Starting phenix.real_space_refine
on Tue Feb 11 05:49:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9k_36110/02_2025/8j9k_36110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9k_36110/02_2025/8j9k_36110.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/8j9k_36110/02_2025/8j9k_36110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9k_36110/02_2025/8j9k_36110.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9k_36110/02_2025/8j9k_36110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9k_36110/02_2025/8j9k_36110.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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2727      2.51       5
     N     744      2.21       5
     O     799      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4284
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 2542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2542
          Classifications: {'peptide': 359}
          Incomplete info: {'truncation_to_alanine': 89}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 332}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 319
          Unresolved non-hydrogen angles: 388
          Unresolved non-hydrogen dihedrals: 262
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 192
    Chain: "B"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 785
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 957
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 3.62, per 1000 atoms: 0.85
  Number of scatterers: 4284
  At special positions: 0
  Unit cell: (70.3779, 107.419, 106.184, 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      14     16.00
     O     799      8.00
     N     744      7.00
     C    2727      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  47 " - pdb=" SG  CYS B 112 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  48 " - pdb=" SG  CYS D 122 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 525.9 milliseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 12 sheets defined
      6.4% alpha, 45.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'C' and resid 46 through 50
      removed outlier: 3.965A  pdb=" N   LEU C  49 " --> pdb=" O   PRO C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
    Processing helix  chain 'C' and resid 99 through 109
    Processing helix  chain 'C' and resid 160 through 162
      No H-bonds generated for 'chain 'C' and resid 160 through 162'
    Processing helix  chain 'B' and resid 103 through 107
    Processing helix  chain 'D' and resid 88 through 91
    Processing helix  chain 'D' and resid 113 through 117
    Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 118
      removed outlier: 3.547A  pdb=" N   GLY C  40 " --> pdb=" O   PHE C 116 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   THR C   7 " --> pdb=" O   VAL C 389 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   GLU C 391 " --> pdb=" O   THR C   7 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   VAL C   9 " --> pdb=" O   GLU C 391 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.687A  pdb=" N   PHE C 145 " --> pdb=" O   ILE C 169 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS C 171 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 9.600A  pdb=" N   VAL C 143 " --> pdb=" O   LYS C 171 " (cutoff:3.500A)
      removed outlier: 16.110A  pdb=" N   GLN C 173 " --> pdb=" O   CYS C 141 " (cutoff:3.500A)
      removed outlier: 20.660A  pdb=" N   CYS C 141 " --> pdb=" O   GLN C 173 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP C 144 " --> pdb=" O   ALA C  61 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   VAL C  54 " --> pdb=" O   GLN C  86 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   GLN C  86 " --> pdb=" O   VAL C  54 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   VAL C  56 " --> pdb=" O   THR C  84 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   THR C  84 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU C  58 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE C  82 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   CYS C  60 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.687A  pdb=" N   PHE C 145 " --> pdb=" O   ILE C 169 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS C 171 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 9.600A  pdb=" N   VAL C 143 " --> pdb=" O   LYS C 171 " (cutoff:3.500A)
      removed outlier: 16.110A  pdb=" N   GLN C 173 " --> pdb=" O   CYS C 141 " (cutoff:3.500A)
      removed outlier: 20.660A  pdb=" N   CYS C 141 " --> pdb=" O   GLN C 173 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   CYS C 141 " --> pdb=" O   LEU C 130 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN C 131 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU C 289 " --> pdb=" O   GLN C 131 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 187 through 190
      removed outlier: 3.514A  pdb=" N   THR C 187 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU C 201 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR C 223 " --> pdb=" O   HIS C 200 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 209 through 211
      removed outlier: 6.365A  pdb=" N   TYR C 210 " --> pdb=" O   MET C 346 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TYR C 323 " --> pdb=" O   PHE C 343 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU C 345 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   VAL C 321 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 209 through 211
      removed outlier: 6.365A  pdb=" N   TYR C 210 " --> pdb=" O   MET C 346 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TYR C 323 " --> pdb=" O   PHE C 343 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU C 345 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   VAL C 321 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS C 232 " --> pdb=" O   VAL C 330 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE C 233 " --> pdb=" O   GLN C 260 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLN C 260 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31
      removed outlier: 3.560A  pdb=" N   THR B  96 " --> pdb=" O   SER B  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 36
      removed outlier: 3.814A  pdb=" N   ALA B 108 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL B  57 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   TYR B  73 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   TRP B  59 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 36
      removed outlier: 3.814A  pdb=" N   ALA B 108 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 31 through 33
      removed outlier: 3.553A  pdb=" N   CYS D  48 " --> pdb=" O   ALA D 105 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA D 105 " --> pdb=" O   CYS D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 86
      removed outlier: 6.837A  pdb=" N   TRP D  62 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   SER D  76 " --> pdb=" O   ILE D  60 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE D  60 " --> pdb=" O   SER D  76 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TYR D 139 " --> pdb=" O   ARG D 124 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 85 through 86
      removed outlier: 6.837A  pdb=" N   TRP D  62 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   SER D  76 " --> pdb=" O   ILE D  60 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE D  60 " --> pdb=" O   SER D  76 " (cutoff:3.500A)

    166 hydrogen bonds defined for protein.
    405 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: 1.40

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1401
        1.34 -     1.46: 1030
        1.46 -     1.58: 1931
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 4380
  Sorted by residual:
  bond pdb=" C   ASP C 136 "
       pdb=" N   THR C 137 "
    ideal  model  delta    sigma   weight residual
    1.331  1.277  0.053 1.40e-02 5.10e+03 1.44e+01
  bond pdb=" N   GLN B 113 "
       pdb=" CA  GLN B 113 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.25e-02 6.40e+03 5.67e+00
  bond pdb=" C   GLN C 131 "
       pdb=" N   PRO C 132 "
    ideal  model  delta    sigma   weight residual
    1.330  1.352 -0.022 1.22e-02 6.72e+03 3.37e+00
  bond pdb=" CA  VAL C 316 "
       pdb=" CB  VAL C 316 "
    ideal  model  delta    sigma   weight residual
    1.542  1.521  0.021 1.33e-02 5.65e+03 2.49e+00
  bond pdb=" CA  VAL C 273 "
       pdb=" CB  VAL C 273 "
    ideal  model  delta    sigma   weight residual
    1.544  1.521  0.023 1.46e-02 4.69e+03 2.41e+00
  ... (remaining 4375 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 5793
        1.84 -     3.68: 153
        3.68 -     5.52: 25
        5.52 -     7.36: 7
        7.36 -     9.20: 3
  Bond angle restraints: 5981
  Sorted by residual:
  angle pdb=" CA  GLN C 131 "
        pdb=" C   GLN C 131 "
        pdb=" N   PRO C 132 "
      ideal   model   delta    sigma   weight residual
     119.06  112.37    6.69 1.05e+00 9.07e-01 4.06e+01
  angle pdb=" O   GLN C 131 "
        pdb=" C   GLN C 131 "
        pdb=" N   PRO C 132 "
      ideal   model   delta    sigma   weight residual
     121.23  128.12   -6.89 1.13e+00 7.83e-01 3.72e+01
  angle pdb=" C   GLN C 131 "
        pdb=" N   PRO C 132 "
        pdb=" CA  PRO C 132 "
      ideal   model   delta    sigma   weight residual
     120.03  114.14    5.89 9.90e-01 1.02e+00 3.54e+01
  angle pdb=" C   SER B  74 "
        pdb=" N   ALA B  75 "
        pdb=" CA  ALA B  75 "
      ideal   model   delta    sigma   weight residual
     121.54  128.99   -7.45 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" CA  GLN B 113 "
        pdb=" C   GLN B 113 "
        pdb=" O   GLN B 113 "
      ideal   model   delta    sigma   weight residual
     120.66  116.66    4.00 1.15e+00 7.56e-01 1.21e+01
  ... (remaining 5976 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 2342
       17.71 -    35.42: 190
       35.42 -    53.13: 54
       53.13 -    70.84: 13
       70.84 -    88.55: 5
  Dihedral angle restraints: 2604
    sinusoidal: 889
      harmonic: 1715
  Sorted by residual:
  dihedral pdb=" CB  CYS B  47 "
           pdb=" SG  CYS B  47 "
           pdb=" SG  CYS B 112 "
           pdb=" CB  CYS B 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   35.49   57.51     1      1.00e+01 1.00e-02 4.44e+01
  dihedral pdb=" CA  TYR D 128 "
           pdb=" C   TYR D 128 "
           pdb=" N   TYR D 129 "
           pdb=" CA  TYR D 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.72   19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" C   GLN B 113 "
           pdb=" N   GLN B 113 "
           pdb=" CA  GLN B 113 "
           pdb=" CB  GLN B 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.19   -9.41     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 2601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 547
       0.051 -    0.101: 112
       0.101 -    0.151: 35
       0.151 -    0.202: 1
       0.202 -    0.252: 1
  Chirality restraints: 696
  Sorted by residual:
  chirality pdb=" CA  GLN B 113 "
            pdb=" N   GLN B 113 "
            pdb=" C   GLN B 113 "
            pdb=" CB  GLN B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  VAL C 339 "
            pdb=" N   VAL C 339 "
            pdb=" C   VAL C 339 "
            pdb=" CB  VAL C 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CB  VAL C 331 "
            pdb=" CA  VAL C 331 "
            pdb=" CG1 VAL C 331 "
            pdb=" CG2 VAL C 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 693 not shown)

  Planarity restraints: 774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 132 "   -0.013 2.00e-02 2.50e+03   2.51e-02 6.31e+00
        pdb=" C   TYR D 132 "    0.043 2.00e-02 2.50e+03
        pdb=" O   TYR D 132 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   MET D 133 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 240 "   -0.015 2.00e-02 2.50e+03   1.72e-02 5.91e+00
        pdb=" CG  TYR C 240 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 240 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 240 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 240 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 240 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 240 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 240 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 182 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO C 183 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO C 183 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 183 "    0.022 5.00e-02 4.00e+02
  ... (remaining 771 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 917
        2.78 -     3.31: 4008
        3.31 -     3.84: 6709
        3.84 -     4.37: 7482
        4.37 -     4.90: 13639
  Nonbonded interactions: 32755
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B  42 "
            pdb=" OG1 THR B  44 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" NH1 ARG D  64 "
            pdb=" OD1 ASP D 116 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" OE1 GLN D 108 "
            pdb=" ND2 ASN D 110 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" N   GLU D  32 "
            pdb=" OE1 GLU D  32 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" O   GLY C 133 "
            pdb=" N   ASP C 136 "
     model   vdw
     2.359 3.120
  ... (remaining 32750 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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.390
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
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      :  0.004   0.055   4380  Z= 0.299
  Angle     :  0.763   9.204   5981  Z= 0.417
  Chirality :  0.046   0.252    696
  Planarity :  0.005   0.040    774
  Dihedral  : 15.318  88.546   1496
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 19.05 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.39 (0.34), residues: 582
  helix: -3.14 (1.02), residues: 17
  sheet: -1.19 (0.31), residues: 263
  loop : -1.82 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  73 
 HIS   0.003   0.001   HIS C 114 
 PHE   0.012   0.002   PHE C  76 
 TYR   0.037   0.002   TYR C 240 
 ARG   0.004   0.001   ARG C 324 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1607
  time to fit residues: 14.7277
Evaluate side-chains
  51 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0020
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 ASN
C 173 GLN
D 108 GLN
D 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.120680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.095458 restraints weight = 9809.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.098500 restraints weight = 5479.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.100429 restraints weight = 3899.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4380  Z= 0.228
  Angle     :  0.641   8.447   5981  Z= 0.321
  Chirality :  0.045   0.156    696
  Planarity :  0.005   0.038    774
  Dihedral  :  4.769  27.722    638
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.05 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.23 (0.34), residues: 582
  helix: -3.07 (0.88), residues: 23
  sheet: -0.93 (0.31), residues: 259
  loop : -1.83 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  62 
 HIS   0.002   0.001   HIS C 114 
 PHE   0.009   0.001   PHE B  95 
 TYR   0.012   0.002   TYR C 240 
 ARG   0.003   0.000   ARG D  64 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 TYR cc_start: 0.8649 (m-10) cc_final: 0.8430 (m-10)
REVERT: B  118 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6711 (m-30)
REVERT: D   95 THR cc_start: 0.8551 (p) cc_final: 0.8307 (p)
REVERT: D  108 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7923 (tm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1513
  time to fit residues: 15.0687
Evaluate side-chains
  64 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0030
   chunk 29 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0770
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.5548

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

Flipped N/Q/H residues before XYZ refinement:
C 114 HIS
C 123 ASN
B  30 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.120690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.095581 restraints weight = 9941.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.098634 restraints weight = 5527.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.100610 restraints weight = 3915.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4380  Z= 0.213
  Angle     :  0.602   7.647   5981  Z= 0.300
  Chirality :  0.043   0.154    696
  Planarity :  0.004   0.038    774
  Dihedral  :  4.540  27.951    638
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.50 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 18.57 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.07 (0.33), residues: 582
  helix: -2.92 (0.94), residues: 23
  sheet: -0.77 (0.31), residues: 260
  loop : -1.77 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 140 
 HIS   0.002   0.000   HIS C 114 
 PHE   0.008   0.001   PHE C 117 
 TYR   0.015   0.001   TYR C 240 
 ARG   0.007   0.000   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 ASN cc_start: 0.8660 (m-40) cc_final: 0.8442 (m-40)
REVERT: C  122 GLN cc_start: 0.7936 (pm20) cc_final: 0.7293 (pt0)
REVERT: B   60 TYR cc_start: 0.8647 (m-10) cc_final: 0.8414 (m-10)
REVERT: B   63 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8598 (mmmm)
REVERT: B  118 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6699 (m-30)
REVERT: D  128 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6538 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1296
  time to fit residues: 13.9306
Evaluate side-chains
  71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  123 ASN
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 44 optimal weight:    0.0980
   chunk 19 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 GLN
D 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.120225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.094912 restraints weight = 9960.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.098009 restraints weight = 5492.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.100014 restraints weight = 3865.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4380  Z= 0.227
  Angle     :  0.591   6.026   5981  Z= 0.300
  Chirality :  0.043   0.151    696
  Planarity :  0.005   0.075    774
  Dihedral  :  4.481  28.201    638
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.50 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 20.24 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -2.03 (0.33), residues: 582
  helix: -2.90 (0.94), residues: 23
  sheet: -0.80 (0.31), residues: 272
  loop : -1.72 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  59 
 HIS   0.005   0.001   HIS C 347 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.013   0.001   TYR C 240 
 ARG   0.006   0.000   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: C   16 ASN cc_start: 0.8678 (m-40) cc_final: 0.8476 (m-40)
REVERT: C  122 GLN cc_start: 0.7838 (pm20) cc_final: 0.7389 (pt0)
REVERT: B   63 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8585 (mmmm)
REVERT: B  118 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6674 (m-30)
REVERT: D  128 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.6582 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1321
  time to fit residues: 12.6325
Evaluate side-chains
  69 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 43 optimal weight:    0.3980
   chunk 50 optimal weight:    0.0270
   chunk 32 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0980
   overall best weight:    0.2438

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

Flipped N/Q/H residues before XYZ refinement:
C 102 GLN
D 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.122758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.097884 restraints weight = 10025.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.101021 restraints weight = 5507.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.103051 restraints weight = 3864.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   4380  Z= 0.153
  Angle     :  0.551   5.976   5981  Z= 0.278
  Chirality :  0.042   0.148    696
  Planarity :  0.005   0.066    774
  Dihedral  :  4.257  27.291    638
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.47 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.95 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -1.77 (0.33), residues: 582
  helix: -2.95 (0.82), residues: 29
  sheet: -0.47 (0.31), residues: 262
  loop : -1.62 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 140 
 HIS   0.006   0.001   HIS C 347 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.014   0.001   TYR C 240 
 ARG   0.004   0.000   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: C   16 ASN cc_start: 0.8663 (m-40) cc_final: 0.8462 (m-40)
REVERT: C  103 ASP cc_start: 0.8326 (t70) cc_final: 0.8084 (t0)
REVERT: C  122 GLN cc_start: 0.7816 (pm20) cc_final: 0.7281 (pt0)
REVERT: C  240 TYR cc_start: 0.8382 (m-80) cc_final: 0.8147 (m-80)
REVERT: D  128 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6943 (m-80)
  outliers start: 16
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1207
  time to fit residues: 13.0531
Evaluate side-chains
  69 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0170
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.6220

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 GLN ** 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 = 0.3780 r_free = 0.3780 target = 0.121117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.096557 restraints weight = 9864.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.099727 restraints weight = 5364.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.101678 restraints weight = 3766.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4380  Z= 0.217
  Angle     :  0.578   7.255   5981  Z= 0.288
  Chirality :  0.043   0.165    696
  Planarity :  0.005   0.055    774
  Dihedral  :  4.312  28.584    638
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.84 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.14 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -1.75 (0.34), residues: 582
  helix: -2.87 (0.82), residues: 29
  sheet: -0.48 (0.31), residues: 267
  loop : -1.62 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  59 
 HIS   0.004   0.001   HIS C 347 
 PHE   0.009   0.001   PHE C 116 
 TYR   0.019   0.001   TYR C 240 
 ARG   0.005   0.000   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: C  103 ASP cc_start: 0.8399 (t70) cc_final: 0.7876 (t0)
REVERT: C  122 GLN cc_start: 0.7876 (pm20) cc_final: 0.7403 (pt0)
REVERT: C  240 TYR cc_start: 0.8532 (m-80) cc_final: 0.8223 (m-80)
REVERT: D  128 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6809 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 70
  average time/residue: 0.1164
  time to fit residues: 11.3589
Evaluate side-chains
  68 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
C  86 GLN
C 182 GLN
D 108 GLN
D 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.119010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.093597 restraints weight = 10024.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096572 restraints weight = 5593.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.098495 restraints weight = 3997.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4380  Z= 0.384
  Angle     :  0.651   6.907   5981  Z= 0.330
  Chirality :  0.045   0.195    696
  Planarity :  0.005   0.037    774
  Dihedral  :  4.742  28.512    638
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.39 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 21.90 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.33), residues: 582
  helix: -2.80 (0.92), residues: 23
  sheet: -0.70 (0.31), residues: 275
  loop : -1.74 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D  73 
 HIS   0.004   0.001   HIS C 114 
 PHE   0.010   0.001   PHE C 117 
 TYR   0.021   0.002   TYR C 240 
 ARG   0.004   0.001   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.491 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8434 (t70) cc_final: 0.7682 (t0)
REVERT: C  122 GLN cc_start: 0.7947 (pm20) cc_final: 0.7469 (pt0)
REVERT: C  240 TYR cc_start: 0.8508 (m-80) cc_final: 0.8094 (m-80)
REVERT: B  118 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6964 (m-30)
REVERT: D  108 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8203 (tm-30)
REVERT: D  128 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7309 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 69
  average time/residue: 0.1202
  time to fit residues: 11.4103
Evaluate side-chains
  66 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  108 GLN
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C 239 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.118723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.094313 restraints weight = 9755.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.097263 restraints weight = 5453.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.099140 restraints weight = 3897.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4380  Z= 0.292
  Angle     :  0.620   7.541   5981  Z= 0.311
  Chirality :  0.044   0.169    696
  Planarity :  0.004   0.036    774
  Dihedral  :  4.644  28.867    638
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.19 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 22.62 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.34), residues: 582
  helix: -2.52 (0.98), residues: 23
  sheet: -0.69 (0.31), residues: 271
  loop : -1.78 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  73 
 HIS   0.008   0.001   HIS C 347 
 PHE   0.009   0.001   PHE C 117 
 TYR   0.019   0.002   TYR C 240 
 ARG   0.004   0.000   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.466 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8352 (t70) cc_final: 0.7555 (t0)
REVERT: C  122 GLN cc_start: 0.7909 (pm20) cc_final: 0.7477 (pt0)
REVERT: C  240 TYR cc_start: 0.8529 (m-80) cc_final: 0.8105 (m-80)
REVERT: C  289 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7909 (pp)
REVERT: B  118 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6941 (m-30)
REVERT: D  128 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7277 (m-80)
  outliers start: 19
  outliers final: 14
  residues processed: 71
  average time/residue: 0.1229
  time to fit residues: 12.0993
Evaluate side-chains
  69 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:   20.0000
   chunk 55 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 GLN ** 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 = 0.3742 r_free = 0.3742 target = 0.117995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.093367 restraints weight = 10017.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.096355 restraints weight = 5577.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.098258 restraints weight = 3998.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4380  Z= 0.321
  Angle     :  0.637   6.934   5981  Z= 0.322
  Chirality :  0.045   0.165    696
  Planarity :  0.004   0.037    774
  Dihedral  :  4.747  28.695    638
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.36 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.81 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.34), residues: 582
  helix: -2.45 (0.98), residues: 23
  sheet: -0.66 (0.31), residues: 271
  loop : -1.80 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  73 
 HIS   0.007   0.001   HIS C 347 
 PHE   0.009   0.001   PHE C 117 
 TYR   0.019   0.002   TYR C 240 
 ARG   0.004   0.000   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.514 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8389 (t70) cc_final: 0.7623 (t0)
REVERT: C  122 GLN cc_start: 0.7920 (pm20) cc_final: 0.7494 (pt0)
REVERT: C  240 TYR cc_start: 0.8555 (m-80) cc_final: 0.8130 (m-80)
REVERT: C  289 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7908 (pp)
REVERT: D  128 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6775 (m-80)
  outliers start: 19
  outliers final: 16
  residues processed: 68
  average time/residue: 0.1208
  time to fit residues: 11.5739
Evaluate side-chains
  68 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 39 optimal weight:    0.3980
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0000
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
C 102 GLN
** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.121617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.096993 restraints weight = 9763.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.100031 restraints weight = 5435.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.101963 restraints weight = 3854.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4380  Z= 0.194
  Angle     :  0.596   8.277   5981  Z= 0.296
  Chirality :  0.043   0.161    696
  Planarity :  0.004   0.037    774
  Dihedral  :  4.477  28.844    638
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.84 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 24.05 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: 582
  helix: -2.13 (1.05), residues: 23
  sheet: -0.46 (0.32), residues: 270
  loop : -1.67 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 140 
 HIS   0.004   0.001   HIS C 114 
 PHE   0.008   0.001   PHE C 116 
 TYR   0.015   0.001   TYR C 240 
 ARG   0.003   0.000   ARG C 100 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.544 
Fit side-chains
REVERT: C  103 ASP cc_start: 0.8404 (t70) cc_final: 0.8068 (t0)
REVERT: C  122 GLN cc_start: 0.7936 (pm20) cc_final: 0.7413 (pt0)
REVERT: C  131 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7590 (tm-30)
REVERT: C  208 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: C  240 TYR cc_start: 0.8603 (m-80) cc_final: 0.8186 (m-80)
REVERT: B   63 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8651 (mmtm)
REVERT: D  128 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6669 (m-80)
  outliers start: 18
  outliers final: 15
  residues processed: 70
  average time/residue: 0.1185
  time to fit residues: 11.5519
Evaluate side-chains
  71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  297 HIS
Chi-restraints excluded: chain C residue  301 ASN
Chi-restraints excluded: chain C residue  330 VAL
Chi-restraints excluded: chain C residue  396 LEU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue  128 TYR
Chi-restraints excluded: chain D residue  148 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    0.0370
   chunk 51 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
C 102 GLN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.119340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.095053 restraints weight = 9769.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.098088 restraints weight = 5404.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.100011 restraints weight = 3838.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4380  Z= 0.232
  Angle     :  0.599   7.675   5981  Z= 0.299
  Chirality :  0.043   0.156    696
  Planarity :  0.004   0.036    774
  Dihedral  :  4.467  28.512    638
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.36 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.81 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.18 %
    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: -1.66 (0.35), residues: 582
  helix: -2.26 (1.05), residues: 23
  sheet: -0.55 (0.31), residues: 285
  loop : -1.55 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  59 
 HIS   0.004   0.001   HIS C 114 
 PHE   0.009   0.001   PHE C 116 
 TYR   0.016   0.001   TYR C 240 
 ARG   0.003   0.000   ARG C 100 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1769.15 seconds
wall clock time: 32 minutes 21.16 seconds (1941.16 seconds total)