Starting phenix.real_space_refine
on Sun Jun  8 18:47:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6c14_7328/06_2025/6c14_7328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6c14_7328/06_2025/6c14_7328.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6c14_7328/06_2025/6c14_7328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6c14_7328/06_2025/6c14_7328.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6c14_7328/06_2025/6c14_7328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6c14_7328/06_2025/6c14_7328.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3678 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4406      2.51       5
     N    1100      2.21       5
     O    1194      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6746
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2110
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 266, 2107
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 11, 'TRANS': 254}
      Conformer: "B"
        Number of residues, atoms: 266, 2107
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 11, 'TRANS': 254}
          bond proxies already assigned to first conformer: 2142
    Chain: "B"
      Number of atoms: 1263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1263
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 4, 'TRANS': 159}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2110
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 266, 2107
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 11, 'TRANS': 254}
      Conformer: "B"
        Number of residues, atoms: 266, 2107
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 11, 'TRANS': 254}
          bond proxies already assigned to first conformer: 2142
    Chain: "D"
      Number of atoms: 1263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1263
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 4, 'TRANS': 159}
          Chain breaks: 2
  Time building chain proxies: 6.63, per 1000 atoms: 0.98
  Number of scatterers: 6746
  At special positions: 0
  Unit cell: (73.84, 80.08, 139.36, 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      46     16.00
     O    1194      8.00
     N    1100      7.00
     C    4406      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  68 " - pdb=" SG  CYS B  79 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  68 " - pdb=" SG  CYS D  79 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 114 " - pdb=" SG  CYS D 130 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.71
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1592

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      49.3% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1180 through 1184
      removed outlier: 3.886A  pdb=" N   ALA A1183 " --> pdb=" O   ASN A1180 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET A1184 " --> pdb=" O   TYR A1181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1180 through 1184'
    Processing helix  chain 'A' and resid 1193 through 1197
    Processing helix  chain 'A' and resid 1231 through 1235
    Processing helix  chain 'A' and resid 1249 through 1253
    Processing helix  chain 'A' and resid 1261 through 1268
    Processing helix  chain 'A' and resid 1268 through 1280
    Processing helix  chain 'A' and resid 1327 through 1337
      removed outlier: 4.074A  pdb=" N   LEU A1335 " --> pdb=" O   LEU A1331 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY A1337 " --> pdb=" O   LYS A1333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1338 through 1344
      removed outlier: 3.889A  pdb=" N   ILE A1342 " --> pdb=" O   LYS A1338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1366 through 1372
      removed outlier: 3.835A  pdb=" N   LYS A1370 " --> pdb=" O   THR A1366 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLY A1372 " --> pdb=" O   ILE A1368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1410
      Proline residue:  A1395  - end of helix
    Processing helix  chain 'B' and resid 16 through 45
    Processing helix  chain 'B' and resid 91 through 117
    Processing helix  chain 'B' and resid 122 through 152
      removed outlier: 3.593A  pdb=" N   LYS B 128 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
      Proline residue:  B 149  - end of helix
    Processing helix  chain 'B' and resid 176 through 199
      removed outlier: 4.125A  pdb=" N   MET B 180 " --> pdb=" O   ARG B 176 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLY B 187 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1180 through 1184
      removed outlier: 3.882A  pdb=" N   ALA C1183 " --> pdb=" O   ASN C1180 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET C1184 " --> pdb=" O   TYR C1181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1180 through 1184'
    Processing helix  chain 'C' and resid 1193 through 1197
    Processing helix  chain 'C' and resid 1231 through 1235
    Processing helix  chain 'C' and resid 1249 through 1253
    Processing helix  chain 'C' and resid 1261 through 1268
    Processing helix  chain 'C' and resid 1268 through 1280
    Processing helix  chain 'C' and resid 1327 through 1337
      removed outlier: 4.073A  pdb=" N   LEU C1335 " --> pdb=" O   LEU C1331 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLY C1337 " --> pdb=" O   LYS C1333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1338 through 1344
      removed outlier: 3.889A  pdb=" N   ILE C1342 " --> pdb=" O   LYS C1338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1366 through 1372
      removed outlier: 3.858A  pdb=" N   LYS C1370 " --> pdb=" O   THR C1366 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY C1372 " --> pdb=" O   ILE C1368 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1377 through 1410
      Proline residue:  C1395  - end of helix
    Processing helix  chain 'D' and resid 16 through 45
    Processing helix  chain 'D' and resid 91 through 117
    Processing helix  chain 'D' and resid 122 through 152
      removed outlier: 3.593A  pdb=" N   LYS D 128 " --> pdb=" O   ALA D 124 " (cutoff:3.500A)
      Proline residue:  D 149  - end of helix
    Processing helix  chain 'D' and resid 176 through 199
      removed outlier: 4.125A  pdb=" N   MET D 180 " --> pdb=" O   ARG D 176 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLY D 187 " --> pdb=" O   ILE D 183 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1148 through 1149
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1153 through 1155
      removed outlier: 3.954A  pdb=" N   LEU A1244 " --> pdb=" O   TYR A1154 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY A1239 " --> pdb=" O   ALA A1229 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A1229 " --> pdb=" O   GLY A1239 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A1243 " --> pdb=" O   PHE A1225 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A1225 " --> pdb=" O   VAL A1243 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1158 through 1159
      removed outlier: 7.252A  pdb=" N   VAL A1158 " --> pdb=" O   VAL A1248 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1202
      removed outlier: 3.564A  pdb=" N   GLY A1199 " --> pdb=" O   ALA A1212 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1311 through 1315
      removed outlier: 3.818A  pdb=" N   SER A1258 " --> pdb=" O   CYS A1311 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A1315 " --> pdb=" O   GLN A1254 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLN A1254 " --> pdb=" O   VAL A1315 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51
    Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 60
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1148 through 1149
    Processing sheet with id=AA9, first strand: chain 'C' and resid 1153 through 1155
      removed outlier: 3.955A  pdb=" N   LEU C1244 " --> pdb=" O   TYR C1154 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY C1239 " --> pdb=" O   ALA C1229 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA C1229 " --> pdb=" O   GLY C1239 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL C1243 " --> pdb=" O   PHE C1225 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE C1225 " --> pdb=" O   VAL C1243 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 1158 through 1159
      removed outlier: 7.252A  pdb=" N   VAL C1158 " --> pdb=" O   VAL C1248 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 1199 through 1202
      removed outlier: 3.580A  pdb=" N   GLY C1199 " --> pdb=" O   ALA C1212 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1311 through 1315
      removed outlier: 3.819A  pdb=" N   SER C1258 " --> pdb=" O   CYS C1311 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL C1315 " --> pdb=" O   GLN C1254 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLN C1254 " --> pdb=" O   VAL C1315 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 1297 through 1299
    Processing sheet with id=AB5, first strand: chain 'D' and resid 50 through 51
    Processing sheet with id=AB6, first strand: chain 'D' and resid 59 through 60

    344 hydrogen bonds defined for protein.
    966 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: 1.80

  Time building geometry restraints manager: 2.01 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: 2088
        1.35 -     1.47: 1769
        1.47 -     1.60: 2967
        1.60 -     1.72: 0
        1.72 -     1.85: 70
  Bond restraints: 6894
  Sorted by residual:
  bond pdb=" CB  MET D  28 "
       pdb=" CG  MET D  28 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.31e+00
  bond pdb=" CB  MET B  28 "
       pdb=" CG  MET B  28 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.30e+00
  bond pdb=" CB  TRP B  29 "
       pdb=" CG  TRP B  29 "
    ideal  model  delta    sigma   weight residual
    1.498  1.446  0.052 3.10e-02 1.04e+03 2.82e+00
  bond pdb=" CB  TRP D  29 "
       pdb=" CG  TRP D  29 "
    ideal  model  delta    sigma   weight residual
    1.498  1.446  0.052 3.10e-02 1.04e+03 2.81e+00
  bond pdb=" C   ILE C1394 "
       pdb=" N   PRO C1395 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.25e-02 6.40e+03 2.77e+00
  ... (remaining 6889 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 9211
        3.55 -     7.10: 113
        7.10 -    10.65: 10
       10.65 -    14.21: 0
       14.21 -    17.76: 2
  Bond angle restraints: 9336
  Sorted by residual:
  angle pdb=" C   ARG C1360 "
        pdb=" N   THR C1361 "
        pdb=" CA  THR C1361 "
      ideal   model   delta    sigma   weight residual
     120.94  138.70  -17.76 1.90e+00 2.77e-01 8.73e+01
  angle pdb=" C   ARG A1360 "
        pdb=" N   THR A1361 "
        pdb=" CA  THR A1361 "
      ideal   model   delta    sigma   weight residual
     120.94  138.36  -17.42 1.90e+00 2.77e-01 8.41e+01
  angle pdb=" CA  ARG B  20 "
        pdb=" CB  ARG B  20 "
        pdb=" CG  ARG B  20 "
      ideal   model   delta    sigma   weight residual
     114.10  123.80   -9.70 2.00e+00 2.50e-01 2.35e+01
  angle pdb=" CA  ARG D  20 "
        pdb=" CB  ARG D  20 "
        pdb=" CG  ARG D  20 "
      ideal   model   delta    sigma   weight residual
     114.10  123.76   -9.66 2.00e+00 2.50e-01 2.33e+01
  angle pdb=" N   SER C1374 "
        pdb=" CA  SER C1374 "
        pdb=" C   SER C1374 "
      ideal   model   delta    sigma   weight residual
     108.34  113.08   -4.74 1.31e+00 5.83e-01 1.31e+01
  ... (remaining 9331 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.34: 3814
       13.34 -    26.69: 200
       26.69 -    40.03: 56
       40.03 -    53.37: 10
       53.37 -    66.71: 2
  Dihedral angle restraints: 4082
    sinusoidal: 1594
      harmonic: 2488
  Sorted by residual:
  dihedral pdb=" CB  CYS B 114 "
           pdb=" SG  CYS B 114 "
           pdb=" SG  CYS B 130 "
           pdb=" CB  CYS B 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.28  -47.28     1      1.00e+01 1.00e-02 3.09e+01
  dihedral pdb=" CB  CYS D 114 "
           pdb=" SG  CYS D 114 "
           pdb=" SG  CYS D 130 "
           pdb=" CB  CYS D 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.28  -47.28     1      1.00e+01 1.00e-02 3.09e+01
  dihedral pdb=" CA  LYS C1344 "
           pdb=" C   LYS C1344 "
           pdb=" N   ASP C1345 "
           pdb=" CA  ASP C1345 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.25  -22.75     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 4079 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 819
       0.061 -    0.122: 203
       0.122 -    0.183: 40
       0.183 -    0.243: 9
       0.243 -    0.304: 3
  Chirality restraints: 1074
  Sorted by residual:
  chirality pdb=" CB  ILE D  45 "
            pdb=" CA  ILE D  45 "
            pdb=" CG1 ILE D  45 "
            pdb=" CG2 ILE D  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.95   -0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CB  ILE B  45 "
            pdb=" CA  ILE B  45 "
            pdb=" CG1 ILE B  45 "
            pdb=" CG2 ILE B  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.95   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CB  ILE C1388 "
            pdb=" CA  ILE C1388 "
            pdb=" CG1 ILE C1388 "
            pdb=" CG2 ILE C1388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 1071 not shown)

  Planarity restraints: 1160
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D  46 "    0.049 5.00e-02 4.00e+02   7.47e-02 8.92e+00
        pdb=" N   PRO D  47 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO D  47 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO D  47 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  46 "   -0.049 5.00e-02 4.00e+02   7.47e-02 8.92e+00
        pdb=" N   PRO B  47 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO B  47 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B  47 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C1347 "   -0.040 5.00e-02 4.00e+02   5.95e-02 5.67e+00
        pdb=" N   PRO C1348 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO C1348 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C1348 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1157 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1611
        2.79 -     3.32: 6290
        3.32 -     3.84: 11324
        3.84 -     4.37: 12852
        4.37 -     4.90: 20646
  Nonbonded interactions: 52723
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A1319 "
            pdb=" OG1 THR A1322 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OD2 ASP C1319 "
            pdb=" OG1 THR C1322 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   TRP D  29 "
            pdb=" OG1 THR D  33 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   TRP B  29 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OE1 GLU A1203 "
            pdb=" OG1 THR A1206 "
     model   vdw
     2.329 3.040
  ... (remaining 52718 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  Number of NCS constrained groups: 2
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.45 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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     22.560
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
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      :  0.005   0.055   6898  Z= 0.256
  Angle     :  1.038  17.757   9344  Z= 0.585
  Chirality :  0.059   0.304   1074
  Planarity :  0.008   0.075   1160
  Dihedral  :  9.458  66.714   2478
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.82 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.44 (0.22), residues: 846
  helix: -2.47 (0.20), residues: 358
  sheet: -3.92 (0.33), residues: 112
  loop : -3.00 (0.27), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP D  49 
 HIS   0.007   0.002   HIS B  15 
 PHE   0.031   0.003   PHE B 100 
 TYR   0.024   0.003   TYR D 148 
 ARG   0.013   0.001   ARG C1371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16525 (  344)
  hydrogen bonds       : angle       7.90256 (  966)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       2.59134 (    8)
  covalent geometry    : bond        0.00507 ( 6894)
  covalent geometry    : angle       1.03575 ( 9336)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A 1149 PHE cc_start: 0.8145 (m-80) cc_final: 0.7934 (m-80)
REVERT: A 1160 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6129 (tp30)
REVERT: A 1186 TYR cc_start: 0.8093 (m-80) cc_final: 0.7751 (m-80)
REVERT: A 1203 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8336 (tm-30)
REVERT: A 1240 LYS cc_start: 0.8893 (pttt) cc_final: 0.8337 (ptmt)
REVERT: A 1249 ASN cc_start: 0.7586 (p0) cc_final: 0.6409 (t0)
REVERT: A 1270 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8697 (pm20)
REVERT: A 1271 ASP cc_start: 0.9376 (m-30) cc_final: 0.9134 (m-30)
REVERT: A 1274 GLU cc_start: 0.9366 (tt0) cc_final: 0.8850 (mt-10)
REVERT: A 1389 ILE cc_start: 0.9392 (mt) cc_final: 0.9080 (tt)
REVERT: A 1393 CYS cc_start: 0.9577 (m) cc_final: 0.9117 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1847
  time to fit residues: 19.0288
Evaluate side-chains
  56 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.262 
Evaluate side-chains
  76 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.6497 (mmp80) cc_final: 0.6060 (tpt170)
REVERT: B   32 LEU cc_start: 0.9639 (mt) cc_final: 0.9127 (mm)
REVERT: B   66 SER cc_start: 0.8171 (p) cc_final: 0.7953 (t)
REVERT: B  123 THR cc_start: 0.8842 (p) cc_final: 0.8601 (p)
REVERT: B  127 TYR cc_start: 0.8919 (m-10) cc_final: 0.8577 (m-80)
REVERT: B  133 MET cc_start: 0.9448 (mmp) cc_final: 0.9235 (mmm)
REVERT: B  180 MET cc_start: 0.7823 (ttp) cc_final: 0.7174 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1050
  time to fit residues: 9.0366
Evaluate side-chains
  52 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0010
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    2.5790
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1254 GLN
A1299 HIS

Total number of N/Q/H flips: 2

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.078062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.061977 restraints weight = 15813.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.064312 restraints weight = 9221.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.066081 restraints weight = 6292.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.109094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.093330 restraints weight = 4599.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.095743 restraints weight = 3223.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.097666 restraints weight = 2416.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6898  Z= 0.204
  Angle     :  0.805   8.199   9344  Z= 0.435
  Chirality :  0.050   0.193   1074
  Planarity :  0.006   0.049   1160
  Dihedral  :  6.397  24.226    936
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  1.65 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.25), residues: 846
  helix: -1.29 (0.23), residues: 368
  sheet: -3.39 (0.36), residues: 122
  loop : -2.63 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B  49 
 HIS   0.002   0.000   HIS A1216 
 PHE   0.043   0.002   PHE B 100 
 TYR   0.019   0.003   TYR D  67 
 ARG   0.008   0.001   ARG A1219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05513 (  344)
  hydrogen bonds       : angle       6.46771 (  966)
  SS BOND              : bond        0.01259 (    4)
  SS BOND              : angle       3.11373 (    8)
  covalent geometry    : bond        0.00430 ( 6894)
  covalent geometry    : angle       0.80007 ( 9336)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1149 PHE cc_start: 0.8356 (m-80) cc_final: 0.8077 (m-80)
REVERT: A 1184 MET cc_start: 0.8323 (mmp) cc_final: 0.8058 (mmm)
REVERT: A 1186 TYR cc_start: 0.7952 (m-80) cc_final: 0.7667 (m-80)
REVERT: A 1271 ASP cc_start: 0.9372 (m-30) cc_final: 0.9034 (m-30)
REVERT: A 1275 ILE cc_start: 0.9520 (mm) cc_final: 0.8938 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1562
  time to fit residues: 11.4939
Evaluate side-chains
  52 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.244 
Evaluate side-chains
  70 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.6558 (mmp80) cc_final: 0.6268 (tpt170)
REVERT: B   32 LEU cc_start: 0.9510 (mt) cc_final: 0.9187 (mt)
REVERT: B   73 LEU cc_start: 0.9038 (mt) cc_final: 0.8574 (pp)
REVERT: B   98 MET cc_start: 0.8985 (ttp) cc_final: 0.8702 (tmm)
REVERT: B  100 PHE cc_start: 0.9042 (m-80) cc_final: 0.8842 (m-80)
REVERT: B  180 MET cc_start: 0.7848 (ttp) cc_final: 0.7125 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1011
  time to fit residues: 7.8478
Evaluate side-chains
  51 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:   30.0000
   chunk 61 optimal weight:    8.9990
   chunk 23 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    0.3980
   overall best weight:    1.3986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.077464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.060334 restraints weight = 27637.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.063300 restraints weight = 12382.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.065469 restraints weight = 7381.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.108700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.092942 restraints weight = 4748.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.095387 restraints weight = 3446.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.097365 restraints weight = 2634.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.099   6898  Z= 0.338
  Angle     :  1.133  29.009   9344  Z= 0.569
  Chirality :  0.053   0.232   1074
  Planarity :  0.011   0.108   1160
  Dihedral  :  6.551  23.970    936
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 24.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  3.57 %
    Favored  : 95.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.25), residues: 846
  helix: -1.51 (0.21), residues: 368
  sheet: -3.23 (0.39), residues: 120
  loop : -2.50 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  29 
 HIS   0.002   0.000   HIS C1216 
 PHE   0.057   0.004   PHE C1165 
 TYR   0.140   0.007   TYR A1154 
 ARG   0.061   0.003   ARG A1163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05808 (  344)
  hydrogen bonds       : angle       6.62180 (  966)
  SS BOND              : bond        0.01659 (    4)
  SS BOND              : angle       1.64615 (    8)
  covalent geometry    : bond        0.00782 ( 6894)
  covalent geometry    : angle       1.13247 ( 9336)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 1149 PHE cc_start: 0.8190 (m-80) cc_final: 0.7986 (m-80)
REVERT: C 1164 MET cc_start: 0.8179 (ptt) cc_final: 0.7085 (pmm)
REVERT: C 1184 MET cc_start: 0.8442 (mmp) cc_final: 0.8134 (mmm)
REVERT: C 1186 TYR cc_start: 0.7996 (m-80) cc_final: 0.7718 (m-80)
REVERT: C 1225 PHE cc_start: 0.9041 (p90) cc_final: 0.8595 (p90)
REVERT: C 1407 PHE cc_start: 0.8568 (t80) cc_final: 0.8110 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1602
  time to fit residues: 10.2262
Evaluate side-chains
  48 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.264 
Evaluate side-chains
  66 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.6438 (mmt-90) cc_final: 0.5978 (tpt170)
REVERT: B   32 LEU cc_start: 0.9502 (mt) cc_final: 0.9252 (mt)
REVERT: B   73 LEU cc_start: 0.9035 (mt) cc_final: 0.8590 (pp)
REVERT: B   98 MET cc_start: 0.9022 (ttp) cc_final: 0.8701 (tmm)
REVERT: B   99 PHE cc_start: 0.8905 (t80) cc_final: 0.8696 (t80)
REVERT: B  113 ILE cc_start: 0.9235 (mp) cc_final: 0.9024 (mp)
REVERT: B  133 MET cc_start: 0.9066 (mmm) cc_final: 0.8800 (mmm)
REVERT: B  141 LEU cc_start: 0.9316 (mt) cc_final: 0.9063 (mt)
REVERT: B  180 MET cc_start: 0.7840 (ttp) cc_final: 0.7159 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 65
  average time/residue: 0.1062
  time to fit residues: 7.9183
Evaluate side-chains
  48 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   chunk 54 optimal weight:    0.2980
   chunk 26 optimal weight:   10.0000
   chunk 25 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0060
   chunk 79 optimal weight:    7.9990
   chunk 41 optimal weight:   20.0000
   chunk 58 optimal weight:    0.3980
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.4198
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.076272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.058990 restraints weight = 30157.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.061815 restraints weight = 13493.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.063857 restraints weight = 8062.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.108706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.093270 restraints weight = 4626.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.095750 restraints weight = 3365.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.097715 restraints weight = 2585.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.4639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.097   6898  Z= 0.298
  Angle     :  1.095  20.700   9344  Z= 0.567
  Chirality :  0.056   0.256   1074
  Planarity :  0.011   0.102   1160
  Dihedral  :  6.540  25.303    936
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 23.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  3.85 %
    Favored  : 95.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.43 (0.25), residues: 846
  helix: -1.79 (0.21), residues: 368
  sheet: -2.89 (0.43), residues: 100
  loop : -2.50 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  29 
 HIS   0.002   0.000   HIS A1216 
 PHE   0.131   0.004   PHE C1165 
 TYR   0.130   0.006   TYR C1154 
 ARG   0.053   0.003   ARG A1163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05874 (  344)
  hydrogen bonds       : angle       6.56754 (  966)
  SS BOND              : bond        0.00342 (    4)
  SS BOND              : angle       3.62263 (    8)
  covalent geometry    : bond        0.00689 ( 6894)
  covalent geometry    : angle       1.09063 ( 9336)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 1164 MET cc_start: 0.8165 (ptt) cc_final: 0.7779 (pmm)
REVERT: C 1184 MET cc_start: 0.8506 (mmp) cc_final: 0.8233 (mmm)
REVERT: C 1186 TYR cc_start: 0.8029 (m-80) cc_final: 0.7722 (m-80)
REVERT: C 1225 PHE cc_start: 0.9029 (p90) cc_final: 0.8583 (p90)
REVERT: C 1407 PHE cc_start: 0.8569 (t80) cc_final: 0.8105 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1695
  time to fit residues: 11.1645
Evaluate side-chains
  44 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.237 
Evaluate side-chains
  67 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.6671 (mmt-90) cc_final: 0.6112 (tpt170)
REVERT: B   32 LEU cc_start: 0.9497 (mt) cc_final: 0.9162 (mt)
REVERT: B   73 LEU cc_start: 0.9049 (mt) cc_final: 0.8603 (pp)
REVERT: B   98 MET cc_start: 0.9020 (ttp) cc_final: 0.8691 (tmm)
REVERT: B   99 PHE cc_start: 0.8901 (t80) cc_final: 0.8681 (t80)
REVERT: B  133 MET cc_start: 0.9124 (mmm) cc_final: 0.8862 (mmm)
REVERT: B  141 LEU cc_start: 0.9330 (mt) cc_final: 0.9078 (mt)
REVERT: B  180 MET cc_start: 0.7875 (ttp) cc_final: 0.7265 (tpp)
  outliers start: 3
  outliers final: 1
  residues processed: 65
  average time/residue: 0.0914
  time to fit residues: 6.7910
Evaluate side-chains
  52 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz
    self.minimization_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs
    ncs_groups                  = ncs_groups)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine
    rms_angles_limit         = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine
    refine_sites                 = True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__
    ignore_line_search_failed_maxfev=True))
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients
    x=self.x)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients
    grad                   = g_data)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads
    compute_gradients = True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2442 > 50:
  distance: 0 - 1:   3.298
  distance: 1 - 2:   5.295
  distance: 2 - 3:   6.741
  distance: 2 - 4:   7.811
  distance: 4 - 5:   8.055
  distance: 5 - 6:  12.643
  distance: 5 - 8:   6.265
  distance: 6 - 7:  12.622
  distance: 6 - 13:  19.953
  distance: 8 - 9:  13.804
  distance: 9 - 10:   4.104
  distance: 10 - 11:   9.589
  distance: 11 - 12:   7.867
  distance: 13 - 14:  24.706
  distance: 14 - 15:  16.994
  distance: 15 - 16:  24.711
  distance: 15 - 17:  13.433
  distance: 17 - 18:  16.865
  distance: 18 - 19:  54.543
  distance: 18 - 21:  28.673
  distance: 19 - 20:  18.727
  distance: 19 - 25:  55.185
  distance: 21 - 22:  27.728
  distance: 22 - 23:  32.415
  distance: 22 - 24:  17.861
  distance: 25 - 26:  26.968
  distance: 26 - 27:   9.508
  distance: 26 - 29:  12.568
  distance: 27 - 28:   9.576
  distance: 27 - 31:   9.568
  distance: 29 - 30:  14.346
  distance: 31 - 32:   7.794
  distance: 33 - 34:  10.862
  distance: 33 - 35:  10.959
  distance: 35 - 36:  17.674
  distance: 36 - 37:  42.203
  distance: 36 - 39:  25.964
  distance: 37 - 38:  33.418
  distance: 37 - 44:  31.016
  distance: 39 - 40:  28.427
  distance: 40 - 41:  51.600
  distance: 41 - 42:  22.733
  distance: 42 - 43:  69.244
  distance: 44 - 45:  20.606
  distance: 45 - 46:  10.306
  distance: 45 - 48:  28.428
  distance: 46 - 47:   3.832
  distance: 46 - 49:  17.087
  distance: 49 - 50:  12.180
  distance: 50 - 51:  28.175
  distance: 50 - 53:  10.061
  distance: 51 - 52:  35.562
  distance: 51 - 57:  31.285
  distance: 53 - 54:   8.655
  distance: 54 - 55:   4.105
  distance: 54 - 56:   6.540
  distance: 57 - 58:  12.068
  distance: 58 - 59:  16.451
  distance: 58 - 61:   8.960
  distance: 59 - 60:  24.319
  distance: 61 - 62:  22.855
  distance: 61 - 63:  16.253