Starting phenix.real_space_refine
on Thu Mar  6 05:07:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gsz_34244/03_2025/8gsz_34244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gsz_34244/03_2025/8gsz_34244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gsz_34244/03_2025/8gsz_34244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gsz_34244/03_2025/8gsz_34244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gsz_34244/03_2025/8gsz_34244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gsz_34244/03_2025/8gsz_34244.cif"
  }
  resolution = 3.65
  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 140 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      26      5.16       5
     C    3118      2.51       5
     N     854      2.21       5
     O     872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2435
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 14, 'TRANS': 295}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.19, per 1000 atoms: 1.07
  Number of scatterers: 4870
  At special positions: 0
  Unit cell: (84.609, 73.899, 106.029, 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      26     16.00
     O     872      8.00
     N     854      7.00
     C    3118      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.17
  Conformation dependent library (CDL) restraints added in 596.4 milliseconds
  

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      62.3% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 31
      removed outlier: 3.551A  pdb=" N   ALA A  21 " --> pdb=" O   GLY A  17 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 3.678A  pdb=" N   GLU A  38 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 65
      removed outlier: 3.593A  pdb=" N   VAL A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   SER A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLY A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 72
      removed outlier: 4.025A  pdb=" N   ARG A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 78
    Processing helix  chain 'A' and resid 80 through 90
      removed outlier: 3.844A  pdb=" N   THR A  84 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 108
      removed outlier: 4.134A  pdb=" N   ARG A  95 " --> pdb=" O   CYS A  91 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU A  98 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   TYR A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 134
      removed outlier: 4.115A  pdb=" N   LEU A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A 132 " --> pdb=" O   GLN A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 151
      removed outlier: 3.505A  pdb=" N   LEU A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 167
      removed outlier: 3.590A  pdb=" N   SER A 162 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 186
      removed outlier: 3.655A  pdb=" N   ARG A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR A 186 " --> pdb=" O   TYR A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 273
      removed outlier: 3.717A  pdb=" N   GLN A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 288
      removed outlier: 3.643A  pdb=" N   ALA A 288 " --> pdb=" O   ARG A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 302
      removed outlier: 3.978A  pdb=" N   GLU A 296 " --> pdb=" O   CYS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 307
      removed outlier: 3.719A  pdb=" N   GLN A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ASN A 307 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 302 through 307'
    Processing helix  chain 'A' and resid 324 through 335
      removed outlier: 4.250A  pdb=" N   GLU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A 335 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 31
      removed outlier: 3.551A  pdb=" N   ALA B  21 " --> pdb=" O   GLY B  17 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU B  23 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL B  24 " --> pdb=" O   LYS B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 38
      removed outlier: 3.678A  pdb=" N   GLU B  38 " --> pdb=" O   TRP B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 65
      removed outlier: 3.593A  pdb=" N   VAL B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   SER B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLY B  57 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 72
      removed outlier: 4.025A  pdb=" N   ARG B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS B  72 " --> pdb=" O   GLU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 78
    Processing helix  chain 'B' and resid 80 through 90
      removed outlier: 3.844A  pdb=" N   THR B  84 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 108
      removed outlier: 4.134A  pdb=" N   ARG B  95 " --> pdb=" O   CYS B  91 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU B  98 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   TYR B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 134
      removed outlier: 4.115A  pdb=" N   LEU B 124 " --> pdb=" O   MET B 120 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE B 132 " --> pdb=" O   GLN B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 151
      removed outlier: 3.505A  pdb=" N   LEU B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 167
      removed outlier: 3.590A  pdb=" N   SER B 162 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 186
      removed outlier: 3.655A  pdb=" N   ARG B 178 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR B 186 " --> pdb=" O   TYR B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 273
      removed outlier: 3.717A  pdb=" N   GLN B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR B 267 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 288
      removed outlier: 3.643A  pdb=" N   ALA B 288 " --> pdb=" O   ARG B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 302
      removed outlier: 3.978A  pdb=" N   GLU B 296 " --> pdb=" O   CYS B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 307
      removed outlier: 3.719A  pdb=" N   GLN B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ASN B 307 " --> pdb=" O   PRO B 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 302 through 307'
    Processing helix  chain 'B' and resid 324 through 335
      removed outlier: 4.250A  pdb=" N   GLU B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN B 335 " --> pdb=" O   ARG B 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 249
      removed outlier: 3.691A  pdb=" N   GLY A 255 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU A 249 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ARG A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A 198 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 249
      removed outlier: 3.691A  pdb=" N   GLY B 255 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU B 249 " --> pdb=" O   ARG B 253 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ARG B 253 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU B 198 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ILE B 312 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    612 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: 1.26

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1588
        1.34 -     1.46: 1126
        1.46 -     1.58: 2226
        1.58 -     1.70: 0
        1.70 -     1.81: 32
  Bond restraints: 4972
  Sorted by residual:
  bond pdb=" N   VAL A 194 "
       pdb=" CA  VAL A 194 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.18e-02 7.18e+03 9.66e+00
  bond pdb=" N   VAL B 194 "
       pdb=" CA  VAL B 194 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.18e-02 7.18e+03 9.66e+00
  bond pdb=" N   HIS B  72 "
       pdb=" CA  HIS B  72 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.18e-02 7.18e+03 8.92e+00
  bond pdb=" N   HIS A  72 "
       pdb=" CA  HIS A  72 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.18e-02 7.18e+03 8.92e+00
  bond pdb=" N   ILE A  73 "
       pdb=" CA  ILE A  73 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.70e+00
  ... (remaining 4967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 6328
        1.58 -     3.16: 326
        3.16 -     4.74: 54
        4.74 -     6.32: 28
        6.32 -     7.90: 4
  Bond angle restraints: 6740
  Sorted by residual:
  angle pdb=" C   TYR A  77 "
        pdb=" N   ARG A  78 "
        pdb=" CA  ARG A  78 "
      ideal   model   delta    sigma   weight residual
     122.08  127.51   -5.43 1.47e+00 4.63e-01 1.37e+01
  angle pdb=" C   TYR B  77 "
        pdb=" N   ARG B  78 "
        pdb=" CA  ARG B  78 "
      ideal   model   delta    sigma   weight residual
     122.08  127.51   -5.43 1.47e+00 4.63e-01 1.37e+01
  angle pdb=" C   GLU B 249 "
        pdb=" N   ASN B 250 "
        pdb=" CA  ASN B 250 "
      ideal   model   delta    sigma   weight residual
     122.46  127.15   -4.69 1.41e+00 5.03e-01 1.11e+01
  angle pdb=" C   GLU A 249 "
        pdb=" N   ASN A 250 "
        pdb=" CA  ASN A 250 "
      ideal   model   delta    sigma   weight residual
     122.46  127.15   -4.69 1.41e+00 5.03e-01 1.11e+01
  angle pdb=" CA  ILE B  73 "
        pdb=" C   ILE B  73 "
        pdb=" O   ILE B  73 "
      ideal   model   delta    sigma   weight residual
     120.95  117.51    3.44 1.04e+00 9.25e-01 1.09e+01
  ... (remaining 6735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.97: 2532
       14.97 -    29.95: 302
       29.95 -    44.92: 106
       44.92 -    59.89: 12
       59.89 -    74.86: 14
  Dihedral angle restraints: 2966
    sinusoidal: 1164
      harmonic: 1802
  Sorted by residual:
  dihedral pdb=" CA  ASN B 154 "
           pdb=" C   ASN B 154 "
           pdb=" N   VAL B 155 "
           pdb=" CA  VAL B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.27  -29.73     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  ASN A 154 "
           pdb=" C   ASN A 154 "
           pdb=" N   VAL A 155 "
           pdb=" CA  VAL A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.27  -29.73     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  GLU B 328 "
           pdb=" C   GLU B 328 "
           pdb=" N   VAL B 329 "
           pdb=" CA  VAL B 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 2963 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 442
       0.040 -    0.079: 242
       0.079 -    0.118: 54
       0.118 -    0.158: 16
       0.158 -    0.197: 8
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CA  LEU A 198 "
            pdb=" N   LEU A 198 "
            pdb=" C   LEU A 198 "
            pdb=" CB  LEU A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" CA  LEU B 198 "
            pdb=" N   LEU B 198 "
            pdb=" C   LEU B 198 "
            pdb=" CB  LEU B 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" CA  ARG B  71 "
            pdb=" N   ARG B  71 "
            pdb=" C   ARG B  71 "
            pdb=" CB  ARG B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.71e-01
  ... (remaining 759 not shown)

  Planarity restraints: 854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 263 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO B 264 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 264 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 264 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 263 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 264 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 264 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 264 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 172 "    0.036 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO B 173 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 173 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 173 "    0.030 5.00e-02 4.00e+02
  ... (remaining 851 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1064
        2.77 -     3.30: 4390
        3.30 -     3.84: 7845
        3.84 -     4.37: 9309
        4.37 -     4.90: 15438
  Nonbonded interactions: 38046
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 197 "
            pdb=" CG  ARG A 310 "
     model   vdw
     2.241 3.520
  nonbonded pdb=" NH2 ARG B 197 "
            pdb=" CG  ARG B 310 "
     model   vdw
     2.241 3.520
  nonbonded pdb=" OE1 GLU B 246 "
            pdb=" OG1 THR B 256 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OE1 GLU A 246 "
            pdb=" OG1 THR A 256 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   LEU B  99 "
            pdb=" OG  SER B 102 "
     model   vdw
     2.365 3.040
  ... (remaining 38041 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.560
  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:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.980
  Find NCS groups from input model:        0.090
  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:             0.000
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099   4972  Z= 0.373
  Angle     :  0.862   7.903   6740  Z= 0.489
  Chirality :  0.051   0.197    762
  Planarity :  0.006   0.063    854
  Dihedral  : 15.613  74.864   1806
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 10.85 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -5.38 (0.24), residues: 596
  helix: -4.27 (0.12), residues: 348
  sheet: -2.93 (0.62), residues: 36
  loop : -1.91 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 119 
 HIS   0.002   0.001   HIS A   7 
 PHE   0.009   0.002   PHE B 117 
 TYR   0.007   0.001   TYR A 107 
 ARG   0.001   0.000   ARG A 169 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 162
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A   42 HIS cc_start: 0.6621 (m-70) cc_final: 0.6383 (m90)
REVERT: A  132 ILE cc_start: 0.8956 (pt) cc_final: 0.8731 (pt)
REVERT: A  223 ASP cc_start: 0.6769 (m-30) cc_final: 0.6561 (m-30)
REVERT: A  269 PHE cc_start: 0.8515 (t80) cc_final: 0.7921 (t80)
REVERT: A  310 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7159 (mmm-85)
REVERT: B   42 HIS cc_start: 0.6619 (m-70) cc_final: 0.6381 (m90)
REVERT: B  132 ILE cc_start: 0.8957 (pt) cc_final: 0.8731 (pt)
REVERT: B  223 ASP cc_start: 0.6768 (m-30) cc_final: 0.6556 (m-30)
REVERT: B  269 PHE cc_start: 0.8517 (t80) cc_final: 0.7924 (t80)
REVERT: B  310 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7159 (mmm-85)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.2094
  time to fit residues: 42.7912
Evaluate side-chains
  116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A   7 HIS
A  61 ASN
A  74 HIS
A 131 ASN
A 154 ASN
A 157 HIS
A 218 ASN
A 273 GLN
A 307 ASN
B   7 HIS
B  61 ASN
B  74 HIS
B 131 ASN
B 154 ASN
B 157 HIS
B 218 ASN
B 273 GLN
B 307 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.155245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.127488 restraints weight = 7816.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.130807 restraints weight = 4759.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133105 restraints weight = 3509.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4972  Z= 0.178
  Angle     :  0.623   6.235   6740  Z= 0.309
  Chirality :  0.041   0.131    762
  Planarity :  0.005   0.042    854
  Dihedral  :  4.830  25.794    684
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.38 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.29), residues: 596
  helix: -2.53 (0.21), residues: 378
  sheet: -2.62 (0.66), residues: 42
  loop : -1.81 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  34 
 HIS   0.002   0.000   HIS A  50 
 PHE   0.026   0.002   PHE B 221 
 TYR   0.011   0.001   TYR B 199 
 ARG   0.004   0.000   ARG B 180 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.555 
Fit side-chains
REVERT: A   42 HIS cc_start: 0.6628 (m-70) cc_final: 0.6426 (m90)
REVERT: A  199 TYR cc_start: 0.7816 (m-80) cc_final: 0.7601 (m-80)
REVERT: A  269 PHE cc_start: 0.8381 (t80) cc_final: 0.7946 (t80)
REVERT: B   42 HIS cc_start: 0.6630 (m-70) cc_final: 0.6423 (m90)
REVERT: B  199 TYR cc_start: 0.7808 (m-80) cc_final: 0.7597 (m-80)
REVERT: B  269 PHE cc_start: 0.8376 (t80) cc_final: 0.7942 (t80)
  outliers start: 10
  outliers final: 4
  residues processed: 134
  average time/residue: 0.1525
  time to fit residues: 26.7916
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  210 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
A  61 ASN
B   3 HIS
B  61 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.152655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.124343 restraints weight = 7983.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.127651 restraints weight = 5006.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.129798 restraints weight = 3748.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   4972  Z= 0.249
  Angle     :  0.640   5.947   6740  Z= 0.308
  Chirality :  0.042   0.124    762
  Planarity :  0.004   0.037    854
  Dihedral  :  4.673  25.127    684
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 21.32 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.87 (0.31), residues: 596
  helix: -1.74 (0.25), residues: 370
  sheet: -2.22 (0.61), residues: 54
  loop : -1.62 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  34 
 HIS   0.004   0.001   HIS A   3 
 PHE   0.014   0.002   PHE B 221 
 TYR   0.010   0.001   TYR B 199 
 ARG   0.005   0.000   ARG A 180 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A  269 PHE cc_start: 0.8453 (t80) cc_final: 0.8014 (t80)
REVERT: B   42 HIS cc_start: 0.6624 (m-70) cc_final: 0.6422 (m90)
REVERT: B  269 PHE cc_start: 0.8447 (t80) cc_final: 0.8012 (t80)
  outliers start: 30
  outliers final: 16
  residues processed: 130
  average time/residue: 0.1653
  time to fit residues: 27.4130
Evaluate side-chains
  121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
A  72 HIS
B   3 HIS
B  72 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.150912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.122466 restraints weight = 8079.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.125771 restraints weight = 4969.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.128048 restraints weight = 3697.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   4972  Z= 0.300
  Angle     :  0.696   7.578   6740  Z= 0.325
  Chirality :  0.043   0.132    762
  Planarity :  0.004   0.037    854
  Dihedral  :  4.677  25.503    684
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 22.87 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.55 (0.32), residues: 596
  helix: -1.41 (0.25), residues: 382
  sheet: -2.61 (0.97), residues: 22
  loop : -1.80 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 119 
 HIS   0.004   0.001   HIS B   3 
 PHE   0.009   0.002   PHE A 117 
 TYR   0.008   0.001   TYR B  81 
 ARG   0.009   0.001   ARG B 180 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A   81 TYR cc_start: 0.7971 (m-80) cc_final: 0.7696 (m-80)
REVERT: A  269 PHE cc_start: 0.8523 (t80) cc_final: 0.8193 (t80)
REVERT: B   42 HIS cc_start: 0.6663 (m-70) cc_final: 0.6451 (m90)
REVERT: B   81 TYR cc_start: 0.7960 (m-80) cc_final: 0.7683 (m-80)
REVERT: B  269 PHE cc_start: 0.8518 (t80) cc_final: 0.8189 (t80)
  outliers start: 30
  outliers final: 26
  residues processed: 137
  average time/residue: 0.1680
  time to fit residues: 30.4442
Evaluate side-chains
  137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 HIS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue    3 HIS
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.0970
   chunk 60 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
A  72 HIS
B   3 HIS
B  72 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.153573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.125828 restraints weight = 8063.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.129051 restraints weight = 5173.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.131259 restraints weight = 3904.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4972  Z= 0.184
  Angle     :  0.621   6.800   6740  Z= 0.285
  Chirality :  0.040   0.127    762
  Planarity :  0.003   0.034    854
  Dihedral  :  4.395  23.807    684
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 26.74 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.12 (0.33), residues: 596
  helix: -0.90 (0.26), residues: 374
  sheet: -2.91 (0.77), residues: 36
  loop : -1.82 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B   3 
 PHE   0.014   0.001   PHE A 117 
 TYR   0.009   0.001   TYR B 199 
 ARG   0.004   0.000   ARG B 180 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A   81 TYR cc_start: 0.7823 (m-80) cc_final: 0.7525 (m-80)
REVERT: A  269 PHE cc_start: 0.8448 (t80) cc_final: 0.8090 (t80)
REVERT: B   81 TYR cc_start: 0.7811 (m-80) cc_final: 0.7510 (m-80)
REVERT: B  269 PHE cc_start: 0.8446 (t80) cc_final: 0.8089 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 135
  average time/residue: 0.1877
  time to fit residues: 34.5215
Evaluate side-chains
  141 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 55 optimal weight:    0.2980
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0270
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.155652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.127235 restraints weight = 7995.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.130734 restraints weight = 4952.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133109 restraints weight = 3678.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   4972  Z= 0.155
  Angle     :  0.596   6.317   6740  Z= 0.275
  Chirality :  0.039   0.135    762
  Planarity :  0.003   0.030    854
  Dihedral  :  4.162  22.199    684
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 26.74 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.34), residues: 596
  helix: -0.46 (0.27), residues: 372
  sheet: -2.85 (0.76), residues: 40
  loop : -1.86 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.006   0.001   PHE A 105 
 TYR   0.008   0.001   TYR A 199 
 ARG   0.003   0.000   ARG B 180 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A  260 GLU cc_start: 0.7932 (pp20) cc_final: 0.7658 (pp20)
REVERT: A  269 PHE cc_start: 0.8415 (t80) cc_final: 0.8012 (t80)
REVERT: B  260 GLU cc_start: 0.7929 (pp20) cc_final: 0.7654 (pp20)
REVERT: B  269 PHE cc_start: 0.8414 (t80) cc_final: 0.8012 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 139
  average time/residue: 0.1736
  time to fit residues: 31.7179
Evaluate side-chains
  143 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0870
   chunk 45 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.154674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.126968 restraints weight = 7963.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.130268 restraints weight = 5005.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.132499 restraints weight = 3744.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4972  Z= 0.174
  Angle     :  0.600   7.066   6740  Z= 0.280
  Chirality :  0.040   0.172    762
  Planarity :  0.004   0.043    854
  Dihedral  :  4.162  22.449    684
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 26.74 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.34), residues: 596
  helix: -0.17 (0.28), residues: 374
  sheet: -2.29 (0.65), residues: 52
  loop : -1.83 (0.45), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 119 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.010   0.001   PHE A 221 
 TYR   0.008   0.001   TYR A 199 
 ARG   0.005   0.000   ARG B 180 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.616 
Fit side-chains
REVERT: A  260 GLU cc_start: 0.7933 (pp20) cc_final: 0.7717 (pp20)
REVERT: A  269 PHE cc_start: 0.8419 (t80) cc_final: 0.8035 (t80)
REVERT: B  260 GLU cc_start: 0.7934 (pp20) cc_final: 0.7716 (pp20)
REVERT: B  269 PHE cc_start: 0.8419 (t80) cc_final: 0.8036 (t80)
  outliers start: 32
  outliers final: 26
  residues processed: 147
  average time/residue: 0.1518
  time to fit residues: 29.0473
Evaluate side-chains
  143 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 8 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0870
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.155338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.127112 restraints weight = 8053.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.130674 restraints weight = 4917.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.133069 restraints weight = 3606.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4972  Z= 0.158
  Angle     :  0.580   5.919   6740  Z= 0.270
  Chirality :  0.040   0.137    762
  Planarity :  0.003   0.029    854
  Dihedral  :  4.075  21.659    684
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 29.07 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.35), residues: 596
  helix:  0.03 (0.28), residues: 374
  sheet: -2.22 (0.67), residues: 52
  loop : -1.74 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A  72 
 PHE   0.008   0.001   PHE B 221 
 TYR   0.007   0.001   TYR B 274 
 ARG   0.004   0.000   ARG B 180 

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A  260 GLU cc_start: 0.7946 (pp20) cc_final: 0.7740 (pp20)
REVERT: A  269 PHE cc_start: 0.8451 (t80) cc_final: 0.8058 (t80)
REVERT: B  260 GLU cc_start: 0.7950 (pp20) cc_final: 0.7740 (pp20)
REVERT: B  269 PHE cc_start: 0.8451 (t80) cc_final: 0.8060 (t80)
  outliers start: 28
  outliers final: 17
  residues processed: 137
  average time/residue: 0.1511
  time to fit residues: 27.1814
Evaluate side-chains
  132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7099 > 50:
  distance: 137 - 141:  27.152
  distance: 138 - 169:  11.552
  distance: 141 - 142:  23.220
  distance: 142 - 143:  20.013
  distance: 142 - 145:   3.737
  distance: 143 - 144:  17.942
  distance: 143 - 152:  19.477
  distance: 145 - 146:  10.945
  distance: 146 - 147:  24.105
  distance: 147 - 148:  19.378
  distance: 149 - 150:   9.300
  distance: 149 - 151:   8.369
  distance: 152 - 153:  32.848
  distance: 153 - 154:  45.552
  distance: 153 - 156:  25.757
  distance: 154 - 155:  31.216
  distance: 154 - 160:  42.573
  distance: 156 - 157:  23.119
  distance: 157 - 158:  45.111
  distance: 157 - 159:  42.240
  distance: 160 - 161:  26.298
  distance: 161 - 162:  38.899
  distance: 161 - 164:  19.721
  distance: 162 - 163:  20.383
  distance: 162 - 169:  31.681
  distance: 164 - 165:  15.354
  distance: 165 - 166:  15.527
  distance: 166 - 167:  10.597
  distance: 166 - 168:  21.258
  distance: 169 - 170:  17.532
  distance: 170 - 171:  11.806
  distance: 170 - 173:  15.780
  distance: 171 - 172:  23.691
  distance: 171 - 178:  19.973
  distance: 173 - 174:   3.685
  distance: 174 - 175:  19.154
  distance: 175 - 176:  10.932
  distance: 175 - 177:  17.229
  distance: 178 - 179:  17.002
  distance: 179 - 180:  24.771
  distance: 179 - 182:  52.297
  distance: 180 - 181:  16.107
  distance: 180 - 183:  16.552
  distance: 183 - 184:  12.943
  distance: 184 - 185:  34.196
  distance: 184 - 187:  23.096
  distance: 185 - 186:  11.455
  distance: 185 - 192:   7.123
  distance: 187 - 188:   6.889
  distance: 188 - 189:  17.862
  distance: 189 - 190:  27.707
  distance: 190 - 191:  11.707
  distance: 192 - 193:  16.575
  distance: 193 - 194:   9.348
  distance: 193 - 196:  27.404
  distance: 194 - 195:  46.342
  distance: 194 - 200:  27.309
  distance: 195 - 228:  27.458
  distance: 196 - 197:  11.334
  distance: 197 - 198:  17.047
  distance: 197 - 199:  11.833
  distance: 200 - 201:  15.708
  distance: 201 - 202:  26.401
  distance: 201 - 204:  12.969
  distance: 202 - 203:  18.473
  distance: 202 - 211:  28.566
  distance: 203 - 235:  25.096
  distance: 204 - 205:   7.607
  distance: 205 - 206:  11.372
  distance: 205 - 207:   8.342
  distance: 206 - 208:  18.305
  distance: 207 - 209:   4.916
  distance: 208 - 210:  12.427
  distance: 209 - 210:  15.486
  distance: 211 - 212:   7.010
  distance: 212 - 213:  23.482
  distance: 212 - 215:  23.863
  distance: 213 - 214:  22.230
  distance: 213 - 217:  19.893
  distance: 215 - 216:  31.875
  distance: 217 - 218:   7.520
  distance: 218 - 219:  21.189
  distance: 218 - 221:  23.800
  distance: 219 - 220:  31.459
  distance: 219 - 228:  30.024
  distance: 220 - 250:  34.132
  distance: 221 - 222:  23.383
  distance: 222 - 223:  21.196
  distance: 223 - 224:  10.781
  distance: 225 - 226:  11.800
  distance: 225 - 227:   7.916