Starting phenix.real_space_refine
on Tue Mar 11 17:22:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k7r_36939/03_2025/8k7r_36939.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k7r_36939/03_2025/8k7r_36939.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k7r_36939/03_2025/8k7r_36939.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k7r_36939/03_2025/8k7r_36939.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k7r_36939/03_2025/8k7r_36939.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k7r_36939/03_2025/8k7r_36939.cif"
  }
  resolution = 3.56
  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=   0.002 sd=   0.056
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      27      5.16       5
     C    4051      2.51       5
     N    1100      2.21       5
     O    1294      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 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: 6472
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1448
          Classifications: {'peptide': 175}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 167}
    Chain: "E"
      Number of atoms: 2382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2382
          Classifications: {'peptide': 304}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 283}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "F"
      Number of atoms: 2376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2376
          Classifications: {'peptide': 303}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 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: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "G"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "H"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.54, per 1000 atoms: 0.70
  Number of scatterers: 6472
  At special positions: 0
  Unit cell: (102.367, 99.6, 124.5, 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      27     16.00
     O    1294      8.00
     N    1100      7.00
     C    4051      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 132 " - pdb=" SG  CYS A 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 121 " - pdb=" SG  CYS F 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 135 " - pdb=" SG  CYS E 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 209 " - pdb=" SG  CYS F 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 239 " - pdb=" SG  CYS E 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 345 " - pdb=" SG  CYS E 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 135 " - pdb=" SG  CYS F 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 239 " - pdb=" SG  CYS F 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 345 " - pdb=" SG  CYS F 405 " 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
  Links applied
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
      " BMA G   3 " - " MAN G   4 "
      " BMA H   3 " - " MAN H   4 "
    ALPHA1-6
      " BMA G   3 " - " MAN G   5 "
      " BMA H   3 " - " MAN H   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 301 " - " ASN A 191 "
      " NAG A 302 " - " ASN A 165 "
      " NAG B   1 " - " ASN A  46 "
      " NAG C   1 " - " ASN A 160 "
      " NAG D   1 " - " ASN A  67 "
      " NAG G   1 " - " ASN E 275 "
      " NAG H   1 " - " ASN F 275 "
  Time building additional restraints: 2.02
  Conformation dependent library (CDL) restraints added in 926.2 milliseconds
  

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1476

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 19 sheets defined
      8.1% alpha, 40.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.763A  pdb=" N   SER A  88 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 217
    Processing helix  chain 'E' and resid 225 through 231
    Processing helix  chain 'E' and resid 287 through 294
      removed outlier: 3.563A  pdb=" N   GLY E 294 " --> pdb=" O   ASP E 290 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 367 through 369
      No H-bonds generated for 'chain 'E' and resid 367 through 369'
    Processing helix  chain 'E' and resid 393 through 399
      removed outlier: 3.646A  pdb=" N   GLN E 399 " --> pdb=" O   ALA E 395 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 181 through 187
    Processing helix  chain 'F' and resid 225 through 231
    Processing helix  chain 'F' and resid 287 through 294
    Processing helix  chain 'F' and resid 394 through 399
      removed outlier: 3.577A  pdb=" N   GLN F 399 " --> pdb=" O   ALA F 395 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35
    Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42
      removed outlier: 6.405A  pdb=" N   ILE A  41 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 65
    Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 117
    Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 155
      removed outlier: 3.917A  pdb=" N   GLU A 150 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   TYR A 145 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   TYR A 154 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   VAL A 143 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   LYS A 142 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   LYS A 179 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 174
    Processing sheet with id=AA7, first strand: chain 'E' and resid 178 through 179
      removed outlier: 6.448A  pdb=" N   GLN E 132 " --> pdb=" O   SER E 119 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 157 through 161
      removed outlier: 4.964A  pdb=" N   GLN E 146 " --> pdb=" O   THR E 196 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 218 through 221
      removed outlier: 3.731A  pdb=" N   ASP E 243 " --> pdb=" O   LEU E 278 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   LEU E 278 " --> pdb=" O   ASP E 243 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR E 279 " --> pdb=" O   GLU E 271 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR E 283 " --> pdb=" O   THR E 267 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 253 through 257
    Processing sheet with id=AB2, first strand: chain 'E' and resid 325 through 330
    Processing sheet with id=AB3, first strand: chain 'E' and resid 325 through 330
    Processing sheet with id=AB4, first strand: chain 'E' and resid 364 through 365
    Processing sheet with id=AB5, first strand: chain 'F' and resid 146 through 151
      removed outlier: 3.996A  pdb=" N   GLN F 146 " --> pdb=" O   THR F 196 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 218 through 222
      removed outlier: 3.863A  pdb=" N   THR F 238 " --> pdb=" O   SER F 222 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 252 through 257
    Processing sheet with id=AB8, first strand: chain 'F' and resid 325 through 330
      removed outlier: 6.039A  pdb=" N   PHE F 384 " --> pdb=" O   ASN F 349 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 325 through 330
      removed outlier: 6.039A  pdb=" N   PHE F 384 " --> pdb=" O   ASN F 349 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 364 through 365

    250 hydrogen bonds defined for protein.
    633 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: 1.97

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2063
        1.35 -     1.47: 1655
        1.47 -     1.58: 2878
        1.58 -     1.70: 2
        1.70 -     1.82: 34
  Bond restraints: 6632
  Sorted by residual:
  bond pdb=" CG  PRO F 332 "
       pdb=" CD  PRO F 332 "
    ideal  model  delta    sigma   weight residual
    1.503  1.329  0.174 3.40e-02 8.65e+02 2.62e+01
  bond pdb=" C1  NAG A 302 "
       pdb=" O5  NAG A 302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.479 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" CB  PRO F 332 "
       pdb=" CG  PRO F 332 "
    ideal  model  delta    sigma   weight residual
    1.492  1.666 -0.174 5.00e-02 4.00e+02 1.22e+01
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.582 -0.063 2.00e-02 2.50e+03 1.01e+01
  bond pdb=" CB  PRO E 332 "
       pdb=" CG  PRO E 332 "
    ideal  model  delta    sigma   weight residual
    1.492  1.649 -0.157 5.00e-02 4.00e+02 9.90e+00
  ... (remaining 6627 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 8958
        3.45 -     6.90: 62
        6.90 -    10.35: 6
       10.35 -    13.80: 1
       13.80 -    17.25: 2
  Bond angle restraints: 9029
  Sorted by residual:
  angle pdb=" CA  PRO F 332 "
        pdb=" N   PRO F 332 "
        pdb=" CD  PRO F 332 "
      ideal   model   delta    sigma   weight residual
     112.00   94.75   17.25 1.40e+00 5.10e-01 1.52e+02
  angle pdb=" CA  PRO E 332 "
        pdb=" N   PRO E 332 "
        pdb=" CD  PRO E 332 "
      ideal   model   delta    sigma   weight residual
     112.00   97.91   14.09 1.40e+00 5.10e-01 1.01e+02
  angle pdb=" N   PRO F 332 "
        pdb=" CD  PRO F 332 "
        pdb=" CG  PRO F 332 "
      ideal   model   delta    sigma   weight residual
     103.20   92.52   10.68 1.50e+00 4.44e-01 5.07e+01
  angle pdb=" N   PRO E 332 "
        pdb=" CD  PRO E 332 "
        pdb=" CG  PRO E 332 "
      ideal   model   delta    sigma   weight residual
     103.20   95.98    7.22 1.50e+00 4.44e-01 2.32e+01
  angle pdb=" CA  PRO F 332 "
        pdb=" CB  PRO F 332 "
        pdb=" CG  PRO F 332 "
      ideal   model   delta    sigma   weight residual
     104.50   95.72    8.78 1.90e+00 2.77e-01 2.13e+01
  ... (remaining 9024 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.62: 3853
       24.62 -    49.24: 306
       49.24 -    73.86: 44
       73.86 -    98.48: 32
       98.48 -   123.10: 21
  Dihedral angle restraints: 4256
    sinusoidal: 1980
      harmonic: 2276
  Sorted by residual:
  dihedral pdb=" CB  CYS E 121 "
           pdb=" SG  CYS E 121 "
           pdb=" SG  CYS F 209 "
           pdb=" CB  CYS F 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -0.49  -85.51     1      1.00e+01 1.00e-02 8.85e+01
  dihedral pdb=" CA  PRO E 332 "
           pdb=" C   PRO E 332 "
           pdb=" N   GLU E 333 "
           pdb=" CA  GLU E 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.94  -23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CB  CYS E 135 "
           pdb=" SG  CYS E 135 "
           pdb=" SG  CYS E 193 "
           pdb=" CB  CYS E 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.08   36.08     1      1.00e+01 1.00e-02 1.84e+01
  ... (remaining 4253 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 883
       0.055 -    0.109: 143
       0.109 -    0.164: 31
       0.164 -    0.219: 3
       0.219 -    0.273: 4
  Chirality restraints: 1064
  Sorted by residual:
  chirality pdb=" C2  BMA D   3 "
            pdb=" C1  BMA D   3 "
            pdb=" C3  BMA D   3 "
            pdb=" O2  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.75   -0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" C5  BMA H   3 "
            pdb=" C4  BMA H   3 "
            pdb=" C6  BMA H   3 "
            pdb=" O5  BMA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 1061 not shown)

  Planarity restraints: 1134
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 331 "    0.088 5.00e-02 4.00e+02   1.19e-01 2.26e+01
        pdb=" N   PRO F 332 "   -0.205 5.00e-02 4.00e+02
        pdb=" CA  PRO F 332 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO F 332 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 331 "    0.074 5.00e-02 4.00e+02   1.03e-01 1.70e+01
        pdb=" N   PRO E 332 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO E 332 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO E 332 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 306 "    0.060 5.00e-02 4.00e+02   8.90e-02 1.27e+01
        pdb=" N   PRO E 307 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO E 307 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO E 307 "    0.048 5.00e-02 4.00e+02
  ... (remaining 1131 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 259
        2.72 -     3.26: 5807
        3.26 -     3.81: 9886
        3.81 -     4.35: 11995
        4.35 -     4.90: 20782
  Nonbonded interactions: 48729
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F 140 "
            pdb=" OG1 THR F 174 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   PHE A  57 "
            pdb=" OG  SER A  61 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG1 THR F 148 "
            pdb=" OE1 GLN F 194 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OH  TYR E 140 "
            pdb=" O   ALA E 172 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   SER F 234 "
            pdb=" OG  SER F 234 "
     model   vdw
     2.326 3.040
  ... (remaining 48724 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
Found NCS groups:
ncs_group {
  reference = (chain 'E' and (resid 113 through 159 or resid 172 through 257 or (resid 258 and \ 
 (name N or name CA or name C or name O )) or resid 259 through 425))
  selection = (chain 'F' and (resid 113 through 231 or (resid 232 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name CD or name NE or name CZ )) or resi \ 
d 233 through 425))
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}

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:             0.270
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.160
  Find NCS groups from input model:        0.230
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.174   6632  Z= 0.354
  Angle     :  0.775  17.253   9029  Z= 0.392
  Chirality :  0.048   0.273   1064
  Planarity :  0.006   0.119   1127
  Dihedral  : 20.110 123.105   2750
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.90 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 20.31 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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 (0.31), residues: 772
  helix: -1.05 (0.90), residues: 35
  sheet:  1.15 (0.28), residues: 353
  loop : -0.71 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 181 
 HIS   0.008   0.001   HIS A  95 
 PHE   0.016   0.001   PHE E 329 
 TYR   0.006   0.001   TYR A 175 
 ARG   0.004   0.000   ARG E 341 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  191 TYR cc_start: 0.8290 (m-80) cc_final: 0.7834 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 78
  average time/residue: 0.1880
  time to fit residues: 19.8556
Evaluate side-chains
  76 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain F residue  146 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 362 ASN
F 182 GLN
F 198 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.160808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.114819 restraints weight = 8154.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.117068 restraints weight = 6095.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.117770 restraints weight = 4794.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6632  Z= 0.282
  Angle     :  0.642   8.656   9029  Z= 0.312
  Chirality :  0.047   0.267   1064
  Planarity :  0.005   0.047   1127
  Dihedral  : 16.118 106.436   1269
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.42 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.46 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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:  0.08 (0.31), residues: 772
  helix: -0.96 (0.78), residues: 43
  sheet:  1.16 (0.27), residues: 349
  loop : -0.92 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  38 
 HIS   0.008   0.001   HIS A  95 
 PHE   0.008   0.001   PHE E 329 
 TYR   0.015   0.001   TYR E 327 
 ARG   0.005   0.000   ARG A 131 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7319 (tp30) cc_final: 0.6990 (tp30)
REVERT: E  311 MET cc_start: 0.6964 (tpp) cc_final: 0.6751 (tpt)
  outliers start: 18
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1790
  time to fit residues: 22.9276
Evaluate side-chains
  80 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain E residue  364 VAL
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  198 GLN
Chi-restraints excluded: chain F residue  202 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 61 optimal weight:    0.4980
   chunk 52 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 198 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 = 0.3771 r_free = 0.3771 target = 0.162932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.127732 restraints weight = 8132.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.123351 restraints weight = 9472.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.125088 restraints weight = 9949.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6632  Z= 0.185
  Angle     :  0.611   9.202   9029  Z= 0.295
  Chirality :  0.045   0.250   1064
  Planarity :  0.004   0.035   1127
  Dihedral  : 15.011 104.085   1264
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.42 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.88 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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:  0.10 (0.31), residues: 772
  helix: -1.13 (0.78), residues: 42
  sheet:  1.16 (0.27), residues: 349
  loop : -0.87 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 291 
 HIS   0.008   0.001   HIS A  95 
 PHE   0.013   0.001   PHE E 329 
 TYR   0.019   0.001   TYR F 197 
 ARG   0.003   0.000   ARG E 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  311 MET cc_start: 0.7072 (tpp) cc_final: 0.6691 (tpt)
REVERT: F  306 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8368 (mp)
  outliers start: 12
  outliers final: 7
  residues processed: 88
  average time/residue: 0.1706
  time to fit residues: 20.6729
Evaluate side-chains
  81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  269 LYS
Chi-restraints excluded: chain E residue  364 VAL
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  306 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 3 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.161016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.114910 restraints weight = 8253.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.117223 restraints weight = 6163.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.118513 restraints weight = 5151.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6632  Z= 0.229
  Angle     :  0.630   9.229   9029  Z= 0.304
  Chirality :  0.046   0.263   1064
  Planarity :  0.004   0.040   1127
  Dihedral  : 14.088 101.588   1264
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.81 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.45 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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:  0.05 (0.30), residues: 772
  helix: -1.18 (0.77), residues: 42
  sheet:  1.13 (0.27), residues: 347
  loop : -0.88 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  38 
 HIS   0.006   0.001   HIS A  95 
 PHE   0.010   0.001   PHE E 329 
 TYR   0.015   0.001   TYR E 327 
 ARG   0.006   0.000   ARG F 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7982 (ttt180)
REVERT: E  183 LYS cc_start: 0.7358 (mttt) cc_final: 0.6929 (tttt)
REVERT: E  311 MET cc_start: 0.7110 (tpp) cc_final: 0.6735 (tpt)
REVERT: F  306 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8574 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1795
  time to fit residues: 23.0287
Evaluate side-chains
  88 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  269 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  364 VAL
Chi-restraints excluded: chain E residue  410 GLU
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  292 ILE
Chi-restraints excluded: chain F residue  306 LEU
Chi-restraints excluded: chain F residue  317 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
F 182 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.161004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.114778 restraints weight = 8215.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.117073 restraints weight = 6154.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.118262 restraints weight = 5127.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6632  Z= 0.216
  Angle     :  0.627   9.228   9029  Z= 0.301
  Chirality :  0.046   0.280   1064
  Planarity :  0.004   0.032   1127
  Dihedral  : 13.189  99.590   1264
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.42 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.88 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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: -0.00 (0.30), residues: 772
  helix: -1.29 (0.76), residues: 42
  sheet:  1.09 (0.27), residues: 344
  loop : -0.89 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  38 
 HIS   0.004   0.001   HIS A  95 
 PHE   0.008   0.001   PHE E 387 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.004   0.000   ARG E 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7996 (ttt180)
REVERT: E  183 LYS cc_start: 0.7472 (mttt) cc_final: 0.6991 (tttt)
REVERT: E  256 SER cc_start: 0.9070 (p) cc_final: 0.8700 (t)
REVERT: E  264 ASN cc_start: 0.8189 (m-40) cc_final: 0.7916 (m110)
REVERT: E  311 MET cc_start: 0.7049 (tpp) cc_final: 0.6650 (tpt)
REVERT: F  306 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8545 (mp)
  outliers start: 20
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1870
  time to fit residues: 22.8641
Evaluate side-chains
  79 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  269 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  306 LEU
Chi-restraints excluded: chain F residue  392 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 40 optimal weight:    0.5980
   chunk 20 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A  95 HIS
** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.160677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.115354 restraints weight = 8220.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.117376 restraints weight = 6069.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.117807 restraints weight = 5003.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6632  Z= 0.199
  Angle     :  0.624   9.250   9029  Z= 0.302
  Chirality :  0.046   0.288   1064
  Planarity :  0.004   0.029   1127
  Dihedral  : 12.514  97.516   1264
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.55 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.60 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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:  0.04 (0.31), residues: 772
  helix: -1.36 (0.76), residues: 42
  sheet:  1.08 (0.27), residues: 352
  loop : -0.84 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 291 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.022   0.002   PHE E 329 
 TYR   0.008   0.001   TYR E 327 
 ARG   0.004   0.000   ARG F 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LYS cc_start: 0.7024 (ttpt) cc_final: 0.6820 (ttpt)
REVERT: A  131 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8017 (ttt180)
REVERT: E  183 LYS cc_start: 0.7608 (mttt) cc_final: 0.7196 (tttt)
REVERT: E  189 ARG cc_start: 0.6044 (mmm-85) cc_final: 0.5650 (mmm-85)
REVERT: E  256 SER cc_start: 0.9053 (p) cc_final: 0.8683 (t)
REVERT: E  311 MET cc_start: 0.6958 (tpp) cc_final: 0.6574 (tpt)
REVERT: F  306 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8541 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 82
  average time/residue: 0.1840
  time to fit residues: 20.4896
Evaluate side-chains
  77 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  269 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  306 LEU
Chi-restraints excluded: chain F residue  392 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 70 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 60 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** E 303 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 = 0.3758 r_free = 0.3758 target = 0.161166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.116146 restraints weight = 8174.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.117967 restraints weight = 6640.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.118878 restraints weight = 5554.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6632  Z= 0.199
  Angle     :  0.623   9.272   9029  Z= 0.301
  Chirality :  0.045   0.293   1064
  Planarity :  0.003   0.027   1127
  Dihedral  : 12.010  95.035   1264
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.42 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.46 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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:  0.02 (0.31), residues: 772
  helix: -1.47 (0.75), residues: 43
  sheet:  1.06 (0.27), residues: 352
  loop : -0.83 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  38 
 HIS   0.003   0.000   HIS A  95 
 PHE   0.018   0.001   PHE E 329 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.004   0.000   ARG F 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.7657 (tt0) cc_final: 0.7456 (tt0)
REVERT: A  131 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7998 (ttt180)
REVERT: E  183 LYS cc_start: 0.7522 (mttt) cc_final: 0.7016 (tttt)
REVERT: E  256 SER cc_start: 0.9049 (p) cc_final: 0.8716 (t)
REVERT: F  306 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8576 (mp)
  outliers start: 16
  outliers final: 13
  residues processed: 83
  average time/residue: 0.1879
  time to fit residues: 21.3302
Evaluate side-chains
  81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  269 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  401 ASP
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  284 LEU
Chi-restraints excluded: chain F residue  306 LEU
Chi-restraints excluded: chain F residue  392 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 213 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.158852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.114854 restraints weight = 8140.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.116879 restraints weight = 6225.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.118171 restraints weight = 5268.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6632  Z= 0.209
  Angle     :  0.628   9.261   9029  Z= 0.304
  Chirality :  0.046   0.292   1064
  Planarity :  0.003   0.027   1127
  Dihedral  : 11.735  96.267   1264
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.68 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.89 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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:  0.01 (0.31), residues: 772
  helix: -1.52 (0.74), residues: 43
  sheet:  1.04 (0.27), residues: 352
  loop : -0.82 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  38 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.016   0.001   PHE E 329 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.004   0.000   ARG F 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 TYR cc_start: 0.7980 (m-10) cc_final: 0.7698 (m-10)
REVERT: A  131 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7944 (ttt180)
REVERT: E  183 LYS cc_start: 0.7646 (mttt) cc_final: 0.7201 (tttt)
REVERT: E  256 SER cc_start: 0.9109 (p) cc_final: 0.8748 (t)
REVERT: F  306 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8509 (mp)
REVERT: F  311 MET cc_start: 0.7578 (tpt) cc_final: 0.7128 (tpp)
  outliers start: 18
  outliers final: 14
  residues processed: 87
  average time/residue: 0.2053
  time to fit residues: 23.8828
Evaluate side-chains
  85 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  269 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  401 ASP
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  213 ASN
Chi-restraints excluded: chain F residue  284 LEU
Chi-restraints excluded: chain F residue  306 LEU
Chi-restraints excluded: chain F residue  392 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 13 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 213 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.154326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.110236 restraints weight = 8301.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.112162 restraints weight = 6410.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.113305 restraints weight = 5437.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6632  Z= 0.402
  Angle     :  0.716   8.968   9029  Z= 0.352
  Chirality :  0.048   0.296   1064
  Planarity :  0.004   0.035   1127
  Dihedral  : 12.195 102.575   1264
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.84 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.46 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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: -0.23 (0.30), residues: 772
  helix: -1.50 (0.73), residues: 43
  sheet:  0.87 (0.27), residues: 352
  loop : -1.00 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  38 
 HIS   0.005   0.001   HIS A  95 
 PHE   0.021   0.002   PHE E 329 
 TYR   0.011   0.002   TYR A 174 
 ARG   0.008   0.001   ARG F 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8527 (ttt180)
REVERT: E  183 LYS cc_start: 0.7823 (mttt) cc_final: 0.7372 (tttt)
REVERT: E  256 SER cc_start: 0.9074 (p) cc_final: 0.8767 (t)
REVERT: E  264 ASN cc_start: 0.8267 (m-40) cc_final: 0.8014 (m110)
REVERT: F  306 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8657 (mp)
REVERT: F  311 MET cc_start: 0.7495 (tpt) cc_final: 0.7028 (tpp)
  outliers start: 16
  outliers final: 10
  residues processed: 84
  average time/residue: 0.1882
  time to fit residues: 21.1972
Evaluate side-chains
  81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  213 ASN
Chi-restraints excluded: chain F residue  284 LEU
Chi-restraints excluded: chain F residue  306 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0040
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 213 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.158554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.114947 restraints weight = 8240.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.116926 restraints weight = 6152.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.118141 restraints weight = 5179.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6632  Z= 0.172
  Angle     :  0.655   9.345   9029  Z= 0.322
  Chirality :  0.046   0.277   1064
  Planarity :  0.004   0.030   1127
  Dihedral  : 11.602  98.998   1264
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.55 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 22.17 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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: -0.10 (0.31), residues: 772
  helix: -1.59 (0.74), residues: 43
  sheet:  0.90 (0.27), residues: 351
  loop : -0.81 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 291 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.012   0.001   PHE F 329 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.007   0.000   ARG F 289 

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  183 LYS cc_start: 0.7715 (mttt) cc_final: 0.7246 (tttt)
REVERT: E  256 SER cc_start: 0.9120 (p) cc_final: 0.8761 (t)
REVERT: F  311 MET cc_start: 0.7574 (tpt) cc_final: 0.7121 (tpp)
  outliers start: 8
  outliers final: 6
  residues processed: 77
  average time/residue: 0.2026
  time to fit residues: 20.9093
Evaluate side-chains
  73 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain E residue  146 GLN
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain F residue  213 ASN
Chi-restraints excluded: chain F residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 213 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.157509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.114787 restraints weight = 8301.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.115955 restraints weight = 6153.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.116232 restraints weight = 5343.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6632  Z= 0.228
  Angle     :  0.676   9.542   9029  Z= 0.330
  Chirality :  0.046   0.274   1064
  Planarity :  0.004   0.030   1127
  Dihedral  : 11.531  98.867   1264
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.68 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 22.32 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.42 %
    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: -0.14 (0.30), residues: 772
  helix: -1.42 (0.73), residues: 43
  sheet:  0.88 (0.27), residues: 352
  loop : -0.88 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 149 
 HIS   0.004   0.001   HIS A  95 
 PHE   0.015   0.002   PHE F 329 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.007   0.000   ARG F 289 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2330.27 seconds
wall clock time: 41 minutes 12.13 seconds (2472.13 seconds total)