Starting phenix.real_space_refine
on Fri Aug 22 19:29:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mg8_9111/08_2025/6mg8_9111.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mg8_9111/08_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_9111/08_2025/6mg8_9111.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mg8_9111/08_2025/6mg8_9111.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mg8_9111/08_2025/6mg8_9111.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mg8_9111/08_2025/6mg8_9111.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 19, 'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 14, 'PHE:plan': 7, 'GLU:plan': 33, 'ASP:plan': 32, 'TRP:plan': 2, 'HIS:plan': 1}
          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: 2.05, per 1000 atoms: 0.29
  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: 0.72
  Conformation dependent library (CDL) restraints added in 445.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.27
  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: 1.21

  Time building geometry restraints manager: 0.91 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:             2.970
  Set stop_for_unknowns flag:              0.010
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.970
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.510
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG A 931 
 TYR   0.015   0.001   TYR A 999 
 PHE   0.015   0.001   PHE A 502 
 TRP   0.009   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A 175 

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

*********************** 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  : 0.248 
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: 0.0553
  time to fit residues: 10.1086
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  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.114004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.091511 restraints weight = 14377.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.094169 restraints weight = 7181.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.095869 restraints weight = 4579.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.096977 restraints weight = 3421.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.097489 restraints weight = 2841.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1221

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     :  0.607   8.158   9963  Z= 0.301
  Chirality :  0.041   0.145   1210
  Planarity :  0.004   0.041   1242
  Dihedral  :  6.436  44.851   1302
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.76 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.26), residues: 981
  helix: -0.53 (0.21), residues: 566
  sheet: -3.87 (0.60), residues: 46
  loop : -2.04 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 280 
 TYR   0.016   0.001   TYR A 870 
 PHE   0.019   0.002   PHE A 781 
 TRP   0.015   0.001   TRP A 849 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7221)
  covalent geometry    : angle       0.60550 ( 9957)
  SS BOND              : bond        0.00539 (    3)
  SS BOND              : angle       1.72395 (    6)
  hydrogen bonds       : bond        0.03336 (  389)
  hydrogen bonds       : angle       4.39488 ( 1122)

*********************** 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
  115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  204 GLN cc_start: 0.7713 (tt0) cc_final: 0.7469 (tt0)
REVERT: A  248 LEU cc_start: 0.9095 (mp) cc_final: 0.8706 (tt)
REVERT: A  358 MET cc_start: 0.8961 (tpt) cc_final: 0.8639 (tpp)
REVERT: A  489 LEU cc_start: 0.8503 (tp) cc_final: 0.8266 (tp)
REVERT: A  819 MET cc_start: 0.8277 (ttm) cc_final: 0.7953 (ttp)
REVERT: A 1002 LEU cc_start: 0.9074 (mt) cc_final: 0.8760 (mt)
REVERT: A 1091 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8514 (pt)
  outliers start: 8
  outliers final: 4
  residues processed: 112
  average time/residue: 0.0590
  time to fit residues: 10.2320
Evaluate side-chains
  94 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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 56 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0070
   chunk 44 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 91 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.4598

-------------------------------------------------------------------------------
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 = 0.113730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.093380 restraints weight = 14426.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.093486 restraints weight = 7267.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.095424 restraints weight = 5198.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.095420 restraints weight = 3790.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.095582 restraints weight = 3628.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1639

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= 0.145
  Angle     :  0.620  10.252   9963  Z= 0.301
  Chirality :  0.041   0.159   1210
  Planarity :  0.004   0.042   1242
  Dihedral  :  6.185  56.420   1302
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.34 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.27), residues: 981
  helix:  0.13 (0.22), residues: 568
  sheet: -3.82 (0.57), residues: 46
  loop : -1.76 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 124 
 TYR   0.018   0.001   TYR A 438 
 PHE   0.014   0.001   PHE A 569 
 TRP   0.008   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7221)
  covalent geometry    : angle       0.61859 ( 9957)
  SS BOND              : bond        0.00143 (    3)
  SS BOND              : angle       1.63669 (    6)
  hydrogen bonds       : bond        0.03191 (  389)
  hydrogen bonds       : angle       4.17613 ( 1122)

*********************** 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
  120 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  358 MET cc_start: 0.8971 (tpt) cc_final: 0.8515 (tpp)
REVERT: A  489 LEU cc_start: 0.8506 (tp) cc_final: 0.8299 (tp)
REVERT: A  569 PHE cc_start: 0.8962 (m-80) cc_final: 0.8653 (m-10)
REVERT: A  819 MET cc_start: 0.8271 (ttm) cc_final: 0.7942 (ttp)
REVERT: A 1002 LEU cc_start: 0.9051 (mt) cc_final: 0.8678 (mt)
REVERT: A 1056 MET cc_start: 0.9088 (mmm) cc_final: 0.8849 (mmm)
REVERT: A 1091 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8580 (pt)
  outliers start: 17
  outliers final: 13
  residues processed: 114
  average time/residue: 0.0512
  time to fit residues: 9.3826
Evaluate side-chains
  102 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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  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 4 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0980
   chunk 79 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   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 = 0.3678 r_free = 0.3678 target = 0.113598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093154 restraints weight = 14497.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.093243 restraints weight = 7149.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.095077 restraints weight = 5171.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.095064 restraints weight = 3758.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.095524 restraints weight = 3682.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7224  Z= 0.147
  Angle     :  0.614   9.619   9963  Z= 0.298
  Chirality :  0.041   0.203   1210
  Planarity :  0.004   0.040   1242
  Dihedral  :  5.982  59.098   1302
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.27), residues: 981
  helix:  0.47 (0.22), residues: 567
  sheet: -3.73 (0.57), residues: 46
  loop : -1.66 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 124 
 TYR   0.033   0.001   TYR A 999 
 PHE   0.022   0.002   PHE A 781 
 TRP   0.008   0.001   TRP A 830 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7221)
  covalent geometry    : angle       0.61380 ( 9957)
  SS BOND              : bond        0.00403 (    3)
  SS BOND              : angle       0.39604 (    6)
  hydrogen bonds       : bond        0.03098 (  389)
  hydrogen bonds       : angle       4.12018 ( 1122)

*********************** 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
  119 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A  278 MET cc_start: 0.8441 (mmt) cc_final: 0.8122 (mmm)
REVERT: A  411 THR cc_start: 0.8827 (p) cc_final: 0.8450 (p)
REVERT: A  561 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8999 (mm)
REVERT: A  569 PHE cc_start: 0.8820 (m-80) cc_final: 0.8469 (m-10)
REVERT: A  906 TYR cc_start: 0.8587 (m-10) cc_final: 0.8275 (m-10)
REVERT: A 1002 LEU cc_start: 0.9116 (mt) cc_final: 0.8750 (mt)
REVERT: A 1056 MET cc_start: 0.8976 (mmm) cc_final: 0.8710 (mmm)
REVERT: A 1091 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8604 (pt)
  outliers start: 21
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0512
  time to fit residues: 9.3550
Evaluate side-chains
  114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  393 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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0870
   chunk 78 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0270
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.4416

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.114225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.092958 restraints weight = 14468.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.094308 restraints weight = 7140.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.095024 restraints weight = 5387.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.095477 restraints weight = 4218.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.095488 restraints weight = 3733.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7224  Z= 0.140
  Angle     :  0.619  10.024   9963  Z= 0.299
  Chirality :  0.041   0.197   1210
  Planarity :  0.003   0.040   1242
  Dihedral  :  5.795  57.147   1302
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 18.74 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.28), residues: 981
  helix:  0.74 (0.22), residues: 566
  sheet: -3.72 (0.54), residues: 50
  loop : -1.49 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 280 
 TYR   0.029   0.001   TYR A 999 
 PHE   0.013   0.001   PHE A1090 
 TRP   0.009   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7221)
  covalent geometry    : angle       0.61548 ( 9957)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       2.71681 (    6)
  hydrogen bonds       : bond        0.02975 (  389)
  hydrogen bonds       : angle       4.00554 ( 1122)

*********************** 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
  134 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  278 MET cc_start: 0.8426 (mmt) cc_final: 0.8101 (mmm)
REVERT: A  556 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8456 (mm)
REVERT: A  561 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8969 (mm)
REVERT: A  569 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8374 (m-10)
REVERT: A  906 TYR cc_start: 0.8586 (m-10) cc_final: 0.8355 (m-10)
REVERT: A 1002 LEU cc_start: 0.9066 (mt) cc_final: 0.8681 (mt)
REVERT: A 1056 MET cc_start: 0.8905 (mmm) cc_final: 0.8692 (mmm)
REVERT: A 1088 LEU cc_start: 0.9464 (mm) cc_final: 0.9252 (mm)
REVERT: A 1091 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8624 (pt)
  outliers start: 28
  outliers final: 18
  residues processed: 123
  average time/residue: 0.0526
  time to fit residues: 10.5044
Evaluate side-chains
  117 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  393 VAL
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  894 VAL
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 16 optimal weight:    0.0980
   chunk 63 optimal weight:    0.8980
   chunk 57 optimal weight:    0.1980
   chunk 91 optimal weight:    0.3980
   chunk 67 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.114236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.093425 restraints weight = 14307.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.094646 restraints weight = 7055.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.095640 restraints weight = 5128.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.096027 restraints weight = 3798.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.096145 restraints weight = 3599.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2146

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= 0.135
  Angle     :  0.610  10.967   9963  Z= 0.293
  Chirality :  0.041   0.184   1210
  Planarity :  0.003   0.039   1242
  Dihedral  :  5.652  54.748   1302
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.19 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.28), residues: 981
  helix:  0.93 (0.22), residues: 564
  sheet: -3.69 (0.57), residues: 45
  loop : -1.39 (0.35), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 280 
 TYR   0.026   0.001   TYR A 999 
 PHE   0.023   0.001   PHE A 781 
 TRP   0.009   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7221)
  covalent geometry    : angle       0.61014 ( 9957)
  SS BOND              : bond        0.00629 (    3)
  SS BOND              : angle       0.72333 (    6)
  hydrogen bonds       : bond        0.02962 (  389)
  hydrogen bonds       : angle       3.97791 ( 1122)

*********************** 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
  121 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  278 MET cc_start: 0.8417 (mmt) cc_final: 0.8091 (mmm)
REVERT: A  561 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8964 (mm)
REVERT: A  569 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8452 (m-10)
REVERT: A 1002 LEU cc_start: 0.9049 (mt) cc_final: 0.8664 (mt)
REVERT: A 1019 SER cc_start: 0.9516 (t) cc_final: 0.9263 (m)
REVERT: A 1056 MET cc_start: 0.8877 (mmm) cc_final: 0.8635 (mmm)
REVERT: A 1088 LEU cc_start: 0.9448 (mm) cc_final: 0.9239 (mm)
REVERT: A 1091 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8625 (pt)
  outliers start: 22
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0527
  time to fit residues: 9.6225
Evaluate side-chains
  116 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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  393 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  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 51 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0060
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.114248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.093653 restraints weight = 14273.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.093652 restraints weight = 7222.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.095584 restraints weight = 5202.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.095419 restraints weight = 3798.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.095871 restraints weight = 3823.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2204

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     :  0.616  11.064   9963  Z= 0.297
  Chirality :  0.041   0.184   1210
  Planarity :  0.003   0.038   1242
  Dihedral  :  5.638  54.081   1302
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 21.37 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.28), residues: 981
  helix:  1.05 (0.23), residues: 563
  sheet: -3.59 (0.55), residues: 50
  loop : -1.38 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 280 
 TYR   0.026   0.001   TYR A 999 
 PHE   0.016   0.001   PHE A1131 
 TRP   0.011   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7221)
  covalent geometry    : angle       0.61553 ( 9957)
  SS BOND              : bond        0.00545 (    3)
  SS BOND              : angle       1.34318 (    6)
  hydrogen bonds       : bond        0.02948 (  389)
  hydrogen bonds       : angle       4.00981 ( 1122)

*********************** 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
  125 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  278 MET cc_start: 0.8374 (mmt) cc_final: 0.8055 (mmm)
REVERT: A  561 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8973 (mm)
REVERT: A  569 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8454 (m-10)
REVERT: A 1002 LEU cc_start: 0.9040 (mt) cc_final: 0.8656 (mt)
REVERT: A 1019 SER cc_start: 0.9509 (t) cc_final: 0.9258 (m)
REVERT: A 1056 MET cc_start: 0.8933 (mmm) cc_final: 0.8556 (mmm)
REVERT: A 1088 LEU cc_start: 0.9486 (mm) cc_final: 0.9270 (mm)
REVERT: A 1091 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8598 (pt)
REVERT: A 1125 MET cc_start: 0.8204 (tpp) cc_final: 0.7867 (tpp)
  outliers start: 27
  outliers final: 22
  residues processed: 117
  average time/residue: 0.0522
  time to fit residues: 9.8234
Evaluate side-chains
  114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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  157 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  393 VAL
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 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 64 optimal weight:    0.4980
   chunk 29 optimal weight:    0.3980
   chunk 31 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0670
   chunk 89 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   overall best weight:    0.3718

-------------------------------------------------------------------------------
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 = 0.3691 r_free = 0.3691 target = 0.114637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.093742 restraints weight = 14281.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.095199 restraints weight = 6875.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.096073 restraints weight = 4946.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.096429 restraints weight = 3937.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.096471 restraints weight = 3550.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7224  Z= 0.127
  Angle     :  0.611  12.797   9963  Z= 0.291
  Chirality :  0.040   0.178   1210
  Planarity :  0.003   0.038   1242
  Dihedral  :  5.581  54.564   1302
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 21.89 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.28), residues: 981
  helix:  1.14 (0.23), residues: 568
  sheet: -3.33 (0.62), residues: 49
  loop : -1.30 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 387 
 TYR   0.024   0.001   TYR A 999 
 PHE   0.016   0.001   PHE A1131 
 TRP   0.009   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7221)
  covalent geometry    : angle       0.61034 ( 9957)
  SS BOND              : bond        0.00441 (    3)
  SS BOND              : angle       1.24864 (    6)
  hydrogen bonds       : bond        0.02870 (  389)
  hydrogen bonds       : angle       3.95777 ( 1122)

*********************** 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
  126 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  278 MET cc_start: 0.8367 (mmt) cc_final: 0.8061 (mmm)
REVERT: A  489 LEU cc_start: 0.8363 (tp) cc_final: 0.8106 (tp)
REVERT: A  561 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8944 (mm)
REVERT: A  569 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8441 (m-10)
REVERT: A  806 TYR cc_start: 0.8124 (m-80) cc_final: 0.7837 (m-80)
REVERT: A  819 MET cc_start: 0.8245 (ttm) cc_final: 0.7998 (ttp)
REVERT: A 1002 LEU cc_start: 0.9016 (mt) cc_final: 0.8638 (mt)
REVERT: A 1019 SER cc_start: 0.9499 (t) cc_final: 0.9255 (m)
REVERT: A 1056 MET cc_start: 0.8911 (mmm) cc_final: 0.8535 (mmm)
REVERT: A 1088 LEU cc_start: 0.9468 (mm) cc_final: 0.9246 (mm)
REVERT: A 1091 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8590 (pt)
REVERT: A 1125 MET cc_start: 0.8267 (tpp) cc_final: 0.7909 (tpp)
  outliers start: 29
  outliers final: 23
  residues processed: 119
  average time/residue: 0.0512
  time to fit residues: 9.8590
Evaluate side-chains
  115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  393 VAL
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 1091 LEU
Chi-restraints excluded: chain A residue 1108 MET
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 28 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0980
   chunk 0 optimal weight:    4.9990
   chunk 90 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 79 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   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 = 0.3687 r_free = 0.3687 target = 0.114427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.093647 restraints weight = 14136.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.094865 restraints weight = 6854.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.095811 restraints weight = 4994.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.096167 restraints weight = 3962.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.096472 restraints weight = 3584.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7224  Z= 0.142
  Angle     :  0.623  12.126   9963  Z= 0.298
  Chirality :  0.041   0.179   1210
  Planarity :  0.003   0.035   1242
  Dihedral  :  5.633  55.267   1302
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 21.37 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.28), residues: 981
  helix:  1.15 (0.23), residues: 568
  sheet: -3.39 (0.62), residues: 49
  loop : -1.29 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 280 
 TYR   0.024   0.001   TYR A 999 
 PHE   0.015   0.001   PHE A1131 
 TRP   0.011   0.001   TRP A 837 
 HIS   0.003   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7221)
  covalent geometry    : angle       0.62248 ( 9957)
  SS BOND              : bond        0.00450 (    3)
  SS BOND              : angle       1.35189 (    6)
  hydrogen bonds       : bond        0.02907 (  389)
  hydrogen bonds       : angle       3.99939 ( 1122)

*********************** 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
  123 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  278 MET cc_start: 0.8378 (mmt) cc_final: 0.8069 (mmm)
REVERT: A  489 LEU cc_start: 0.8382 (tp) cc_final: 0.8110 (tp)
REVERT: A  561 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8969 (mm)
REVERT: A  569 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8474 (m-10)
REVERT: A 1002 LEU cc_start: 0.9023 (mt) cc_final: 0.8644 (mt)
REVERT: A 1019 SER cc_start: 0.9498 (t) cc_final: 0.9260 (m)
REVERT: A 1049 MET cc_start: 0.8808 (ttp) cc_final: 0.8321 (ttm)
REVERT: A 1056 MET cc_start: 0.8901 (mmm) cc_final: 0.8527 (mmm)
REVERT: A 1088 LEU cc_start: 0.9458 (mm) cc_final: 0.9239 (mm)
REVERT: A 1091 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8597 (pt)
REVERT: A 1125 MET cc_start: 0.8338 (tpp) cc_final: 0.7946 (tpp)
  outliers start: 31
  outliers final: 23
  residues processed: 115
  average time/residue: 0.0510
  time to fit residues: 9.5358
Evaluate side-chains
  116 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  393 VAL
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 1091 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0980
   chunk 20 optimal weight:    0.4980
   chunk 54 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.112323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091558 restraints weight = 14294.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.092480 restraints weight = 7111.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.093418 restraints weight = 5186.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.093575 restraints weight = 4013.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.094837 restraints weight = 3810.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7224  Z= 0.193
  Angle     :  0.661  12.673   9963  Z= 0.319
  Chirality :  0.043   0.189   1210
  Planarity :  0.004   0.039   1242
  Dihedral  :  5.812  57.215   1302
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 22.24 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.28), residues: 981
  helix:  1.11 (0.23), residues: 567
  sheet: -3.57 (0.60), residues: 50
  loop : -1.36 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 835 
 TYR   0.022   0.001   TYR A 999 
 PHE   0.014   0.002   PHE A1131 
 TRP   0.015   0.001   TRP A 837 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 7221)
  covalent geometry    : angle       0.66051 ( 9957)
  SS BOND              : bond        0.00559 (    3)
  SS BOND              : angle       1.54185 (    6)
  hydrogen bonds       : bond        0.03125 (  389)
  hydrogen bonds       : angle       4.11950 ( 1122)

********************** REFINEMENT MACRO_CYCLE 10 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: 27
    poor density    : 89
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  278 MET cc_start: 0.8390 (mmt) cc_final: 0.8077 (mmm)
REVERT: A  489 LEU cc_start: 0.8427 (tp) cc_final: 0.8154 (tp)
REVERT: A  561 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9025 (mm)
REVERT: A  569 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8485 (m-10)
REVERT: A 1002 LEU cc_start: 0.9077 (mt) cc_final: 0.8668 (mt)
REVERT: A 1019 SER cc_start: 0.9507 (t) cc_final: 0.9251 (m)
REVERT: A 1056 MET cc_start: 0.8893 (mmm) cc_final: 0.8529 (mmm)
REVERT: A 1088 LEU cc_start: 0.9469 (mm) cc_final: 0.9243 (mm)
REVERT: A 1091 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8576 (pt)
  outliers start: 27
  outliers final: 23
  residues processed: 111
  average time/residue: 0.0517
  time to fit residues: 9.3143
Evaluate side-chains
  116 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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  393 VAL
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  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 1108 MET
Chi-restraints excluded: chain A residue 1113 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0570
   chunk 68 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0000
   overall best weight:    0.5702

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.113460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.092826 restraints weight = 14363.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.092827 restraints weight = 7261.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.094692 restraints weight = 5288.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.094541 restraints weight = 3886.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.095030 restraints weight = 3913.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7224  Z= 0.163
  Angle     :  0.644  12.559   9963  Z= 0.308
  Chirality :  0.042   0.187   1210
  Planarity :  0.004   0.036   1242
  Dihedral  :  5.826  59.644   1302
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 22.94 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.28), residues: 981
  helix:  1.14 (0.23), residues: 568
  sheet: -3.48 (0.65), residues: 45
  loop : -1.33 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 835 
 TYR   0.022   0.001   TYR A 999 
 PHE   0.015   0.002   PHE A 743 
 TRP   0.012   0.001   TRP A 837 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7221)
  covalent geometry    : angle       0.64328 ( 9957)
  SS BOND              : bond        0.00492 (    3)
  SS BOND              : angle       1.44895 (    6)
  hydrogen bonds       : bond        0.03013 (  389)
  hydrogen bonds       : angle       4.07957 ( 1122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1270.61 seconds
wall clock time: 22 minutes 41.04 seconds (1361.04 seconds total)