25.203
  distance: 90 - 91:  26.722
  distance: 90 - 93:  18.648
  distance: 91 - 92:  56.107
  distance: 91 - 97:  21.101
  distance: 93 - 94:  43.050
  distance: 94 - 95:  41.355
  distance: 94 - 96:  23.319
  distance: 97 - 98:  40.729
  distance: 98 - 99:  52.943
  distance: 98 - 101:  33.540
  distance: 99 - 100:  29.109
  distance: 99 - 102:  10.634
  distance: 103 - 104:   3.057
  distance: 103 - 106:  44.778
  distance: 104 - 110:  40.441
  distance: 106 - 107:  12.668
  distance: 106 - 108:  38.784
  distance: 107 - 109:  50.944
  distance: 110 - 111:  32.702
  distance: 110 - 116:  32.348
  distance: 111 - 112:  36.297
  distance: 111 - 114:  48.250
  distance: 112 - 117:  16.962
  distance: 115 - 116:  51.162
  distance: 118 - 119:  47.853
  distance: 118 - 121:  13.778
  distance: 119 - 120:  29.415
  distance: 119 - 122:  30.217