Starting phenix.real_space_refine
on Wed Mar  5 23:08:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6q_35203/03_2025/8i6q_35203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6q_35203/03_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_35203/03_2025/8i6q_35203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6q_35203/03_2025/8i6q_35203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6q_35203/03_2025/8i6q_35203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6q_35203/03_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-5624/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: 3.59, per 1000 atoms: 0.90
  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: 1.34
  Conformation dependent library (CDL) restraints added in 726.5 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: 0.43
  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: 1.04

  Time building geometry restraints manager: 1.52 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:             2.010
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.170
  Find NCS groups from input model:        0.160
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.300
-------------------------------------------------------------------------------
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  : 0.467 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0421
  time to fit residues: 2.0060
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  : 0.464 
-------------------------------------------------------------------------------
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:    1.9990
   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:    3.8066

-------------------------------------------------------------------------------
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 = 0.2938 r_free = 0.2938 target = 0.034930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027587 restraints weight = 62595.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.027675 restraints weight = 58376.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.027779 restraints weight = 55043.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   3968  Z= 0.163
  Angle     :  0.480   6.729   5493  Z= 0.307
  Chirality :  0.039   0.130    728
  Planarity :  0.003   0.012    803
  Dihedral  :  5.089  25.836    803
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.53 %
    Favored  : 95.34 %
  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: -0.41 (0.30), residues: 794
  helix:  0.91 (0.23), residues: 491
  sheet: -2.69 (0.86), residues: 34
  loop : -2.18 (0.36), residues: 269

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  : 0.420 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0363
  time to fit residues: 1.8026
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  : 0.423 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 24 optimal weight:   50.0000
   chunk 13 optimal weight:   20.0000
   chunk 66 optimal weight:    8.9990
   chunk 9 optimal weight:   20.0000
   chunk 49 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   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 = 0.2925 r_free = 0.2925 target = 0.034406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.027270 restraints weight = 63908.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.027380 restraints weight = 58712.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.027514 restraints weight = 54924.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3968  Z= 0.272
  Angle     :  0.542   7.166   5493  Z= 0.359
  Chirality :  0.040   0.135    728
  Planarity :  0.003   0.012    803
  Dihedral  :  5.103  24.907    803
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.81 %
    Favored  : 92.07 %
  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: -0.84 (0.29), residues: 794
  helix:  0.54 (0.22), residues: 488
  sheet: -2.80 (0.81), residues: 46
  loop : -2.18 (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   0.013   0.001   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  : 0.450 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0692
  time to fit residues: 2.9728
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  : 0.459 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0870
   chunk 68 optimal weight:    6.9990
   chunk 42 optimal weight:   30.0000
   chunk 66 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 70 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    3.7564

-------------------------------------------------------------------------------
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 = 0.2766 r_free = 0.2766 target = 0.033251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.025177 restraints weight = 70817.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.025177 restraints weight = 68635.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.025177 restraints weight = 68635.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.2494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   3968  Z= 0.135
  Angle     :  0.418   6.396   5493  Z= 0.264
  Chirality :  0.039   0.133    728
  Planarity :  0.002   0.010    803
  Dihedral  :  4.442  24.500    803
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.91 %
    Favored  : 94.96 %
  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:  0.28 (0.31), residues: 794
  helix:  1.57 (0.23), residues: 491
  sheet: -2.29 (0.84), residues: 43
  loop : -2.17 (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   0.025   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  : 0.471 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0394
  time to fit residues: 1.9801
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  : 0.474 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 23 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:   30.0000
   chunk 60 optimal weight:    0.8980
   chunk 76 optimal weight:    0.3980
   chunk 36 optimal weight:    0.7980
   chunk 26 optimal weight:   40.0000
   chunk 73 optimal weight:    9.9990
   overall best weight:    3.0184

-------------------------------------------------------------------------------
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 = 0.2822 r_free = 0.2822 target = 0.034433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.028235 restraints weight = 83500.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.028341 restraints weight = 75229.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.028437 restraints weight = 69059.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   3968  Z= 0.114
  Angle     :  0.383   5.724   5493  Z= 0.242
  Chirality :  0.039   0.128    728
  Planarity :  0.002   0.008    803
  Dihedral  :  3.902  23.073    803
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.42 %
    Favored  : 94.46 %
  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:  1.11 (0.32), residues: 794
  helix:  2.37 (0.24), residues: 491
  sheet: -2.30 (0.76), residues: 52
  loop : -2.06 (0.39), residues: 251

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   0.021   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  : 0.473 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0393
  time to fit residues: 2.0009
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  : 0.439 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 25 optimal weight:   20.0000
   chunk 46 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:   20.0000
   chunk 3 optimal weight:   30.0000
   chunk 15 optimal weight:   30.0000
   chunk 11 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.2946 r_free = 0.2946 target = 0.034639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.027403 restraints weight = 65039.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.027552 restraints weight = 58985.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.027634 restraints weight = 54659.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3968  Z= 0.209
  Angle     :  0.458   5.943   5493  Z= 0.301
  Chirality :  0.039   0.127    728
  Planarity :  0.002   0.009    803
  Dihedral  :  4.244  23.479    803
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.42 %
    Favored  : 93.45 %
  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:  0.67 (0.31), residues: 794
  helix:  1.98 (0.23), residues: 491
  sheet: -2.37 (0.82), residues: 43
  loop : -2.17 (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   0.020   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  : 0.421 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0363
  time to fit residues: 1.8063
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:   40.0000
   chunk 71 optimal weight:    0.0980
   chunk 51 optimal weight:   40.0000
   chunk 18 optimal weight:   50.0000
   chunk 62 optimal weight:    5.9990
   chunk 73 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 41 optimal weight:   30.0000
   chunk 53 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   overall best weight:    7.4190

-------------------------------------------------------------------------------
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 = 0.2939 r_free = 0.2939 target = 0.034585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027328 restraints weight = 65675.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.027501 restraints weight = 59764.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.027613 restraints weight = 54893.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3968  Z= 0.256
  Angle     :  0.503   6.815   5493  Z= 0.333
  Chirality :  0.039   0.130    728
  Planarity :  0.003   0.010    803
  Dihedral  :  4.593  23.941    803
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.81 %
    Favored  : 92.07 %
  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:  0.07 (0.30), residues: 794
  helix:  1.41 (0.22), residues: 490
  sheet: -2.80 (0.92), residues: 34
  loop : -2.21 (0.37), 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   0.020   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  : 0.426 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0364
  time to fit residues: 1.8208
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  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 15 optimal weight:   20.0000
   chunk 78 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 47 optimal weight:   50.0000
   chunk 68 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.034772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.027487 restraints weight = 63962.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.027600 restraints weight = 58731.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.027724 restraints weight = 54813.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3095

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= 0.121
  Angle     :  0.396   5.673   5493  Z= 0.249
  Chirality :  0.039   0.129    728
  Planarity :  0.002   0.007    803
  Dihedral  :  4.109  23.365    803
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.54 %
    Favored  : 94.33 %
  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:  1.06 (0.32), residues: 794
  helix:  2.31 (0.23), residues: 492
  sheet: -2.19 (0.88), residues: 38
  loop : -2.12 (0.38), residues: 264

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   0.017   0.002   TYR D  11 

*********************** REFINEMENT MACRO_CYCLE 8 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  : 0.450 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0369
  time to fit residues: 1.8525
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  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 61 optimal weight:   40.0000
   chunk 31 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 54 optimal weight:   40.0000
   chunk 40 optimal weight:   20.0000
   chunk 51 optimal weight:   40.0000
   chunk 29 optimal weight:   20.0000
   chunk 8 optimal weight:   20.0000
   overall best weight:   11.1792

-------------------------------------------------------------------------------
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 = 0.2927 r_free = 0.2927 target = 0.034171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.027183 restraints weight = 66749.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.027325 restraints weight = 61130.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.027430 restraints weight = 56827.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3968  Z= 0.367
  Angle     :  0.609   7.169   5493  Z= 0.415
  Chirality :  0.040   0.140    728
  Planarity :  0.004   0.014    803
  Dihedral  :  4.962  24.800    803
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.82 %
    Favored  : 90.05 %
  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: -0.73 (0.29), residues: 794
  helix:  0.68 (0.22), residues: 485
  sheet: -3.05 (0.74), residues: 51
  loop : -2.16 (0.38), residues: 258

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 9 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  : 0.497 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0382
  time to fit residues: 1.8700
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  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 26 optimal weight:   40.0000
   chunk 34 optimal weight:    9.9990
   chunk 65 optimal weight:   30.0000
   chunk 14 optimal weight:    0.0050
   chunk 6 optimal weight:    5.9990
   chunk 61 optimal weight:   40.0000
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.7400

-------------------------------------------------------------------------------
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 = 0.2944 r_free = 0.2944 target = 0.034782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.027419 restraints weight = 64359.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.027536 restraints weight = 58607.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.027650 restraints weight = 54596.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3326

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= 0.089
  Angle     :  0.392   5.620   5493  Z= 0.243
  Chirality :  0.039   0.131    728
  Planarity :  0.002   0.007    803
  Dihedral  :  4.166  22.878    803
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.04 %
    Favored  : 94.84 %
  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:  1.08 (0.32), residues: 794
  helix:  2.33 (0.23), residues: 493
  sheet: -2.38 (0.88), residues: 38
  loop : -2.12 (0.38), residues: 263

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   0.015   0.002   TYR D  11 

********************** REFINEMENT MACRO_CYCLE 10 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  : 0.458 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0365
  time to fit residues: 1.8834
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  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 26 optimal weight:   30.0000
   chunk 55 optimal weight:   50.0000
   chunk 6 optimal weight:    0.0770
   chunk 33 optimal weight:   20.0000
   chunk 31 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    5.8146

-------------------------------------------------------------------------------
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 = 0.2937 r_free = 0.2937 target = 0.034459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.027275 restraints weight = 65788.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.027435 restraints weight = 59608.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.027564 restraints weight = 53576.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3968  Z= 0.195
  Angle     :  0.445   6.045   5493  Z= 0.291
  Chirality :  0.039   0.127    728
  Planarity :  0.002   0.009    803
  Dihedral  :  4.194  23.161    803
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.44 %
    Favored  : 91.44 %
  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:  0.83 (0.31), residues: 794
  helix:  2.13 (0.23), residues: 492
  sheet: -2.43 (0.86), residues: 38
  loop : -2.20 (0.38), residues: 264

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   0.016   0.002   TYR D  11 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1334.37 seconds
wall clock time: 23 minutes 41.16 seconds (1421.16 seconds total)