Starting phenix.real_space_refine
on Sat Aug 23 04:59:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6c14_7328/08_2025/6c14_7328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6c14_7328/08_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_7328/08_2025/6c14_7328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6c14_7328/08_2025/6c14_7328.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6c14_7328/08_2025/6c14_7328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6c14_7328/08_2025/6c14_7328.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.01, per 1000 atoms: 0.30
  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: 0.35
  Conformation dependent library (CDL) restraints added in 365.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.20
  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: 1.13

  Time building geometry restraints manager: 0.48 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: 0.01
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:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.670
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.140
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.013   0.001   ARG C1371 
 TYR   0.024   0.003   TYR D 148 
 PHE   0.031   0.003   PHE B 100 
 TRP   0.020   0.004   TRP D  49 
 HIS   0.007   0.002   HIS B  15 

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

*********************** 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  : 0.091 
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: 0.0715
  time to fit residues: 7.3820
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  : 0.050 
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  : 0.027 
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: 0.0349
  time to fit residues: 3.0530
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  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0010
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:    0.3980
   overall best weight:    1.2388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 1

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 = 0.3523 r_free = 0.3523 target = 0.079546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.062073 restraints weight = 20861.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.064722 restraints weight = 11263.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.066722 restraints weight = 7387.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.068254 restraints weight = 5350.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.069422 restraints weight = 4152.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.111787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.095707 restraints weight = 4712.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.097993 restraints weight = 3369.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.099946 restraints weight = 2599.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.101434 restraints weight = 2062.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.102774 restraints weight = 1677.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6898  Z= 0.192
  Angle     :  0.793   9.081   9344  Z= 0.427
  Chirality :  0.049   0.183   1074
  Planarity :  0.006   0.047   1160
  Dihedral  :  6.311  23.502    936
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  1.37 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.34 (0.26), residues: 846
  helix: -1.33 (0.23), residues: 368
  sheet: -3.34 (0.35), residues: 142
  loop : -2.54 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C1219 
 TYR   0.022   0.003   TYR C1308 
 PHE   0.045   0.002   PHE D 100 
 TRP   0.009   0.002   TRP B  29 
 HIS   0.002   0.000   HIS C1216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6894)
  covalent geometry    : angle       0.78724 ( 9336)
  SS BOND              : bond        0.01845 (    4)
  SS BOND              : angle       3.31986 (    8)
  hydrogen bonds       : bond        0.05592 (  344)
  hydrogen bonds       : angle       6.42064 (  966)

*********************** 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
  66 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1149 PHE cc_start: 0.8255 (m-80) cc_final: 0.7955 (m-80)
REVERT: A 1184 MET cc_start: 0.8428 (mmp) cc_final: 0.8114 (mmm)
REVERT: A 1186 TYR cc_start: 0.7965 (m-80) cc_final: 0.7662 (m-80)
REVERT: A 1203 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8455 (tm-30)
REVERT: A 1267 LYS cc_start: 0.9527 (tttt) cc_final: 0.9311 (ttpp)
REVERT: A 1271 ASP cc_start: 0.9381 (m-30) cc_final: 0.9044 (m-30)
REVERT: A 1275 ILE cc_start: 0.9472 (mm) cc_final: 0.8894 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0639
  time to fit residues: 4.7718
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  : 0.086 
Evaluate side-chains
  72 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.045 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.6466 (mmp80) cc_final: 0.6130 (tpt170)
REVERT: B   32 LEU cc_start: 0.9485 (mt) cc_final: 0.9181 (mm)
REVERT: B   98 MET cc_start: 0.8945 (ttp) cc_final: 0.8681 (tmm)
REVERT: B  180 MET cc_start: 0.7867 (ttp) cc_final: 0.7164 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0389
  time to fit residues: 3.1426
Evaluate side-chains
  49 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0870
   chunk 65 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 72 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0070
   chunk 5 optimal weight:   20.0000
   chunk 39 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.1780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C1299 HIS

Total number of N/Q/H flips: 1

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 = 0.3535 r_free = 0.3535 target = 0.080023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.063403 restraints weight = 19065.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.066046 restraints weight = 9851.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.068007 restraints weight = 6297.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.069474 restraints weight = 4492.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.070584 restraints weight = 3466.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.109537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.093422 restraints weight = 4719.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.095841 restraints weight = 3326.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.098045 restraints weight = 2558.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.099619 restraints weight = 2018.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.101115 restraints weight = 1647.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3370
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.106   6898  Z= 0.276
  Angle     :  1.012  13.500   9344  Z= 0.537
  Chirality :  0.055   0.271   1074
  Planarity :  0.011   0.116   1160
  Dihedral  :  6.528  23.570    936
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 20.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.26), residues: 846
  helix: -1.45 (0.22), residues: 368
  sheet: -2.88 (0.42), residues: 120
  loop : -2.47 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.056   0.003   ARG A1163 
 TYR   0.133   0.006   TYR A1154 
 PHE   0.084   0.004   PHE C1165 
 TRP   0.024   0.002   TRP D  29 
 HIS   0.017   0.002   HIS A1299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 6894)
  covalent geometry    : angle       1.00843 ( 9336)
  SS BOND              : bond        0.00471 (    4)
  SS BOND              : angle       3.05208 (    8)
  hydrogen bonds       : bond        0.05884 (  344)
  hydrogen bonds       : angle       6.38886 (  966)

*********************** 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
  58 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 1149 PHE cc_start: 0.8064 (m-80) cc_final: 0.7851 (m-80)
REVERT: C 1160 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7125 (mm-30)
REVERT: C 1164 MET cc_start: 0.7949 (ptt) cc_final: 0.7619 (ppp)
REVERT: C 1184 MET cc_start: 0.8487 (mmp) cc_final: 0.8195 (mmm)
REVERT: C 1186 TYR cc_start: 0.7913 (m-80) cc_final: 0.7619 (m-80)
REVERT: C 1225 PHE cc_start: 0.8972 (p90) cc_final: 0.8522 (p90)
REVERT: C 1407 PHE cc_start: 0.8558 (t80) cc_final: 0.8114 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0661
  time to fit residues: 4.3686
Evaluate side-chains
  47 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.086 
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  : 0.046 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.6547 (mmt-90) cc_final: 0.6089 (tpt170)
REVERT: B   32 LEU cc_start: 0.9488 (mt) cc_final: 0.9149 (mt)
REVERT: B   73 LEU cc_start: 0.9031 (mt) cc_final: 0.8550 (pp)
REVERT: B   98 MET cc_start: 0.8959 (ttp) cc_final: 0.8665 (tmm)
REVERT: B   99 PHE cc_start: 0.8882 (t80) cc_final: 0.8643 (t80)
REVERT: B  113 ILE cc_start: 0.9206 (mp) cc_final: 0.8987 (mp)
REVERT: B  133 MET cc_start: 0.9117 (mmm) cc_final: 0.8877 (mmm)
REVERT: B  180 MET cc_start: 0.7883 (ttp) cc_final: 0.7209 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 65
  average time/residue: 0.0347
  time to fit residues: 2.5975
Evaluate side-chains
  50 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 51 optimal weight:    0.0060
   chunk 66 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    0.3980
   chunk 58 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0060
   chunk 52 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    0.3612
-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.078754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.063192 restraints weight = 18247.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.065692 restraints weight = 10088.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.067475 restraints weight = 6590.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.068818 restraints weight = 4792.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.069824 restraints weight = 3726.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.109341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.093842 restraints weight = 4541.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.096382 restraints weight = 3268.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.098224 restraints weight = 2492.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.099766 restraints weight = 1994.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.100809 restraints weight = 1623.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.042   2.366   6898  Z= 2.082
  Angle     :  1.290  41.119   9344  Z= 0.658
  Chirality :  0.055   0.271   1074
  Planarity :  0.011   0.116   1160
  Dihedral  :  6.528  23.570    936
  Min Nonbonded Distance : 0.789

Molprobity Statistics.
  All-atom Clashscore : 39.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.26), residues: 846
  helix: -1.45 (0.22), residues: 368
  sheet: -2.88 (0.42), residues: 120
  loop : -2.47 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.056   0.003   ARG C1163 
 TYR   0.133   0.006   TYR A1154 
 PHE   0.084   0.004   PHE A1165 
 TRP   0.024   0.002   TRP D  29 
 HIS   0.017   0.002   HIS A1299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 6894)
  covalent geometry    : angle       1.00822 ( 9336)
  SS BOND              : bond        1.71428 (    4)
  SS BOND              : angle      27.52410 (    8)
  hydrogen bonds       : bond        0.05884 (  344)
  hydrogen bonds       : angle       6.38897 (  966)

*********************** 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
  58 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C 1160 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7175 (mm-30)
REVERT: C 1164 MET cc_start: 0.7195 (ptt) cc_final: 0.6667 (ppp)
REVERT: C 1184 MET cc_start: 0.8564 (mmp) cc_final: 0.8211 (mmm)
REVERT: C 1186 TYR cc_start: 0.7945 (m-80) cc_final: 0.7648 (m-80)
REVERT: C 1407 PHE cc_start: 0.8512 (t80) cc_final: 0.8106 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0572
  time to fit residues: 3.8069
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  : 0.049 
Evaluate side-chains
  61 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.027 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.6575 (mmt-90) cc_final: 0.6109 (tpt170)
REVERT: B   32 LEU cc_start: 0.9438 (mt) cc_final: 0.9188 (mt)
REVERT: B   73 LEU cc_start: 0.9053 (mt) cc_final: 0.8569 (pp)
REVERT: B   98 MET cc_start: 0.8954 (ttp) cc_final: 0.8654 (tmm)
REVERT: B   99 PHE cc_start: 0.8862 (t80) cc_final: 0.8651 (t80)
REVERT: B  113 ILE cc_start: 0.9142 (mp) cc_final: 0.8881 (mp)
REVERT: B  133 MET cc_start: 0.9031 (mmm) cc_final: 0.8779 (mmm)
REVERT: B  180 MET cc_start: 0.7875 (ttp) cc_final: 0.7195 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0337
  time to fit residues: 2.3807
Evaluate side-chains
  50 residues out of total 134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz
    self.minimization_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs
    weight = real_space_weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine
    minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__
    minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients
    t,g = self.target_and_grads_object.target_and_gradients(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients
    t_restraints, g_restraints = restraints_target_and_grads(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads
    ef = restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5307 > 50:
  distance: 0 - 1:  30.105
  distance: 1 - 2:  12.788
  distance: 1 - 4:  25.854
  distance: 2 - 3:  20.701
  distance: 2 - 8:  32.601
  distance: 4 - 5:  20.449
  distance: 5 - 6:  24.559
  distance: 5 - 7:  22.019
  distance: 8 - 9:  21.493
  distance: 9 - 10:  29.274
  distance: 9 - 12:  16.742
  distance: 10 - 11:  19.486
  distance: 10 - 15:  23.327
  distance: 12 - 13:  48.642
  distance: 12 - 14:  47.928
  distance: 15 - 18:  24.854
  distance: 15 - 21:  29.185
  distance: 16 - 17:  28.192
  distance: 16 - 18:  12.049
  distance: 16 - 21:  12.959
  distance: 16 - 24:  33.561
  distance: 18 - 19:  30.642
  distance: 19 - 20:  26.162
  distance: 21 - 22:  36.123
  distance: 22 - 23:  31.209
  distance: 24 - 25:  30.321
  distance: 25 - 26:  20.520
  distance: 25 - 28:  21.071
  distance: 26 - 27:  18.793
  distance: 26 - 31:  13.532
  distance: 28 - 29:  21.381
  distance: 28 - 30:  33.354
  distance: 31 - 32:   9.406
  distance: 32 - 33:  16.907
  distance: 32 - 35:   9.233
  distance: 33 - 34:  20.551
  distance: 33 - 38:  19.019
  distance: 35 - 36:  18.062
  distance: 35 - 37:  18.187
  distance: 38 - 39:  17.760
  distance: 39 - 40:  18.260
  distance: 39 - 42:  27.645
  distance: 40 - 41:  46.217
  distance: 41 - 63:  29.244
  distance: 42 - 43:  31.884
  distance: 43 - 44:  12.618
  distance: 43 - 45:  19.350
  distance: 46 - 47:  20.810
  distance: 47 - 48:   5.084
  distance: 47 - 50:  18.550
  distance: 48 - 49:  11.322
  distance: 48 - 55:  14.564
  distance: 49 - 71:  13.196
  distance: 50 - 51:   9.323
  distance: 51 - 52:  10.658
  distance: 52 - 53:  20.356
  distance: 52 - 54:  16.190
  distance: 55 - 56:  44.150
  distance: 56 - 57:  20.690
  distance: 56 - 59:  16.342
  distance: 57 - 58:  16.383
  distance: 57 - 63:   5.924
  distance: 59 - 60:  11.674
  distance: 60 - 61:  19.548
  distance: 60 - 62:  17.266
  distance: 63 - 64:   8.239
  distance: 64 - 65:   6.135
  distance: 64 - 67:  13.075
  distance: 65 - 66:  10.276
  distance: 65 - 71:  18.438
  distance: 67 - 68:  10.295
  distance: 68 - 69:  13.816
  distance: 68 - 70:   6.042
  distance: 71 - 72:  10.655
  distance: 72 - 73:   5.814
  distance: 72 - 75:   9.685
  distance: 73 - 74:   8.625
  distance: 75 - 76:   4.384
  distance: 76 - 77:  13.764
  distance: 77 - 78:  12.215