Starting phenix.real_space_refine
on Thu Mar  6 08:23:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yi7_39311/03_2025/8yi7_39311_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yi7_39311/03_2025/8yi7_39311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yi7_39311/03_2025/8yi7_39311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yi7_39311/03_2025/8yi7_39311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yi7_39311/03_2025/8yi7_39311_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yi7_39311/03_2025/8yi7_39311_neut.cif"
  }
  resolution = 3.57
  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=   0.003 sd=   0.049
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      43      5.16       5
     C    3514      2.51       5
     N     943      2.21       5
     O    1086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 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: 5586
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1485
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 6, 'TRANS': 178}
    Chain: "B"
      Number of atoms: 2413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2413
          Classifications: {'peptide': 303}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 764
          Classifications: {'peptide': 98}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 94}
    Chain: "D"
      Number of atoms: 871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 871
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 6, 'TRANS': 104}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.04, per 1000 atoms: 0.72
  Number of scatterers: 5586
  At special positions: 0
  Unit cell: (117.41, 97.4064, 101.755, 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      43     16.00
     O    1086      8.00
     N     943      7.00
     C    3514      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  37 " - pdb=" SG  CYS A 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS B 199 " distance=2.25
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 142 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 170 " - pdb=" SG  CYS B 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  28 " - pdb=" SG  CYS C 114 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  51 " - pdb=" SG  CYS C 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C 105 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  29 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  52 " - pdb=" SG  CYS D  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D  86 " distance=2.05

  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
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG C 401 " - " ASN C  48 "
      " NAG E   1 " - " ASN B 222 "
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 702.9 milliseconds
  

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1332

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 13 sheets defined
      17.4% alpha, 31.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 59
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 117 through 147
      removed outlier: 4.010A  pdb=" N   MET A 147 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
    Processing helix  chain 'A' and resid 187 through 218
      removed outlier: 3.937A  pdb=" N   THR A 191 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 228 through 233
    Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 27
      removed outlier: 6.270A  pdb=" N   ILE B  23 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLU B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLU B  25 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL B  32 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS B  27 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   VAL B  96 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LYS B  92 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   HIS B  91 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY B  70 " --> pdb=" O   TRP B  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27
      removed outlier: 6.270A  pdb=" N   ILE B  23 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLU B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLU B  25 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL B  32 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS B  27 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 49
    Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 133
      removed outlier: 6.526A  pdb=" N   GLU B 188 " --> pdb=" O   SER B 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160
    Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 245
      removed outlier: 5.333A  pdb=" N   ASN B 240 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLU B 257 " --> pdb=" O   ASN B 240 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291
      removed outlier: 4.262A  pdb=" N   ALA B 304 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS B 327 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 306 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 34
    Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 42
      removed outlier: 5.755A  pdb=" N   ILE C  41 " --> pdb=" O   GLY C 121 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   GLN C 112 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU C 103 " --> pdb=" O   GLN C 112 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS C 114 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY C  95 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   LEU C  68 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   PHE C  79 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU C  70 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 56
      removed outlier: 4.035A  pdb=" N   LEU D  50 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   SER D  63 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS D  52 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU D  61 " --> pdb=" O   CYS D  52 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ARG D  54 " --> pdb=" O   ARG D  59 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ARG D  59 " --> pdb=" O   ARG D  54 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88
    Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 88
      removed outlier: 3.765A  pdb=" N   VAL D 111 " --> pdb=" O   LEU D 131 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    543 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: 1.75 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1072
        1.32 -     1.45: 1396
        1.45 -     1.57: 3181
        1.57 -     1.69: 0
        1.69 -     1.82: 55
  Bond restraints: 5704
  Sorted by residual:
  bond pdb=" CA  VAL D 107 "
       pdb=" CB  VAL D 107 "
    ideal  model  delta    sigma   weight residual
    1.537  1.479  0.058 1.24e-02 6.50e+03 2.20e+01
  bond pdb=" CA  VAL D 105 "
       pdb=" CB  VAL D 105 "
    ideal  model  delta    sigma   weight residual
    1.541  1.488  0.053 1.30e-02 5.92e+03 1.65e+01
  bond pdb=" CA  PRO B 237 "
       pdb=" C   PRO B 237 "
    ideal  model  delta    sigma   weight residual
    1.514  1.536 -0.022 5.50e-03 3.31e+04 1.60e+01
  bond pdb=" N   VAL B 325 "
       pdb=" CA  VAL B 325 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 9.00e-03 1.23e+04 1.54e+01
  bond pdb=" N   THR B  52 "
       pdb=" CA  THR B  52 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 9.20e-03 1.18e+04 1.49e+01
  ... (remaining 5699 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 6213
        2.13 -     4.26: 1422
        4.26 -     6.38: 77
        6.38 -     8.51: 7
        8.51 -    10.64: 2
  Bond angle restraints: 7721
  Sorted by residual:
  angle pdb=" N   ARG C  65 "
        pdb=" CA  ARG C  65 "
        pdb=" C   ARG C  65 "
      ideal   model   delta    sigma   weight residual
     114.62  106.84    7.78 1.14e+00 7.69e-01 4.65e+01
  angle pdb=" C   THR D 123 "
        pdb=" CA  THR D 123 "
        pdb=" CB  THR D 123 "
      ideal   model   delta    sigma   weight residual
     110.78  100.14   10.64 1.60e+00 3.91e-01 4.42e+01
  angle pdb=" CA  GLY B  72 "
        pdb=" C   GLY B  72 "
        pdb=" O   GLY B  72 "
      ideal   model   delta    sigma   weight residual
     122.23  117.93    4.30 6.90e-01 2.10e+00 3.89e+01
  angle pdb=" CA  THR D 112 "
        pdb=" C   THR D 112 "
        pdb=" O   THR D 112 "
      ideal   model   delta    sigma   weight residual
     121.81  115.62    6.19 1.18e+00 7.18e-01 2.75e+01
  angle pdb=" N   SER D 106 "
        pdb=" CA  SER D 106 "
        pdb=" C   SER D 106 "
      ideal   model   delta    sigma   weight residual
     109.59  117.10   -7.51 1.47e+00 4.63e-01 2.61e+01
  ... (remaining 7716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.20: 3301
       20.20 -    40.40: 196
       40.40 -    60.60: 37
       60.60 -    80.80: 8
       80.80 -   101.00: 6
  Dihedral angle restraints: 3548
    sinusoidal: 1498
      harmonic: 2050
  Sorted by residual:
  dihedral pdb=" CB  CYS C  59 "
           pdb=" SG  CYS C  59 "
           pdb=" SG  CYS C 105 "
           pdb=" CB  CYS C 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.24  -73.24     1      1.00e+01 1.00e-02 6.83e+01
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 327 "
           pdb=" CB  CYS B 327 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.42   61.42     1      1.00e+01 1.00e-02 5.01e+01
  dihedral pdb=" CB  CYS B  50 "
           pdb=" SG  CYS B  50 "
           pdb=" SG  CYS B  90 "
           pdb=" CB  CYS B  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.54  -60.54     1      1.00e+01 1.00e-02 4.88e+01
  ... (remaining 3545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 396
       0.076 -    0.151: 318
       0.151 -    0.227: 119
       0.227 -    0.302: 38
       0.302 -    0.378: 3
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" CA  THR D 123 "
            pdb=" N   THR D 123 "
            pdb=" C   THR D 123 "
            pdb=" CB  THR D 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.90   -0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  ASN B 184 "
            pdb=" N   ASN B 184 "
            pdb=" C   ASN B 184 "
            pdb=" CB  ASN B 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CB  VAL B 180 "
            pdb=" CA  VAL B 180 "
            pdb=" CG1 VAL B 180 "
            pdb=" CG2 VAL B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.96e+00
  ... (remaining 871 not shown)

  Planarity restraints: 979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 100 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.22e+00
        pdb=" C   SER D 100 "    0.053 2.00e-02 2.50e+03
        pdb=" O   SER D 100 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP D 101 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 196 "   -0.014 2.00e-02 2.50e+03   2.96e-02 8.76e+00
        pdb=" C   ASP B 196 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASP B 196 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 197 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 265 "    0.014 2.00e-02 2.50e+03   2.80e-02 7.83e+00
        pdb=" C   PRO B 265 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   PRO B 265 "    0.018 2.00e-02 2.50e+03
        pdb=" N   HIS B 266 "    0.016 2.00e-02 2.50e+03
  ... (remaining 976 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 138
        2.68 -     3.23: 4878
        3.23 -     3.79: 8010
        3.79 -     4.34: 11305
        4.34 -     4.90: 17923
  Nonbonded interactions: 42254
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU B 117 "
            pdb=" CG2 THR B 146 "
     model   vdw
     2.122 3.880
  nonbonded pdb=" CG2 THR B 141 "
            pdb=" OE1 GLU B 192 "
     model   vdw
     2.338 3.460
  nonbonded pdb=" O   ASP A 187 "
            pdb=" OD1 ASP A 187 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NZ  LYS B 157 "
            pdb=" OD2 ASP B 213 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O5  NAG C 401 "
            pdb=" O6  NAG C 401 "
     model   vdw
     2.447 2.432
  ... (remaining 42249 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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.400
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
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      :  0.013   0.058   5704  Z= 0.861
  Angle     :  1.602  10.638   7721  Z= 1.206
  Chirality :  0.114   0.378    874
  Planarity :  0.005   0.030    977
  Dihedral  : 13.654 100.996   2174
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.81 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.60 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.32), residues: 687
  helix:  3.02 (0.48), residues: 119
  sheet:  0.51 (0.35), residues: 230
  loop : -0.76 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  60 
 HIS   0.004   0.001   HIS A  71 
 PHE   0.026   0.002   PHE D  99 
 TYR   0.025   0.002   TYR B 268 
 ARG   0.004   0.001   ARG A 205 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 THR cc_start: 0.8516 (p) cc_final: 0.8123 (p)
REVERT: B  114 THR cc_start: 0.8475 (m) cc_final: 0.8270 (p)
REVERT: B  271 LEU cc_start: 0.8973 (mt) cc_final: 0.8768 (mt)
REVERT: B  275 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (m)
REVERT: B  276 GLN cc_start: 0.7301 (tt0) cc_final: 0.7020 (pp30)
REVERT: D   51 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7787 (ptp-110)
REVERT: D   63 SER cc_start: 0.8564 (t) cc_final: 0.8130 (m)
REVERT: D   65 GLN cc_start: 0.7776 (tt0) cc_final: 0.7498 (mt0)
REVERT: D   96 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7495 (ptp90)
REVERT: D   98 GLN cc_start: 0.8315 (mt0) cc_final: 0.7879 (mt0)
  outliers start: 11
  outliers final: 1
  residues processed: 183
  average time/residue: 0.2004
  time to fit residues: 46.1458
Evaluate side-chains
  113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0470
   chunk 20 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0670
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  87 GLN
B  99 HIS
D 102 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.171401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141536 restraints weight = 6761.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.140768 restraints weight = 6316.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141493 restraints weight = 5860.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5704  Z= 0.205
  Angle     :  0.590   7.245   7721  Z= 0.319
  Chirality :  0.042   0.157    874
  Planarity :  0.004   0.040    977
  Dihedral  :  7.781  64.229    836
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.53 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.32), residues: 687
  helix:  3.55 (0.43), residues: 109
  sheet:  0.59 (0.35), residues: 226
  loop : -0.67 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 118 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.012   0.001   PHE A 118 
 TYR   0.024   0.002   TYR B 314 
 ARG   0.005   0.001   ARG C  75 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6441 (mp10)
REVERT: B  114 THR cc_start: 0.8430 (m) cc_final: 0.8072 (p)
REVERT: B  271 LEU cc_start: 0.8870 (mt) cc_final: 0.8651 (mt)
REVERT: B  288 ARG cc_start: 0.7346 (ptp-170) cc_final: 0.6691 (mtt180)
REVERT: D   98 GLN cc_start: 0.8429 (mt0) cc_final: 0.8205 (mt0)
REVERT: D  123 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.7020 (m)
  outliers start: 15
  outliers final: 7
  residues processed: 114
  average time/residue: 0.1812
  time to fit residues: 26.7473
Evaluate side-chains
  102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0670
   chunk 6 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0670
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
C  39 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.168379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.138338 restraints weight = 6886.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.139072 restraints weight = 6175.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.139806 restraints weight = 5723.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5704  Z= 0.171
  Angle     :  0.518   6.994   7721  Z= 0.281
  Chirality :  0.040   0.193    874
  Planarity :  0.004   0.041    977
  Dihedral  :  5.595  38.603    834
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.92 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.31), residues: 687
  helix:  3.35 (0.45), residues: 109
  sheet:  0.61 (0.34), residues: 226
  loop : -0.69 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  60 
 HIS   0.010   0.001   HIS B  91 
 PHE   0.011   0.001   PHE B 140 
 TYR   0.015   0.002   TYR C  71 
 ARG   0.004   0.000   ARG D  48 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.6326 (mp10)
REVERT: B  114 THR cc_start: 0.8481 (m) cc_final: 0.7979 (p)
REVERT: B  275 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7841 (m)
REVERT: B  288 ARG cc_start: 0.7437 (ptp-170) cc_final: 0.7075 (mtt180)
REVERT: D  122 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7313 (mp10)
  outliers start: 20
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1699
  time to fit residues: 26.3226
Evaluate side-chains
  105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  135 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0470
   chunk 3 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** B  78 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 = 0.3793 r_free = 0.3793 target = 0.162731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.128052 restraints weight = 7054.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.129937 restraints weight = 5625.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.131312 restraints weight = 4898.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5704  Z= 0.191
  Angle     :  0.529   7.918   7721  Z= 0.281
  Chirality :  0.039   0.170    874
  Planarity :  0.004   0.040    977
  Dihedral  :  4.537  28.312    834
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 19.71 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.32), residues: 687
  helix:  3.34 (0.45), residues: 112
  sheet:  0.67 (0.34), residues: 232
  loop : -0.73 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  60 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.012   0.001   PHE A  35 
 TYR   0.014   0.001   TYR C  71 
 ARG   0.002   0.000   ARG B 230 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
REVERT: B  114 THR cc_start: 0.8316 (m) cc_final: 0.7966 (p)
REVERT: B  118 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7890 (ptmt)
REVERT: B  288 ARG cc_start: 0.7493 (ptp-170) cc_final: 0.7175 (mtt180)
  outliers start: 14
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1862
  time to fit residues: 24.6411
Evaluate side-chains
  101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  135 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0670
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.8126

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
B 166 GLN
B 276 GLN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.150471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.114478 restraints weight = 7016.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.116126 restraints weight = 5866.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.116840 restraints weight = 5248.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   5704  Z= 0.392
  Angle     :  0.646   6.954   7721  Z= 0.343
  Chirality :  0.044   0.211    874
  Planarity :  0.005   0.048    977
  Dihedral  :  4.638  19.126    834
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.24 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.32), residues: 687
  helix:  2.58 (0.47), residues: 119
  sheet:  0.43 (0.34), residues: 228
  loop : -0.96 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 256 
 HIS   0.013   0.003   HIS B 216 
 PHE   0.029   0.003   PHE B 228 
 TYR   0.020   0.002   TYR B 189 
 ARG   0.006   0.001   ARG B 230 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6673 (mp10)
REVERT: A  215 TYR cc_start: 0.9010 (t80) cc_final: 0.8804 (t80)
REVERT: B  114 THR cc_start: 0.8473 (m) cc_final: 0.8124 (p)
REVERT: B  258 TYR cc_start: 0.8777 (m-80) cc_final: 0.8459 (m-80)
REVERT: B  288 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7605 (mtt180)
REVERT: D   85 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7639 (mtp-110)
  outliers start: 24
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1712
  time to fit residues: 25.7046
Evaluate side-chains
  108 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  192 GLU
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS
** B  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 166 GLN
B 276 GLN
D  98 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.154270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.119832 restraints weight = 6895.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.118804 restraints weight = 6650.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.119710 restraints weight = 6389.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   5704  Z= 0.208
  Angle     :  0.546   7.352   7721  Z= 0.289
  Chirality :  0.040   0.198    874
  Planarity :  0.004   0.042    977
  Dihedral  :  4.395  18.756    834
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.83 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.32), residues: 687
  helix:  2.73 (0.47), residues: 118
  sheet:  0.63 (0.36), residues: 215
  loop : -0.95 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  60 
 HIS   0.012   0.001   HIS B  91 
 PHE   0.012   0.001   PHE B 228 
 TYR   0.013   0.001   TYR C  71 
 ARG   0.004   0.000   ARG D  51 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6652 (mp10)
REVERT: B  114 THR cc_start: 0.8278 (m) cc_final: 0.7884 (p)
REVERT: B  258 TYR cc_start: 0.8782 (m-80) cc_final: 0.8454 (m-80)
REVERT: B  288 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7668 (mtt180)
  outliers start: 22
  outliers final: 12
  residues processed: 107
  average time/residue: 0.1882
  time to fit residues: 25.8826
Evaluate side-chains
  101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0870
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0050
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.9774

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
** B  99 HIS ** 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 = 0.3672 r_free = 0.3672 target = 0.152328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.115455 restraints weight = 6903.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.117354 restraints weight = 5499.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.118415 restraints weight = 4826.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.4805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   5704  Z= 0.233
  Angle     :  0.547   7.442   7721  Z= 0.288
  Chirality :  0.040   0.216    874
  Planarity :  0.004   0.044    977
  Dihedral  :  4.276  18.004    834
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.62 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.32), residues: 687
  helix:  2.78 (0.47), residues: 118
  sheet:  0.60 (0.36), residues: 215
  loop : -0.97 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.016   0.001   PHE B 228 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.008   0.001   ARG D  85 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6637 (mp10)
REVERT: B  114 THR cc_start: 0.8387 (m) cc_final: 0.7991 (p)
REVERT: B  258 TYR cc_start: 0.8779 (m-80) cc_final: 0.8482 (m-80)
REVERT: B  288 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7672 (mtt180)
REVERT: D  128 GLU cc_start: 0.7520 (pp20) cc_final: 0.6739 (pp20)
  outliers start: 16
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1929
  time to fit residues: 24.1975
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0470
   chunk 19 optimal weight:    0.1980
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.154746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.118809 restraints weight = 6890.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.120610 restraints weight = 5654.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.121510 restraints weight = 5008.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   5704  Z= 0.175
  Angle     :  0.536   9.968   7721  Z= 0.278
  Chirality :  0.039   0.226    874
  Planarity :  0.004   0.046    977
  Dihedral  :  4.117  17.700    834
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.94 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.32), residues: 687
  helix:  2.78 (0.47), residues: 118
  sheet:  0.72 (0.37), residues: 215
  loop : -0.88 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 143 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.010   0.001   PHE B 140 
 TYR   0.009   0.001   TYR C  71 
 ARG   0.007   0.000   ARG D  85 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6626 (mp10)
REVERT: B  114 THR cc_start: 0.8253 (m) cc_final: 0.7837 (p)
REVERT: B  258 TYR cc_start: 0.8723 (m-80) cc_final: 0.8439 (m-80)
REVERT: D  128 GLU cc_start: 0.7548 (pp20) cc_final: 0.6808 (pp20)
  outliers start: 17
  outliers final: 12
  residues processed: 98
  average time/residue: 0.2293
  time to fit residues: 29.0506
Evaluate side-chains
  101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
B  99 HIS
B 276 GLN
C  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.152376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.114675 restraints weight = 6937.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.116851 restraints weight = 5440.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.117968 restraints weight = 4725.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   5704  Z= 0.232
  Angle     :  0.560   8.275   7721  Z= 0.289
  Chirality :  0.040   0.236    874
  Planarity :  0.004   0.047    977
  Dihedral  :  4.144  18.232    834
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.78 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.32), residues: 687
  helix:  2.77 (0.48), residues: 119
  sheet:  0.64 (0.36), residues: 215
  loop : -0.93 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  60 
 HIS   0.012   0.001   HIS B  91 
 PHE   0.017   0.001   PHE B 228 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.007   0.000   ARG D  85 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6676 (mp10)
REVERT: B  258 TYR cc_start: 0.8785 (m-80) cc_final: 0.8514 (m-80)
REVERT: D  128 GLU cc_start: 0.7596 (pp20) cc_final: 0.6890 (pp20)
  outliers start: 17
  outliers final: 13
  residues processed: 95
  average time/residue: 0.1934
  time to fit residues: 23.5970
Evaluate side-chains
  99 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   26 ASP
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.154048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.118189 restraints weight = 6977.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.119904 restraints weight = 5705.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.121000 restraints weight = 5082.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   5704  Z= 0.203
  Angle     :  0.533   8.187   7721  Z= 0.277
  Chirality :  0.040   0.229    874
  Planarity :  0.004   0.050    977
  Dihedral  :  4.082  17.922    834
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.26 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.32), residues: 687
  helix:  2.80 (0.48), residues: 119
  sheet:  0.49 (0.35), residues: 235
  loop : -0.83 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.012   0.001   PHE B 228 
 TYR   0.011   0.001   TYR C  71 
 ARG   0.006   0.000   ARG D  85 

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6629 (mp10)
REVERT: B  258 TYR cc_start: 0.8758 (m-80) cc_final: 0.8482 (m-80)
REVERT: D  128 GLU cc_start: 0.7501 (pp20) cc_final: 0.6865 (pp20)
  outliers start: 15
  outliers final: 13
  residues processed: 94
  average time/residue: 0.1969
  time to fit residues: 23.7286
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   26 ASP
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 43 optimal weight:    0.1980
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B  91 HIS
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.154258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.117304 restraints weight = 6961.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.120051 restraints weight = 5701.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.120349 restraints weight = 4883.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   5704  Z= 0.199
  Angle     :  0.529   8.228   7721  Z= 0.275
  Chirality :  0.040   0.226    874
  Planarity :  0.004   0.049    977
  Dihedral  :  4.057  17.890    834
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.94 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.32), residues: 687
  helix:  2.73 (0.48), residues: 119
  sheet:  0.45 (0.36), residues: 221
  loop : -0.78 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 256 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.013   0.001   PHE B 228 
 TYR   0.011   0.001   TYR C  71 
 ARG   0.006   0.000   ARG D  85 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2211.74 seconds
wall clock time: 38 minutes 57.73 seconds (2337.73 seconds total)