Starting phenix.real_space_refine
on Mon Jan 13 20:44:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6q_35203/01_2025/8i6q_35203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6q_35203/01_2025/8i6q_35203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i6q_35203/01_2025/8i6q_35203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6q_35203/01_2025/8i6q_35203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6q_35203/01_2025/8i6q_35203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6q_35203/01_2025/8i6q_35203.cif"
  }
  resolution = 4.23
  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=  -0.001 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    2354      2.51       5
     N     810      2.21       5
     O     811      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3975
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 884
          Classifications: {'peptide': 181}
          Incomplete info: {'truncation_to_alanine': 148}
          Link IDs: {'PTRANS': 4, 'TRANS': 176}
          Chain breaks: 2
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 551
          Unresolved non-hydrogen angles: 724
          Unresolved non-hydrogen dihedrals: 456
          Unresolved non-hydrogen chiralities: 73
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 276
    Chain: "B"
      Number of atoms: 1090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1090
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 184}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 659
          Unresolved non-hydrogen angles: 837
          Unresolved non-hydrogen dihedrals: 522
          Unresolved non-hydrogen chiralities: 74
          Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 8, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 341
    Chain: "C"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 904
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 153}
          Link IDs: {'PTRANS': 4, 'TRANS': 180}
          Chain breaks: 2
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 566
          Unresolved non-hydrogen angles: 742
          Unresolved non-hydrogen dihedrals: 468
          Unresolved non-hydrogen chiralities: 74
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 8, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 285
    Chain: "D"
      Number of atoms: 1097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1097
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 183}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 651
          Unresolved non-hydrogen angles: 826
          Unresolved non-hydrogen dihedrals: 514
          Unresolved non-hydrogen chiralities: 74
          Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 8, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 334
  Time building chain proxies: 3.82, per 1000 atoms: 0.96
  Number of scatterers: 3975
  At special positions: 0
  Unit cell: (81.51, 76.362, 120.978, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     811      8.00
     N     810      7.00
     C    2354      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.33
  Conformation dependent library (CDL) restraints added in 686.5 milliseconds
  

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1456

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 3 sheets defined
      64.3% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 54
    Processing helix  chain 'A' and resid 55 through 78
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 190 through 194
      removed outlier: 3.509A  pdb=" N   TRP A 193 " --> pdb=" O   ASP A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 196
      No H-bonds generated for 'chain 'A' and resid 195 through 196'
    Processing helix  chain 'A' and resid 197 through 206
      removed outlier: 3.754A  pdb=" N   LEU A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LYS A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ARG A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 233
      removed outlier: 4.248A  pdb=" N   ILE A 213 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 245
    Processing helix  chain 'A' and resid 247 through 283
      Proline residue:  A 254  - end of helix
      removed outlier: 3.649A  pdb=" N   MET A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR A 262 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA A 272 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ALA A 275 " --> pdb=" O   TRP A 271 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   TRP A 280 " --> pdb=" O   TYR A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 333
      removed outlier: 4.128A  pdb=" N   THR A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ALA A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 49
    Processing helix  chain 'B' and resid 72 through 79
      removed outlier: 4.011A  pdb=" N   PHE B  76 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 101
    Processing helix  chain 'B' and resid 101 through 108
      removed outlier: 3.514A  pdb=" N   GLN B 105 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 125
      removed outlier: 4.231A  pdb=" N   ARG B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 153
    Processing helix  chain 'B' and resid 169 through 186
    Processing helix  chain 'B' and resid 197 through 203
      removed outlier: 4.020A  pdb=" N   ARG B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 54
    Processing helix  chain 'C' and resid 57 through 87
      Proline residue:  C  73  - end of helix
      removed outlier: 4.532A  pdb=" N   LEU C  76 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER C  77 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ASN C  81 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY C  87 " --> pdb=" O   VAL C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 200
    Processing helix  chain 'C' and resid 202 through 233
      removed outlier: 4.312A  pdb=" N   ARG C 206 " --> pdb=" O   LYS C 202 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   PHE C 207 " --> pdb=" O   LEU C 203 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU C 211 " --> pdb=" O   PHE C 207 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE C 213 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU C 215 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU C 217 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR C 218 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 245
    Processing helix  chain 'C' and resid 247 through 283
      Proline residue:  C 254  - end of helix
      removed outlier: 3.882A  pdb=" N   MET C 258 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ALA C 275 " --> pdb=" O   TRP C 271 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR C 276 " --> pdb=" O   ALA C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 309
    Processing helix  chain 'C' and resid 310 through 330
      removed outlier: 5.363A  pdb=" N   ALA C 321 " --> pdb=" O   GLY C 317 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   TRP C 322 " --> pdb=" O   TRP C 318 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA C 326 " --> pdb=" O   TRP C 322 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ARG C 327 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 49
    Processing helix  chain 'D' and resid 72 through 81
      removed outlier: 4.431A  pdb=" N   PHE D  76 " --> pdb=" O   ALA D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 108
      Proline residue:  D 103  - end of helix
    Processing helix  chain 'D' and resid 110 through 125
      removed outlier: 4.097A  pdb=" N   ARG D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 138
    Processing helix  chain 'D' and resid 139 through 153
    Processing helix  chain 'D' and resid 169 through 186
    Processing helix  chain 'D' and resid 197 through 203
      removed outlier: 3.518A  pdb=" N   MET D 203 " --> pdb=" O   LEU D 199 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 25
      removed outlier: 5.130A  pdb=" N   PHE B   4 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU B  60 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLN B   6 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 159
      removed outlier: 3.502A  pdb=" N   LEU B 191 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LEU B  31 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   SER B 194 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL B  33 " --> pdb=" O   SER B 194 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU B 208 " --> pdb=" O   PHE B  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 9 through 11
      removed outlier: 5.823A  pdb=" N   LYS D   9 " --> pdb=" O   GLY D  17 " (cutoff:3.500A)

    352 hydrogen bonds defined for protein.
    1032 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: 1.08

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 810
        1.29 -     1.36: 802
        1.36 -     1.42: 7
        1.42 -     1.48: 810
        1.48 -     1.55: 1539
  Bond restraints: 3968
  Sorted by residual:
  bond pdb=" N   GLN B 142 "
       pdb=" CA  GLN B 142 "
    ideal  model  delta    sigma   weight residual
    1.459  1.433  0.026 1.21e-02 6.83e+03 4.53e+00
  bond pdb=" CA  GLN B 155 "
       pdb=" C   GLN B 155 "
    ideal  model  delta    sigma   weight residual
    1.531  1.517  0.014 7.40e-03 1.83e+04 3.68e+00
  bond pdb=" CA  GLY C 249 "
       pdb=" C   GLY C 249 "
    ideal  model  delta    sigma   weight residual
    1.516  1.500  0.016 1.12e-02 7.97e+03 2.12e+00
  bond pdb=" C   GLU D 163 "
       pdb=" N   PRO D 164 "
    ideal  model  delta    sigma   weight residual
    1.334  1.301  0.033 2.34e-02 1.83e+03 1.98e+00
  bond pdb=" C   GLN D 155 "
       pdb=" O   GLN D 155 "
    ideal  model  delta    sigma   weight residual
    1.235  1.228  0.006 4.70e-03 4.53e+04 1.91e+00
  ... (remaining 3963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 5178
        1.35 -     2.71: 266
        2.71 -     4.06: 36
        4.06 -     5.41: 9
        5.41 -     6.76: 4
  Bond angle restraints: 5493
  Sorted by residual:
  angle pdb=" C   THR B  55 "
        pdb=" CA  THR B  55 "
        pdb=" CB  THR B  55 "
      ideal   model   delta    sigma   weight residual
     116.54  110.07    6.47 1.15e+00 7.56e-01 3.16e+01
  angle pdb=" N   GLY B  57 "
        pdb=" CA  GLY B  57 "
        pdb=" C   GLY B  57 "
      ideal   model   delta    sigma   weight residual
     111.85  116.48   -4.63 1.06e+00 8.90e-01 1.91e+01
  angle pdb=" CA  TYR D  11 "
        pdb=" CB  TYR D  11 "
        pdb=" CG  TYR D  11 "
      ideal   model   delta    sigma   weight residual
     113.90  119.62   -5.72 1.80e+00 3.09e-01 1.01e+01
  angle pdb=" C   GLY C 245 "
        pdb=" N   GLY C 246 "
        pdb=" CA  GLY C 246 "
      ideal   model   delta    sigma   weight residual
     121.32  116.43    4.89 1.58e+00 4.01e-01 9.56e+00
  angle pdb=" N   GLU B 132 "
        pdb=" CA  GLU B 132 "
        pdb=" C   GLU B 132 "
      ideal   model   delta    sigma   weight residual
     111.36  114.66   -3.30 1.09e+00 8.42e-01 9.15e+00
  ... (remaining 5488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.91: 2043
        5.91 -    11.82: 172
       11.82 -    17.73: 35
       17.73 -    23.64: 8
       23.64 -    29.55: 3
  Dihedral angle restraints: 2261
    sinusoidal: 2
      harmonic: 2259
  Sorted by residual:
  dihedral pdb=" CA  ARG D  10 "
           pdb=" C   ARG D  10 "
           pdb=" N   TYR D  11 "
           pdb=" CA  TYR D  11 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.45   29.55     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  ARG D 185 "
           pdb=" C   ARG D 185 "
           pdb=" N   LEU D 186 "
           pdb=" CA  LEU D 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.06   27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  ARG B 185 "
           pdb=" C   ARG B 185 "
           pdb=" N   LEU B 186 "
           pdb=" CA  LEU B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.60   27.40     0      5.00e+00 4.00e-02 3.00e+01
  ... (remaining 2258 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 437
       0.026 -    0.053: 143
       0.053 -    0.079: 102
       0.079 -    0.106: 39
       0.106 -    0.132: 7
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  PRO D 170 "
            pdb=" N   PRO D 170 "
            pdb=" C   PRO D 170 "
            pdb=" CB  PRO D 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE D  30 "
            pdb=" N   ILE D  30 "
            pdb=" C   ILE D  30 "
            pdb=" CB  ILE D  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.35e-01
  chirality pdb=" CA  VAL C 301 "
            pdb=" N   VAL C 301 "
            pdb=" C   VAL C 301 "
            pdb=" CB  VAL C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.30e-01
  ... (remaining 725 not shown)

  Planarity restraints: 803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  11 "    0.016 2.00e-02 2.50e+03   1.30e-02 3.39e+00
        pdb=" CG  TYR D  11 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  11 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  11 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  11 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  11 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  11 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D  11 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  21 "    0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   VAL B  21 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   VAL B  21 "    0.011 2.00e-02 2.50e+03
        pdb=" N   SER B  22 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 122 "    0.008 2.00e-02 2.50e+03   1.58e-02 2.49e+00
        pdb=" C   LEU D 122 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   LEU D 122 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLU D 123 "    0.009 2.00e-02 2.50e+03
  ... (remaining 800 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 44
        2.60 -     3.18: 4580
        3.18 -     3.75: 6332
        3.75 -     4.33: 7457
        4.33 -     4.90: 10306
  Nonbonded interactions: 28719
  Sorted by model distance:
  nonbonded pdb=" O   HIS C  55 "
            pdb=" N   SER C  59 "
     model   vdw
     2.031 3.120
  nonbonded pdb=" O   ILE D   2 "
            pdb=" N   VAL D  25 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   LEU A  70 "
            pdb=" N   MET A  74 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" N   HIS B  19 "
            pdb=" O   GLY B 213 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" N   GLN D   6 "
            pdb=" O   VAL D  21 "
     model   vdw
     2.332 3.120
  ... (remaining 28714 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 35 through 283 or resid 298 through 332))
  selection = (chain 'C' and (resid 35 through 83 or resid 190 through 283 or resid 298 throug \ 
h 332))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and ((resid 1 through 13 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 14 through 222))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.240
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
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   0.033   3968  Z= 0.374
  Angle     :  0.734   6.764   5493  Z= 0.518
  Chirality :  0.040   0.132    728
  Planarity :  0.004   0.017    803
  Dihedral  :  6.123  29.547    805
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.30 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.63 (0.28), residues: 794
  helix: -0.21 (0.23), residues: 449
  sheet: -2.80 (0.88), residues: 34
  loop : -2.13 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 193 
 PHE   0.000   0.000   PHE A  53 
 TYR   0.031   0.004   TYR D  11 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.453 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0403
  time to fit residues: 1.9436
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0370
   chunk 33 optimal weight:   20.0000
   chunk 20 optimal weight:   50.0000
   chunk 40 optimal weight:   20.0000
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:   50.0000
   chunk 38 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    3.5864

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.034992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.027623 restraints weight = 62398.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.027711 restraints weight = 58238.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.027814 restraints weight = 54991.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   3968  Z= 0.159
  Angle     :  0.478   6.568   5493  Z= 0.305
  Chirality :  0.039   0.128    728
  Planarity :  0.003   0.013    803
  Dihedral  :  5.064  25.824    803
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.32 (0.30), residues: 794
  helix:  1.00 (0.23), residues: 490
  sheet: -2.66 (0.86), residues: 34
  loop : -2.18 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 193 
 PHE   0.000   0.000   PHE A  53 
 TYR   0.012   0.001   TYR D  11 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.429 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0365
  time to fit residues: 1.8175
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:   50.0000
   chunk 13 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 49 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 69 optimal weight:   20.0000
   chunk 18 optimal weight:   50.0000
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    8.1992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.034449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.027283 restraints weight = 64040.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.027429 restraints weight = 58327.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.027513 restraints weight = 53847.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3968  Z= 0.279
  Angle     :  0.548   6.902   5493  Z= 0.363
  Chirality :  0.040   0.134    728
  Planarity :  0.003   0.012    803
  Dihedral  :  5.074  24.949    803
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.06 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 100.00 %
    Favored  :  0.00 %
  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: -0.83 (0.29), residues: 794
  helix:  0.53 (0.22), residues: 488
  sheet: -2.81 (0.81), residues: 46
  loop : -2.15 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 193 
 PHE   0.000   0.000   PHE A  53 
 TYR   0.014   0.002   TYR D  11 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.461 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0346
  time to fit residues: 1.7956
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0040
   chunk 62 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 68 optimal weight:    8.9990
   chunk 42 optimal weight:   30.0000
   chunk 66 optimal weight:    0.0030
   chunk 43 optimal weight:   10.0000
   chunk 70 optimal weight:   20.0000
   chunk 74 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7604

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.035290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.027692 restraints weight = 61466.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.027839 restraints weight = 56160.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.027930 restraints weight = 52298.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.012   3968  Z= 0.085
  Angle     :  0.382   5.241   5493  Z= 0.236
  Chirality :  0.039   0.131    728
  Planarity :  0.002   0.011    803
  Dihedral  :  4.142  22.712    803
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.90 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.00 (0.32), residues: 794
  helix:  2.22 (0.24), residues: 492
  sheet: -2.30 (0.76), residues: 52
  loop : -1.98 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 193 
 PHE   0.000   0.000   PHE A  53 
 TYR   0.027   0.003   TYR D  11 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.452 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0376
  time to fit residues: 1.9239
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 23 optimal weight:    0.0010
   chunk 54 optimal weight:   40.0000
   chunk 63 optimal weight:   20.0000
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:   30.0000
   chunk 60 optimal weight:   50.0000
   chunk 76 optimal weight:    0.8980
   chunk 36 optimal weight:   20.0000
   chunk 26 optimal weight:    0.2980
   chunk 73 optimal weight:    8.9990
   overall best weight:    2.6390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.035065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.027545 restraints weight = 63538.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.027693 restraints weight = 57789.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.027780 restraints weight = 53694.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.009   3968  Z= 0.101
  Angle     :  0.369   5.064   5493  Z= 0.232
  Chirality :  0.039   0.123    728
  Planarity :  0.002   0.007    803
  Dihedral  :  3.847  22.710    803
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.28 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.37 (0.32), residues: 794
  helix:  2.53 (0.24), residues: 493
  sheet: -2.25 (0.76), residues: 52
  loop : -1.87 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 193 
 PHE   0.000   0.000   PHE A  53 
 TYR   0.018   0.002   TYR D  11 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.446 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0375
  time to fit residues: 1.8649
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    0.0470
   chunk 25 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 3 optimal weight:   30.0000
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 45 optimal weight:   30.0000
   chunk 10 optimal weight:   10.0000
   overall best weight:    4.6086

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.034823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.027542 restraints weight = 64236.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.027666 restraints weight = 59419.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.027729 restraints weight = 55901.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3968  Z= 0.160
  Angle     :  0.413   5.558   5493  Z= 0.268
  Chirality :  0.039   0.123    728
  Planarity :  0.002   0.008    803
  Dihedral  :  3.982  22.996    803
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.79 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.29 (0.32), residues: 794
  helix:  2.48 (0.23), residues: 491
  sheet: -2.19 (0.84), residues: 43
  loop : -1.93 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 193 
 PHE   0.000   0.000   PHE A  53 
 TYR   0.018   0.002   TYR D  11 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.469 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0387
  time to fit residues: 1.8964
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:   40.0000
   chunk 71 optimal weight:   30.0000
   chunk 51 optimal weight:   40.0000
   chunk 18 optimal weight:   50.0000
   chunk 62 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 41 optimal weight:   30.0000
   chunk 53 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    6.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.034865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.027520 restraints weight = 64895.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.027669 restraints weight = 59019.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.027797 restraints weight = 53298.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3968  Z= 0.222
  Angle     :  0.470   6.292   5493  Z= 0.309
  Chirality :  0.039   0.129    728
  Planarity :  0.002   0.011    803
  Dihedral  :  4.339  23.390    803
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.05 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.75 (0.31), residues: 794
  helix:  2.01 (0.23), residues: 490
  sheet: -2.83 (0.86), residues: 34
  loop : -2.01 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 193 
 PHE   0.000   0.000   PHE A  53 
 TYR   0.019   0.002   TYR D  11 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.434 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0386
  time to fit residues: 1.9839
Evaluate side-chains
  18 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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: 54.7229 > 50:
  distance: 2 - 17:  19.505
  distance: 6 - 22:  24.693
  distance: 14 - 17:  18.093
  distance: 17 - 18:  10.955
  distance: 18 - 19:  22.032
  distance: 18 - 21:  36.030
  distance: 19 - 20:   5.315
  distance: 19 - 22:  25.151
  distance: 22 - 23:  22.660
  distance: 23 - 24:  34.753
  distance: 23 - 26:  22.050
  distance: 24 - 25:   5.339
  distance: 24 - 27:  11.476
  distance: 27 - 28:   7.453
  distance: 28 - 29:  28.798
  distance: 29 - 30:  36.775
  distance: 29 - 31:   7.777
  distance: 31 - 32:  28.238
  distance: 32 - 33:  26.032
  distance: 32 - 35:  38.505
  distance: 33 - 34:  24.226
  distance: 36 - 37:  36.619
  distance: 37 - 38:  10.847
  distance: 37 - 40:  28.926
  distance: 38 - 39:  11.329
  distance: 38 - 41:  23.031
  distance: 41 - 42:  19.862
  distance: 42 - 43:  31.363
  distance: 42 - 45:  19.975
  distance: 43 - 44:  21.835
  distance: 43 - 46:  29.073
  distance: 46 - 47:  21.754
  distance: 47 - 48:  31.235
  distance: 47 - 50:  27.124
  distance: 48 - 49:  41.674
  distance: 48 - 51:  29.168
  distance: 51 - 52:  13.039
  distance: 52 - 53:   5.167
  distance: 52 - 55:  19.412
  distance: 53 - 54:  23.770
  distance: 53 - 56:  15.888
  distance: 56 - 57:  13.820
  distance: 57 - 58:   3.542
  distance: 57 - 60:  37.414
  distance: 58 - 59:  10.179
  distance: 58 - 61:  14.184
  distance: 61 - 62:  31.787
  distance: 62 - 63:  54.723
  distance: 62 - 65:  12.827
  distance: 63 - 64:  32.682
  distance: 63 - 66:  34.708