Starting phenix.real_space_refine
on Sat Aug 23 10:54:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dtm_27705/08_2025/8dtm_27705_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dtm_27705/08_2025/8dtm_27705.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dtm_27705/08_2025/8dtm_27705.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dtm_27705/08_2025/8dtm_27705.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dtm_27705/08_2025/8dtm_27705_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dtm_27705/08_2025/8dtm_27705_neut.cif"
  }
  resolution = 3.5
  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
  Anisotropic ADP refinement not supported. Converting 6304 atoms to isotropic.
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      51      5.16       5
     C    4129      2.51       5
     N    1113      2.21       5
     O    1205      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 6498
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 3560
          Classifications: {'peptide': 444}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 424}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2793
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 23, 'TRANS': 316}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 145
          Classifications: {'peptide': 18}
          Link IDs: {'TRANS': 17}
  Time building chain proxies: 1.41, per 1000 atoms: 0.22
  Number of scatterers: 6498
  At special positions: 0
  Unit cell: (89.64, 89.64, 145.8, 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      51     16.00
     O    1205      8.00
     N    1113      7.00
     C    4129      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 304 " - pdb=" SG  CYS A 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 649 " - pdb=" SG  CYS B 862 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 788 " - pdb=" SG  CYS B 797 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  11 " - pdb=" SG  CYS C  18 " distance=2.03

  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: 0.35
  Conformation dependent library (CDL) restraints added in 318.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1516

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 15 sheets defined
      12.6% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 24
      removed outlier: 3.564A  pdb=" N   LEU A  23 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 225
      removed outlier: 3.716A  pdb=" N   LYS A 224 " --> pdb=" O   ASP A 221 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   CYS A 225 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 221 through 225'
    Processing helix  chain 'A' and resid 255 through 265
      removed outlier: 3.578A  pdb=" N   CYS A 259 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 3.619A  pdb=" N   GLY A 317 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 329
      removed outlier: 4.344A  pdb=" N   GLU A 329 " --> pdb=" O   THR A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 359
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.550A  pdb=" N   ILE A 439 " --> pdb=" O   CYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 500
      removed outlier: 3.768A  pdb=" N   LEU B 500 " --> pdb=" O   PHE B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 646
      removed outlier: 4.063A  pdb=" N   LEU B 646 " --> pdb=" O   LEU B 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 697 through 711
      removed outlier: 4.006A  pdb=" N   LEU B 711 " --> pdb=" O   PHE B 707 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 872
    Processing helix  chain 'C' and resid 2 through 13
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 14
      removed outlier: 7.155A  pdb=" N   CYS A   8 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   HIS A  32 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLY A  10 " --> pdb=" O   HIS A  32 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   GLN A  34 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ASP A  12 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU A  36 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ARG A  14 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   MET A  38 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 14
      removed outlier: 7.155A  pdb=" N   CYS A   8 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   HIS A  32 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLY A  10 " --> pdb=" O   HIS A  32 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   GLN A  34 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ASP A  12 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU A  36 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ARG A  14 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   MET A  38 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
      removed outlier: 8.775A  pdb=" N   LEU A  62 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   LEU A  33 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   PHE A  64 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ILE A  35 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   VAL A  66 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   LEU A  37 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   PHE A  96 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU A  63 " --> pdb=" O   PHE A  96 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL A 117 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   VAL A 146 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ILE A 119 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233
    Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248
    Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279
    Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312
    Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 321
      removed outlier: 7.648A  pdb=" N   PHE A 427 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TYR A 401 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   HIS A 429 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   LEU A 403 " --> pdb=" O   HIS A 429 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 471 through 473
      removed outlier: 3.668A  pdb=" N   LYS B 584 " --> pdb=" O   GLU B 471 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480
      removed outlier: 3.889A  pdb=" N   PHE B 477 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 532 through 534
      removed outlier: 3.765A  pdb=" N   GLY B 502 " --> pdb=" O   LEU B 571 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 601 through 606
      removed outlier: 5.533A  pdb=" N   ASP B 602 " --> pdb=" O   LYS B 618 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 618 " --> pdb=" O   ASP B 602 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 761 through 765
      removed outlier: 4.318A  pdb=" N   GLY B 780 " --> pdb=" O   GLN B 637 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 821 through 824
    Processing sheet with id=AB6, first strand: chain 'B' and resid 859 through 864
      removed outlier: 3.640A  pdb=" N   LEU B 846 " --> pdb=" O   THR B 891 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG B 852 " --> pdb=" O   SER B 885 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   SER B 885 " --> pdb=" O   ARG B 852 " (cutoff:3.500A)

    150 hydrogen bonds defined for protein.
    384 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: 0.96

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2125
        1.35 -     1.47: 1605
        1.47 -     1.59: 2861
        1.59 -     1.71: 0
        1.71 -     1.83: 63
  Bond restraints: 6654
  Sorted by residual:
  bond pdb=" C   ARG B 759 "
       pdb=" N   PRO B 760 "
    ideal  model  delta    sigma   weight residual
    1.333  1.323  0.010 1.01e-02 9.80e+03 1.06e+00
  bond pdb=" CB  ASP A 404 "
       pdb=" CG  ASP A 404 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.75e-01
  bond pdb=" CG  LEU A   2 "
       pdb=" CD1 LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.42e-01
  bond pdb=" CA  ASP B 483 "
       pdb=" CB  ASP B 483 "
    ideal  model  delta    sigma   weight residual
    1.533  1.550 -0.017 2.15e-02 2.16e+03 6.33e-01
  bond pdb=" C   SER B 792 "
       pdb=" N   PRO B 793 "
    ideal  model  delta    sigma   weight residual
    1.334  1.351 -0.017 2.34e-02 1.83e+03 5.34e-01
  ... (remaining 6649 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 8751
        1.42 -     2.84: 205
        2.84 -     4.26: 42
        4.26 -     5.68: 7
        5.68 -     7.10: 4
  Bond angle restraints: 9009
  Sorted by residual:
  angle pdb=" C   ASP B 647 "
        pdb=" N   TYR B 648 "
        pdb=" CA  TYR B 648 "
      ideal   model   delta    sigma   weight residual
     122.09  116.72    5.37 1.79e+00 3.12e-01 9.00e+00
  angle pdb=" C   ILE A  35 "
        pdb=" N   LEU A  36 "
        pdb=" CA  LEU A  36 "
      ideal   model   delta    sigma   weight residual
     121.62  116.98    4.64 1.83e+00 2.99e-01 6.43e+00
  angle pdb=" C   TYR B 633 "
        pdb=" N   TRP B 634 "
        pdb=" CA  TRP B 634 "
      ideal   model   delta    sigma   weight residual
     122.37  118.19    4.18 1.72e+00 3.38e-01 5.91e+00
  angle pdb=" CA  GLU C  12 "
        pdb=" CB  GLU C  12 "
        pdb=" CG  GLU C  12 "
      ideal   model   delta    sigma   weight residual
     114.10  118.61   -4.51 2.00e+00 2.50e-01 5.08e+00
  angle pdb=" CA  CYS B 797 "
        pdb=" CB  CYS B 797 "
        pdb=" SG  CYS B 797 "
      ideal   model   delta    sigma   weight residual
     114.40  119.49   -5.09 2.30e+00 1.89e-01 4.89e+00
  ... (remaining 9004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 3496
       17.75 -    35.50: 415
       35.50 -    53.26: 95
       53.26 -    71.01: 24
       71.01 -    88.76: 11
  Dihedral angle restraints: 4041
    sinusoidal: 1698
      harmonic: 2343
  Sorted by residual:
  dihedral pdb=" CB  CYS A 196 "
           pdb=" SG  CYS A 196 "
           pdb=" SG  CYS A 207 "
           pdb=" CB  CYS A 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.51   57.51     1      1.00e+01 1.00e-02 4.44e+01
  dihedral pdb=" CB  CYS A 169 "
           pdb=" SG  CYS A 169 "
           pdb=" SG  CYS A 188 "
           pdb=" CB  CYS A 188 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -28.88  -57.12     1      1.00e+01 1.00e-02 4.39e+01
  dihedral pdb=" CB  CYS B 649 "
           pdb=" SG  CYS B 649 "
           pdb=" SG  CYS B 862 "
           pdb=" CB  CYS B 862 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.78   54.22     1      1.00e+01 1.00e-02 3.99e+01
  ... (remaining 4038 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 540
       0.027 -    0.054: 244
       0.054 -    0.081: 98
       0.081 -    0.109: 53
       0.109 -    0.136: 38
  Chirality restraints: 973
  Sorted by residual:
  chirality pdb=" CA  ILE A  35 "
            pdb=" N   ILE A  35 "
            pdb=" C   ILE A  35 "
            pdb=" CB  ILE A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  ASP B 483 "
            pdb=" N   ASP B 483 "
            pdb=" C   ASP B 483 "
            pdb=" CB  ASP B 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ILE A 112 "
            pdb=" N   ILE A 112 "
            pdb=" C   ILE A 112 "
            pdb=" CB  ILE A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 970 not shown)

  Planarity restraints: 1162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 634 "    0.015 2.00e-02 2.50e+03   1.90e-02 9.07e+00
        pdb=" CG  TRP B 634 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 634 "    0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 634 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 634 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 634 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 634 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 634 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 634 "    0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 634 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 483 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.37e+00
        pdb=" CG  ASP B 483 "    0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 483 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 483 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 404 "    0.006 2.00e-02 2.50e+03   1.32e-02 1.74e+00
        pdb=" C   ASP A 404 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ASP A 404 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN A 405 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1159 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 130
        2.69 -     3.24: 5885
        3.24 -     3.79: 9349
        3.79 -     4.35: 12659
        4.35 -     4.90: 21518
  Nonbonded interactions: 49541
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  41 "
            pdb=" O   TYR A  67 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" O   SER B 880 "
            pdb=" OH  TYR B 884 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" O   VAL B 888 "
            pdb=" OG1 THR B 900 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" NH2 ARG A 372 "
            pdb=" OD1 ASP B 533 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OG  SER A 339 "
            pdb=" O   PHE A 367 "
     model   vdw
     2.262 3.040
  ... (remaining 49536 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.500
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6672  Z= 0.136
  Angle     :  0.566   7.103   9045  Z= 0.296
  Chirality :  0.045   0.136    973
  Planarity :  0.004   0.030   1162
  Dihedral  : 16.330  88.760   2471
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 18.49 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.79 (0.31), residues: 780
  helix:  0.63 (0.62), residues: 73
  sheet:  0.22 (0.38), residues: 196
  loop : -1.04 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 267 
 TYR   0.010   0.001   TYR B 507 
 PHE   0.015   0.001   PHE B 703 
 TRP   0.049   0.002   TRP B 634 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6654)
  covalent geometry    : angle       0.56392 ( 9009)
  SS BOND              : bond        0.00254 (   18)
  SS BOND              : angle       0.98835 (   36)
  hydrogen bonds       : bond        0.12292 (  150)
  hydrogen bonds       : angle       6.88299 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.160 
Fit side-chains
REVERT: C   16 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7381 (mtt180)
  outliers start: 3
  outliers final: 3
  residues processed: 59
  average time/residue: 0.0676
  time to fit residues: 5.6739
Evaluate side-chains
  57 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ASN
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain B residue  816 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
A 337 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.135409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.104257 restraints weight = 9482.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.107077 restraints weight = 6730.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108481 restraints weight = 4735.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.108649 restraints weight = 4049.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.110765 restraints weight = 3903.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.0514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6672  Z= 0.150
  Angle     :  0.550   6.769   9045  Z= 0.287
  Chirality :  0.045   0.144    973
  Planarity :  0.004   0.031   1162
  Dihedral  :  4.741  26.784    879
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.99 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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 (0.31), residues: 780
  helix:  0.58 (0.59), residues: 79
  sheet:  0.12 (0.37), residues: 195
  loop : -1.03 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  19 
 TYR   0.012   0.001   TYR B 507 
 PHE   0.013   0.001   PHE B 707 
 TRP   0.007   0.001   TRP B 634 
 HIS   0.004   0.001   HIS A 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6654)
  covalent geometry    : angle       0.54731 ( 9009)
  SS BOND              : bond        0.00297 (   18)
  SS BOND              : angle       0.97719 (   36)
  hydrogen bonds       : bond        0.03398 (  150)
  hydrogen bonds       : angle       5.80773 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  185 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7457 (t-90)
REVERT: A  233 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7613 (tp)
REVERT: C   16 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7496 (mtt180)
  outliers start: 17
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0840
  time to fit residues: 8.5357
Evaluate side-chains
  71 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  799 VAL
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6140

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.136301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.104690 restraints weight = 9374.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108184 restraints weight = 5789.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.110583 restraints weight = 4283.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112142 restraints weight = 3504.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.113168 restraints weight = 3071.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.0728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6672  Z= 0.119
  Angle     :  0.519   6.700   9045  Z= 0.272
  Chirality :  0.044   0.142    973
  Planarity :  0.003   0.030   1162
  Dihedral  :  4.514  22.320    876
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.40 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.72 (0.31), residues: 780
  helix:  0.64 (0.59), residues: 79
  sheet:  0.17 (0.37), residues: 195
  loop : -0.95 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 853 
 TYR   0.009   0.001   TYR A  60 
 PHE   0.013   0.001   PHE B 707 
 TRP   0.006   0.001   TRP B 834 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6654)
  covalent geometry    : angle       0.51745 ( 9009)
  SS BOND              : bond        0.00258 (   18)
  SS BOND              : angle       0.85881 (   36)
  hydrogen bonds       : bond        0.03146 (  150)
  hydrogen bonds       : angle       5.53793 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7433 (t-90)
REVERT: B  701 SER cc_start: 0.8267 (m) cc_final: 0.7802 (p)
REVERT: C   16 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7544 (mtt180)
  outliers start: 18
  outliers final: 11
  residues processed: 78
  average time/residue: 0.0841
  time to fit residues: 8.9978
Evaluate side-chains
  70 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.1980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B 786 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.135789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.104193 restraints weight = 9394.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.107740 restraints weight = 5789.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.110062 restraints weight = 4254.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.111640 restraints weight = 3490.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112573 restraints weight = 3052.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6672  Z= 0.129
  Angle     :  0.518   6.634   9045  Z= 0.271
  Chirality :  0.044   0.146    973
  Planarity :  0.003   0.030   1162
  Dihedral  :  4.564  22.102    876
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.67 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.78 (0.31), residues: 780
  helix:  0.60 (0.59), residues: 79
  sheet:  0.06 (0.37), residues: 197
  loop : -0.96 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 853 
 TYR   0.010   0.001   TYR A 401 
 PHE   0.014   0.001   PHE B 703 
 TRP   0.005   0.001   TRP B 834 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6654)
  covalent geometry    : angle       0.51591 ( 9009)
  SS BOND              : bond        0.00286 (   18)
  SS BOND              : angle       0.93989 (   36)
  hydrogen bonds       : bond        0.03033 (  150)
  hydrogen bonds       : angle       5.41800 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7430 (t-90)
REVERT: A  233 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7672 (tp)
REVERT: C   16 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7456 (mtt180)
  outliers start: 18
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0809
  time to fit residues: 8.4421
Evaluate side-chains
  73 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain C residue    9 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0670
   chunk 66 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
A 337 ASN
B 786 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.136023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.104315 restraints weight = 9474.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.107898 restraints weight = 5799.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.110246 restraints weight = 4261.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.111700 restraints weight = 3494.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.112814 restraints weight = 3079.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6672  Z= 0.128
  Angle     :  0.516   6.662   9045  Z= 0.270
  Chirality :  0.044   0.146    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.517  21.617    876
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.40 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.78 (0.30), residues: 780
  helix:  0.63 (0.59), residues: 79
  sheet:  0.13 (0.37), residues: 195
  loop : -0.99 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 853 
 TYR   0.010   0.001   TYR B 507 
 PHE   0.014   0.001   PHE B 703 
 TRP   0.005   0.001   TRP B 834 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6654)
  covalent geometry    : angle       0.51395 ( 9009)
  SS BOND              : bond        0.00269 (   18)
  SS BOND              : angle       0.93257 (   36)
  hydrogen bonds       : bond        0.02956 (  150)
  hydrogen bonds       : angle       5.32565 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8064 (t0)
REVERT: A  185 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7486 (t-90)
REVERT: A  233 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7648 (tp)
REVERT: C   16 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7492 (mtt180)
  outliers start: 19
  outliers final: 14
  residues processed: 77
  average time/residue: 0.0781
  time to fit residues: 8.3574
Evaluate side-chains
  74 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain C residue    9 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0970
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
A  32 HIS
B 786 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.136504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.104869 restraints weight = 9458.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.108435 restraints weight = 5775.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110794 restraints weight = 4240.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112383 restraints weight = 3478.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113217 restraints weight = 3043.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6672  Z= 0.117
  Angle     :  0.514   6.575   9045  Z= 0.270
  Chirality :  0.044   0.144    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.472  22.037    876
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.26 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.74 (0.30), residues: 780
  helix:  0.69 (0.59), residues: 79
  sheet:  0.15 (0.37), residues: 195
  loop : -0.98 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 853 
 TYR   0.009   0.001   TYR B 507 
 PHE   0.013   0.001   PHE B 703 
 TRP   0.005   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6654)
  covalent geometry    : angle       0.51202 ( 9009)
  SS BOND              : bond        0.00250 (   18)
  SS BOND              : angle       0.85900 (   36)
  hydrogen bonds       : bond        0.02849 (  150)
  hydrogen bonds       : angle       5.23908 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8073 (t0)
REVERT: A  185 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7481 (t-90)
REVERT: C   16 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7522 (mtm180)
  outliers start: 22
  outliers final: 17
  residues processed: 83
  average time/residue: 0.0984
  time to fit residues: 10.8031
Evaluate side-chains
  81 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  876 LEU
Chi-restraints excluded: chain C residue    9 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B 786 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.133038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.103024 restraints weight = 9397.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.106409 restraints weight = 5696.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.108614 restraints weight = 4161.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.110154 restraints weight = 3410.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.111105 restraints weight = 2979.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6672  Z= 0.182
  Angle     :  0.558   6.574   9045  Z= 0.291
  Chirality :  0.046   0.149    973
  Planarity :  0.004   0.030   1162
  Dihedral  :  4.689  23.883    876
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.40 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.89 (0.30), residues: 780
  helix:  0.56 (0.60), residues: 80
  sheet:  0.04 (0.37), residues: 192
  loop : -1.07 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 877 
 TYR   0.014   0.001   TYR A 401 
 PHE   0.015   0.002   PHE B 703 
 TRP   0.004   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 6654)
  covalent geometry    : angle       0.55521 ( 9009)
  SS BOND              : bond        0.00343 (   18)
  SS BOND              : angle       1.03326 (   36)
  hydrogen bonds       : bond        0.03157 (  150)
  hydrogen bonds       : angle       5.40972 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8097 (t0)
REVERT: A  185 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.7503 (t-90)
REVERT: A  233 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7721 (tp)
REVERT: C   16 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7557 (mtm180)
  outliers start: 25
  outliers final: 17
  residues processed: 81
  average time/residue: 0.0918
  time to fit residues: 9.9360
Evaluate side-chains
  77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  435 CYS
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
Chi-restraints excluded: chain C residue    9 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0970
   chunk 18 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 49 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
A 440 HIS
B 786 GLN
B 822 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.136653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.104971 restraints weight = 9419.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.108525 restraints weight = 5800.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.110885 restraints weight = 4272.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.112399 restraints weight = 3500.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113474 restraints weight = 3077.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6672  Z= 0.100
  Angle     :  0.512   6.610   9045  Z= 0.267
  Chirality :  0.044   0.145    973
  Planarity :  0.003   0.030   1162
  Dihedral  :  4.481  21.337    876
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.32 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.75 (0.30), residues: 780
  helix:  0.66 (0.59), residues: 79
  sheet:  0.11 (0.37), residues: 192
  loop : -0.96 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 853 
 TYR   0.009   0.001   TYR A 107 
 PHE   0.013   0.001   PHE B 703 
 TRP   0.006   0.001   TRP A 251 
 HIS   0.003   0.001   HIS B 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6654)
  covalent geometry    : angle       0.51017 ( 9009)
  SS BOND              : bond        0.00221 (   18)
  SS BOND              : angle       0.78518 (   36)
  hydrogen bonds       : bond        0.02760 (  150)
  hydrogen bonds       : angle       5.24699 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8041 (t0)
REVERT: A  185 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7460 (t-90)
REVERT: B  852 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.5965 (ttm-80)
REVERT: C   16 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7521 (mtm180)
  outliers start: 14
  outliers final: 11
  residues processed: 75
  average time/residue: 0.0931
  time to fit residues: 9.3158
Evaluate side-chains
  73 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
Chi-restraints excluded: chain B residue  852 ARG
Chi-restraints excluded: chain C residue    9 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    0.1980
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 68 optimal weight:    0.2980
   chunk 34 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.137146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.105463 restraints weight = 9527.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.109080 restraints weight = 5856.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.111456 restraints weight = 4292.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.113004 restraints weight = 3514.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.114035 restraints weight = 3077.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6672  Z= 0.100
  Angle     :  0.509   6.459   9045  Z= 0.265
  Chirality :  0.044   0.142    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.428  21.453    876
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.59 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.70 (0.31), residues: 780
  helix:  0.69 (0.59), residues: 79
  sheet:  0.12 (0.37), residues: 192
  loop : -0.91 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 875 
 TYR   0.010   0.001   TYR B 884 
 PHE   0.013   0.001   PHE B 703 
 TRP   0.005   0.001   TRP A 251 
 HIS   0.009   0.001   HIS B 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6654)
  covalent geometry    : angle       0.50803 ( 9009)
  SS BOND              : bond        0.00223 (   18)
  SS BOND              : angle       0.77468 (   36)
  hydrogen bonds       : bond        0.02725 (  150)
  hydrogen bonds       : angle       5.20030 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8035 (t0)
REVERT: A  185 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7452 (t-90)
REVERT: A  233 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7734 (tp)
REVERT: B  852 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.5877 (ttm-80)
REVERT: C   16 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7517 (mtm180)
  outliers start: 14
  outliers final: 9
  residues processed: 73
  average time/residue: 0.0962
  time to fit residues: 9.3577
Evaluate side-chains
  73 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
Chi-restraints excluded: chain B residue  852 ARG
Chi-restraints excluded: chain C residue    9 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 786 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.135298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103881 restraints weight = 9327.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.107368 restraints weight = 5745.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.109723 restraints weight = 4240.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111242 restraints weight = 3472.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112157 restraints weight = 3051.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6672  Z= 0.145
  Angle     :  0.538   6.641   9045  Z= 0.280
  Chirality :  0.045   0.144    973
  Planarity :  0.003   0.030   1162
  Dihedral  :  4.538  21.871    876
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.32 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.79 (0.30), residues: 780
  helix:  0.57 (0.60), residues: 80
  sheet:  0.08 (0.37), residues: 192
  loop : -0.98 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 875 
 TYR   0.011   0.001   TYR A 401 
 PHE   0.014   0.001   PHE B 703 
 TRP   0.005   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6654)
  covalent geometry    : angle       0.53558 ( 9009)
  SS BOND              : bond        0.00287 (   18)
  SS BOND              : angle       0.91591 (   36)
  hydrogen bonds       : bond        0.02910 (  150)
  hydrogen bonds       : angle       5.24318 (  384)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8055 (t0)
REVERT: A  185 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7525 (t-90)
REVERT: A  233 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7768 (tp)
REVERT: B  852 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5866 (ttm-80)
REVERT: C   16 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7538 (mtm180)
  outliers start: 17
  outliers final: 13
  residues processed: 77
  average time/residue: 0.0907
  time to fit residues: 9.3113
Evaluate side-chains
  79 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  645 GLU
Chi-restraints excluded: chain B residue  648 TYR
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
Chi-restraints excluded: chain B residue  849 VAL
Chi-restraints excluded: chain B residue  852 ARG
Chi-restraints excluded: chain C residue    9 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 60 optimal weight:    0.1980
   chunk 77 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 42 optimal weight:    0.3980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B 786 GLN
B 822 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.137169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.106079 restraints weight = 9424.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.109364 restraints weight = 6068.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.111591 restraints weight = 4572.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.113025 restraints weight = 3792.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.114002 restraints weight = 3357.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6672  Z= 0.103
  Angle     :  0.511   6.587   9045  Z= 0.267
  Chirality :  0.044   0.144    973
  Planarity :  0.003   0.030   1162
  Dihedral  :  4.416  21.380    876
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.86 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.69 (0.31), residues: 780
  helix:  0.59 (0.60), residues: 80
  sheet:  0.16 (0.38), residues: 192
  loop : -0.90 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 875 
 TYR   0.009   0.001   TYR B 633 
 PHE   0.013   0.001   PHE B 703 
 TRP   0.006   0.001   TRP A 251 
 HIS   0.002   0.001   HIS B 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6654)
  covalent geometry    : angle       0.51000 ( 9009)
  SS BOND              : bond        0.00218 (   18)
  SS BOND              : angle       0.77534 (   36)
  hydrogen bonds       : bond        0.02673 (  150)
  hydrogen bonds       : angle       5.12818 (  384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1335.49 seconds
wall clock time: 23 minutes 43.61 seconds (1423.61 seconds total)