Starting phenix.real_space_refine
on Tue Jul 29 19:12:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dtm_27705/07_2025/8dtm_27705_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dtm_27705/07_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_27705/07_2025/8dtm_27705.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dtm_27705/07_2025/8dtm_27705.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dtm_27705/07_2025/8dtm_27705_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dtm_27705/07_2025/8dtm_27705_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.21, per 1000 atoms: 0.65
  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: 1.35
  Conformation dependent library (CDL) restraints added in 859.2 milliseconds
  

  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: 0.72
  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: 1.84

  Time building geometry restraints manager: 1.66 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:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.270
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.640
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (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
 TRP   0.049   0.002   TRP B 634 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.015   0.001   PHE B 703 
 TYR   0.010   0.001   TYR B 507 
 ARG   0.004   0.000   ARG A 267 

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

*********************** 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  : 0.767 
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: 0.1848
  time to fit residues: 15.3142
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  : 0.756 
-------------------------------------------------------------------------------
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 66 optimal weight:    0.0970
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   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 337 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.136731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.104858 restraints weight = 9322.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108353 restraints weight = 5791.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.110705 restraints weight = 4278.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.0512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6672  Z= 0.120
  Angle     :  0.530   6.742   9045  Z= 0.277
  Chirality :  0.044   0.149    973
  Planarity :  0.003   0.031   1162
  Dihedral  :  4.629  24.463    879
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.26 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.31), residues: 780
  helix:  0.59 (0.59), residues: 79
  sheet:  0.19 (0.37), residues: 195
  loop : -1.00 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 834 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.013   0.001   PHE B 707 
 TYR   0.010   0.001   TYR B 507 
 ARG   0.004   0.000   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  150)
  hydrogen bonds       : angle       5.77407 (  384)
  SS BOND              : bond        0.00265 (   18)
  SS BOND              : angle       0.89397 (   36)
  covalent geometry    : bond        0.00287 ( 6654)
  covalent geometry    : angle       0.52825 ( 9009)

*********************** 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
  75 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7414 (t-90)
REVERT: B  634 TRP cc_start: 0.8808 (p90) cc_final: 0.8162 (p90)
REVERT: C   16 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7465 (mtt180)
  outliers start: 14
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1783
  time to fit residues: 18.0328
Evaluate side-chains
  67 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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  280 HIS
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  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 37 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0020
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0770
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    0.5146

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.137140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.105387 restraints weight = 9441.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.108941 restraints weight = 5798.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.111308 restraints weight = 4275.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.0771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6672  Z= 0.107
  Angle     :  0.507   6.677   9045  Z= 0.265
  Chirality :  0.044   0.140    973
  Planarity :  0.003   0.030   1162
  Dihedral  :  4.419  21.687    876
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.26 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.31), residues: 780
  helix:  0.68 (0.59), residues: 79
  sheet:  0.24 (0.37), residues: 195
  loop : -0.93 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 834 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.013   0.001   PHE B 707 
 TYR   0.008   0.001   TYR B 507 
 ARG   0.006   0.000   ARG B 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03050 (  150)
  hydrogen bonds       : angle       5.45855 (  384)
  SS BOND              : bond        0.00242 (   18)
  SS BOND              : angle       0.82408 (   36)
  covalent geometry    : bond        0.00255 ( 6654)
  covalent geometry    : angle       0.50547 ( 9009)

*********************** 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  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7397 (t-90)
REVERT: A  233 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7611 (tp)
REVERT: B  701 SER cc_start: 0.8240 (m) cc_final: 0.7815 (p)
REVERT: C   16 ARG cc_start: 0.7962 (mtm180) cc_final: 0.7564 (mtt180)
  outliers start: 18
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1859
  time to fit residues: 20.2739
Evaluate side-chains
  72 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
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  233 LEU
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.133780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.102210 restraints weight = 9544.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.105703 restraints weight = 5871.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.108007 restraints weight = 4327.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6672  Z= 0.215
  Angle     :  0.577   6.744   9045  Z= 0.300
  Chirality :  0.046   0.150    973
  Planarity :  0.004   0.030   1162
  Dihedral  :  4.758  24.550    876
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.30), residues: 780
  helix:  0.49 (0.59), residues: 80
  sheet: -0.01 (0.37), residues: 197
  loop : -1.04 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 834 
 HIS   0.005   0.001   HIS A 247 
 PHE   0.015   0.002   PHE B 703 
 TYR   0.015   0.001   TYR A 401 
 ARG   0.003   0.000   ARG B 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  150)
  hydrogen bonds       : angle       5.56526 (  384)
  SS BOND              : bond        0.00389 (   18)
  SS BOND              : angle       1.16131 (   36)
  covalent geometry    : bond        0.00528 ( 6654)
  covalent geometry    : angle       0.57298 ( 9009)

*********************** 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
  78 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7517 (t-90)
REVERT: A  233 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7703 (tp)
REVERT: B  538 GLN cc_start: 0.7429 (mt0) cc_final: 0.7172 (mt0)
REVERT: B  634 TRP cc_start: 0.8988 (p90) cc_final: 0.8098 (p90)
  outliers start: 18
  outliers final: 13
  residues processed: 76
  average time/residue: 0.1702
  time to fit residues: 18.0416
Evaluate side-chains
  72 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
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  148 ASN
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 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 51 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.135724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.103912 restraints weight = 9448.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107439 restraints weight = 5814.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.109766 restraints weight = 4287.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.0923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6672  Z= 0.132
  Angle     :  0.526   6.681   9045  Z= 0.275
  Chirality :  0.045   0.145    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.612  23.383    876
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.36 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.30), residues: 780
  helix:  0.62 (0.59), residues: 79
  sheet:  0.02 (0.37), residues: 197
  loop : -1.01 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.014   0.001   PHE B 703 
 TYR   0.010   0.001   TYR A  60 
 ARG   0.003   0.000   ARG B 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03038 (  150)
  hydrogen bonds       : angle       5.39612 (  384)
  SS BOND              : bond        0.00276 (   18)
  SS BOND              : angle       0.97819 (   36)
  covalent geometry    : bond        0.00321 ( 6654)
  covalent geometry    : angle       0.52358 ( 9009)

*********************** 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
  76 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8071 (t0)
REVERT: A  185 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7492 (t-90)
REVERT: A  233 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7690 (tp)
REVERT: B  538 GLN cc_start: 0.7501 (mt0) cc_final: 0.7278 (mt0)
REVERT: C   16 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7620 (mtm180)
  outliers start: 16
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1789
  time to fit residues: 18.3318
Evaluate side-chains
  72 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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  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  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.135082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.103406 restraints weight = 9385.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.106952 restraints weight = 5801.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.109282 restraints weight = 4274.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6672  Z= 0.148
  Angle     :  0.533   6.639   9045  Z= 0.278
  Chirality :  0.045   0.146    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.616  23.180    876
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.95 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.30), residues: 780
  helix:  0.61 (0.59), residues: 79
  sheet: -0.02 (0.37), residues: 197
  loop : -1.02 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.014   0.001   PHE B 703 
 TYR   0.011   0.001   TYR A 401 
 ARG   0.003   0.000   ARG B 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  150)
  hydrogen bonds       : angle       5.35735 (  384)
  SS BOND              : bond        0.00298 (   18)
  SS BOND              : angle       0.97518 (   36)
  covalent geometry    : bond        0.00362 ( 6654)
  covalent geometry    : angle       0.53097 ( 9009)

*********************** 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
  81 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8107 (t0)
REVERT: A  185 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7505 (t-90)
REVERT: A  233 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7670 (tp)
REVERT: C   16 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7656 (mtm180)
  outliers start: 19
  outliers final: 13
  residues processed: 77
  average time/residue: 0.2073
  time to fit residues: 21.5854
Evaluate side-chains
  77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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  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  816 ILE
Chi-restraints excluded: chain B residue  822 HIS
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 20 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0770
   chunk 53 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.9542

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.134486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.102923 restraints weight = 9388.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.106399 restraints weight = 5801.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.108739 restraints weight = 4277.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6672  Z= 0.163
  Angle     :  0.544   6.665   9045  Z= 0.284
  Chirality :  0.045   0.149    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.650  22.955    876
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.67 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.30), residues: 780
  helix:  0.52 (0.59), residues: 80
  sheet:  0.03 (0.38), residues: 192
  loop : -1.06 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 247 
 PHE   0.014   0.001   PHE B 703 
 TYR   0.011   0.001   TYR A 401 
 ARG   0.003   0.000   ARG B 875 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  150)
  hydrogen bonds       : angle       5.38671 (  384)
  SS BOND              : bond        0.00316 (   18)
  SS BOND              : angle       1.02272 (   36)
  covalent geometry    : bond        0.00397 ( 6654)
  covalent geometry    : angle       0.54112 ( 9009)

*********************** 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
  83 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8121 (t0)
REVERT: A  185 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7510 (t-90)
REVERT: A  233 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7691 (tp)
REVERT: C   16 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7684 (mtm180)
  outliers start: 24
  outliers final: 16
  residues processed: 79
  average time/residue: 0.1904
  time to fit residues: 20.4227
Evaluate side-chains
  77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  278 VAL
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  535 ASP
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  876 LEU
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 39 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 57 optimal weight:    0.3980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 822 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.135277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103768 restraints weight = 9371.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.107317 restraints weight = 5764.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.109663 restraints weight = 4246.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1173

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= 0.140
  Angle     :  0.532   6.564   9045  Z= 0.277
  Chirality :  0.045   0.151    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.606  22.126    876
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.22 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.30), residues: 780
  helix:  0.52 (0.59), residues: 80
  sheet:  0.06 (0.38), residues: 192
  loop : -1.03 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 247 
 PHE   0.014   0.001   PHE B 703 
 TYR   0.010   0.001   TYR B 507 
 ARG   0.005   0.000   ARG B 877 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02982 (  150)
  hydrogen bonds       : angle       5.32072 (  384)
  SS BOND              : bond        0.00283 (   18)
  SS BOND              : angle       0.95715 (   36)
  covalent geometry    : bond        0.00342 ( 6654)
  covalent geometry    : angle       0.52938 ( 9009)

*********************** 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
  82 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8110 (t0)
REVERT: A  185 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7546 (t-90)
REVERT: A  233 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7738 (tp)
  outliers start: 21
  outliers final: 18
  residues processed: 80
  average time/residue: 0.1901
  time to fit residues: 20.7563
Evaluate side-chains
  81 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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  116 SER
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  226 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  278 VAL
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  568 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 76 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3638 r_free = 0.3638 target = 0.134447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.102765 restraints weight = 9594.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.106320 restraints weight = 5878.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.108613 restraints weight = 4311.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1206

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= 0.172
  Angle     :  0.565   6.562   9045  Z= 0.296
  Chirality :  0.045   0.147    973
  Planarity :  0.004   0.045   1162
  Dihedral  :  4.675  22.457    876
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.30), residues: 780
  helix:  0.51 (0.59), residues: 80
  sheet: -0.02 (0.38), residues: 192
  loop : -1.06 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 247 
 PHE   0.014   0.001   PHE B 703 
 TYR   0.012   0.001   TYR B 884 
 ARG   0.006   0.000   ARG C  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03082 (  150)
  hydrogen bonds       : angle       5.38015 (  384)
  SS BOND              : bond        0.00326 (   18)
  SS BOND              : angle       1.03212 (   36)
  covalent geometry    : bond        0.00418 ( 6654)
  covalent geometry    : angle       0.56204 ( 9009)

*********************** 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
  83 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8104 (t0)
REVERT: A  185 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7579 (t-90)
REVERT: A  233 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7765 (tp)
  outliers start: 21
  outliers final: 18
  residues processed: 81
  average time/residue: 0.1901
  time to fit residues: 20.7327
Evaluate side-chains
  78 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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  116 SER
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  226 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  278 VAL
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  568 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.8786

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.134724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.103061 restraints weight = 9514.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.106609 restraints weight = 5837.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.108993 restraints weight = 4288.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6672  Z= 0.156
  Angle     :  0.558   6.572   9045  Z= 0.293
  Chirality :  0.045   0.151    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.661  22.430    876
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.36 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.30), residues: 780
  helix:  0.52 (0.59), residues: 80
  sheet: -0.03 (0.38), residues: 192
  loop : -1.04 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 834 
 HIS   0.003   0.001   HIS A 247 
 PHE   0.014   0.001   PHE B 703 
 TYR   0.011   0.001   TYR A 401 
 ARG   0.003   0.000   ARG B 875 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03010 (  150)
  hydrogen bonds       : angle       5.35701 (  384)
  SS BOND              : bond        0.00304 (   18)
  SS BOND              : angle       1.01848 (   36)
  covalent geometry    : bond        0.00379 ( 6654)
  covalent geometry    : angle       0.55587 ( 9009)

********************** 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
  81 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8092 (t0)
REVERT: A  185 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7526 (t-90)
REVERT: A  233 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7777 (tp)
  outliers start: 22
  outliers final: 19
  residues processed: 79
  average time/residue: 0.1815
  time to fit residues: 19.7641
Evaluate side-chains
  81 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
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  116 SER
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  226 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  278 VAL
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  568 VAL
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  807 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 57 optimal weight:    0.3980
   chunk 69 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 822 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.134867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.103327 restraints weight = 9585.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.106851 restraints weight = 5845.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.109226 restraints weight = 4292.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
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      :  0.003   0.027   6672  Z= 0.143
  Angle     :  0.550   6.565   9045  Z= 0.287
  Chirality :  0.045   0.149    973
  Planarity :  0.003   0.029   1162
  Dihedral  :  4.634  22.275    876
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.08 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.30), residues: 780
  helix:  0.53 (0.59), residues: 80
  sheet: -0.01 (0.38), residues: 192
  loop : -1.03 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 834 
 HIS   0.003   0.001   HIS A 247 
 PHE   0.014   0.001   PHE B 703 
 TYR   0.010   0.001   TYR A 401 
 ARG   0.003   0.000   ARG B 875 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02955 (  150)
  hydrogen bonds       : angle       5.32520 (  384)
  SS BOND              : bond        0.00294 (   18)
  SS BOND              : angle       0.99373 (   36)
  covalent geometry    : bond        0.00348 ( 6654)
  covalent geometry    : angle       0.54784 ( 9009)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2352.93 seconds
wall clock time: 41 minutes 22.74 seconds (2482.74 seconds total)