Starting phenix.real_space_refine
on Sun May 11 01:41:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8umd_42376/05_2025/8umd_42376.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8umd_42376/05_2025/8umd_42376.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8umd_42376/05_2025/8umd_42376.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8umd_42376/05_2025/8umd_42376.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8umd_42376/05_2025/8umd_42376.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8umd_42376/05_2025/8umd_42376.cif"
  }
  resolution = 3.6
  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=   0.006 sd=   0.086
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4528      2.51       5
     N    1287      2.21       5
     O    1359      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7201
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 393
          Classifications: {'peptide': 47}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2583
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2348
          Classifications: {'peptide': 290}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 267}
    Chain: "D"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 625
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
    Chain: "E"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 625
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 627
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
  Time building chain proxies: 6.49, per 1000 atoms: 0.90
  Number of scatterers: 7201
  At special positions: 0
  Unit cell: (106.496, 109.824, 168.064, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1359      8.00
     N    1287      7.00
     C    4528      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: 1.72
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      51.6% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 514 through 543
    Processing helix  chain 'A' and resid 543 through 558
    Processing helix  chain 'B' and resid 5 through 18
      removed outlier: 3.832A  pdb=" N   GLY B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 27
    Processing helix  chain 'B' and resid 30 through 43
    Processing helix  chain 'B' and resid 48 through 67
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.574A  pdb=" N   ARG B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   GLU B  87 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 9.440A  pdb=" N   GLU B  88 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ARG B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ARG B 101 " --> pdb=" O   ILE B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 113
      removed outlier: 3.667A  pdb=" N   THR B 109 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN B 111 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 123
    Processing helix  chain 'B' and resid 126 through 137
      removed outlier: 3.635A  pdb=" N   HIS B 136 " --> pdb=" O   THR B 132 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU B 137 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 147
    Processing helix  chain 'B' and resid 150 through 163
    Processing helix  chain 'B' and resid 168 through 183
    Processing helix  chain 'B' and resid 198 through 204
    Processing helix  chain 'B' and resid 207 through 222
    Processing helix  chain 'B' and resid 222 through 235
      removed outlier: 3.517A  pdb=" N   LEU B 235 " --> pdb=" O   ASP B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 241
    Processing helix  chain 'B' and resid 242 through 252
      removed outlier: 4.062A  pdb=" N   SER B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE B 247 " --> pdb=" O   ASP B 243 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLN B 252 " --> pdb=" O   GLN B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 266
      removed outlier: 3.647A  pdb=" N   LYS B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   GLY B 265 " --> pdb=" O   ILE B 261 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 276
    Processing helix  chain 'B' and resid 279 through 293
    Processing helix  chain 'B' and resid 297 through 318
      removed outlier: 3.510A  pdb=" N   THR B 318 " --> pdb=" O   ARG B 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 74
    Processing helix  chain 'C' and resid 89 through 95
      removed outlier: 3.619A  pdb=" N   ASN C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 131
    Processing helix  chain 'C' and resid 147 through 171
      removed outlier: 4.016A  pdb=" N   ALA C 171 " --> pdb=" O   ASP C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 189
    Processing helix  chain 'C' and resid 221 through 225
    Processing helix  chain 'C' and resid 227 through 233
      removed outlier: 3.854A  pdb=" N   ASN C 233 " --> pdb=" O   GLU C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 255
    Processing helix  chain 'C' and resid 271 through 278
    Processing helix  chain 'D' and resid 74 through 81
    Processing helix  chain 'D' and resid 127 through 134
    Processing helix  chain 'E' and resid 75 through 81
    Processing helix  chain 'E' and resid 130 through 135
      removed outlier: 3.630A  pdb=" N   ARG E 134 " --> pdb=" O   GLU E 130 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU E 135 " --> pdb=" O   ARG E 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 130 through 135'
    Processing helix  chain 'F' and resid 75 through 81
    Processing helix  chain 'F' and resid 127 through 136
    Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36
      removed outlier: 5.517A  pdb=" N   LEU E 105 " --> pdb=" O   ILE E 101 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE E 101 " --> pdb=" O   LEU E 105 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA E 107 " --> pdb=" O   ILE E  99 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP E  98 " --> pdb=" O   GLU E  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 86 through 92
      removed outlier: 4.973A  pdb=" N   TYR F 118 " --> pdb=" O   LEU E  89 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLN F 108 " --> pdb=" O   THR F 123 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   ILE F 125 " --> pdb=" O   ILE F 106 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   ILE F 106 " --> pdb=" O   ILE F 125 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ILE F  99 " --> pdb=" O   ILE F 106 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   GLN F 108 " --> pdb=" O   LEU F  97 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LEU F  97 " --> pdb=" O   GLN F 108 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL F  62 " --> pdb=" O   ARG E  72 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   ARG E  72 " --> pdb=" O   VAL F  62 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU F  64 " --> pdb=" O   ARG E  70 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   ARG E  70 " --> pdb=" O   LEU F  64 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   VAL F  66 " --> pdb=" O   LEU E  68 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL E  66 " --> pdb=" O   LEU F  68 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP E  98 " --> pdb=" O   GLU E  67 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA E 107 " --> pdb=" O   ILE E  99 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE E 101 " --> pdb=" O   LEU E 105 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   LEU E 105 " --> pdb=" O   ILE E 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 81
    Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 81
      removed outlier: 4.011A  pdb=" N   ARG C 181 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   HIS C 106 " --> pdb=" O   TYR C 179 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   TYR C 179 " --> pdb=" O   HIS C 106 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   LYS C 108 " --> pdb=" O   VAL C 177 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   VAL C 177 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 283 through 284
      removed outlier: 3.509A  pdb=" N   VAL D 120 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   GLN D 108 " --> pdb=" O   THR D 123 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   ILE D 125 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   ILE D 106 " --> pdb=" O   ILE D 125 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   LEU D 105 " --> pdb=" O   ILE D 101 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   ILE D 101 " --> pdb=" O   LEU D 105 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA D 107 " --> pdb=" O   ILE D  99 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASP D  98 " --> pdb=" O   GLU D  67 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   VAL D  62 " --> pdb=" O   PRO C 269 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU D  64 " --> pdb=" O   ASP C 267 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   ASP C 267 " --> pdb=" O   LEU D  64 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL D  66 " --> pdb=" O   PHE C 265 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ALA C 263 " --> pdb=" O   LEU D  68 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ARG D  70 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU C 261 " --> pdb=" O   ARG D  70 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE C 293 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   VAL C 296 " --> pdb=" O   PRO C 300 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   VAL C 301 " --> pdb=" O   LEU C 320 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   LEU C 320 " --> pdb=" O   VAL C 301 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   THR C 303 " --> pdb=" O   GLU C 318 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   TYR C 313 " --> pdb=" O   LEU D  89 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1152 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: 2.02

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2499
        1.34 -     1.46: 1323
        1.46 -     1.58: 3415
        1.58 -     1.70: 0
        1.70 -     1.82: 53
  Bond restraints: 7290
  Sorted by residual:
  bond pdb=" N   THR B 103 "
       pdb=" CA  THR B 103 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.020 1.29e-02 6.01e+03 2.32e+00
  bond pdb=" CB  ASP E  59 "
       pdb=" CG  ASP E  59 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.89e+00
  bond pdb=" CA  ASP D 116 "
       pdb=" CB  ASP D 116 "
    ideal  model  delta    sigma   weight residual
    1.530  1.553 -0.022 1.69e-02 3.50e+03 1.76e+00
  bond pdb=" CA  MET E  58 "
       pdb=" CB  MET E  58 "
    ideal  model  delta    sigma   weight residual
    1.537  1.560 -0.023 1.85e-02 2.92e+03 1.54e+00
  bond pdb=" CB  ASP D 116 "
       pdb=" CG  ASP D 116 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.49e+00
  ... (remaining 7285 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 9691
        2.44 -     4.89: 148
        4.89 -     7.33: 19
        7.33 -     9.77: 5
        9.77 -    12.21: 2
  Bond angle restraints: 9865
  Sorted by residual:
  angle pdb=" CA  MET E  58 "
        pdb=" CB  MET E  58 "
        pdb=" CG  MET E  58 "
      ideal   model   delta    sigma   weight residual
     114.10  122.99   -8.89 2.00e+00 2.50e-01 1.97e+01
  angle pdb=" CA  MET D 132 "
        pdb=" CB  MET D 132 "
        pdb=" CG  MET D 132 "
      ideal   model   delta    sigma   weight residual
     114.10  121.40   -7.30 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" CA  LEU A 549 "
        pdb=" CB  LEU A 549 "
        pdb=" CG  LEU A 549 "
      ideal   model   delta    sigma   weight residual
     116.30  128.51  -12.21 3.50e+00 8.16e-02 1.22e+01
  angle pdb=" C   MET E  58 "
        pdb=" CA  MET E  58 "
        pdb=" CB  MET E  58 "
      ideal   model   delta    sigma   weight residual
     109.80  114.97   -5.17 1.61e+00 3.86e-01 1.03e+01
  angle pdb=" CA  MET A 532 "
        pdb=" CB  MET A 532 "
        pdb=" CG  MET A 532 "
      ideal   model   delta    sigma   weight residual
     114.10  120.23   -6.13 2.00e+00 2.50e-01 9.39e+00
  ... (remaining 9860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3892
       17.85 -    35.70: 492
       35.70 -    53.55: 125
       53.55 -    71.41: 21
       71.41 -    89.26: 8
  Dihedral angle restraints: 4538
    sinusoidal: 1903
      harmonic: 2635
  Sorted by residual:
  dihedral pdb=" CA  PRO C 234 "
           pdb=" C   PRO C 234 "
           pdb=" N   PRO C 235 "
           pdb=" CA  PRO C 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.64  -23.36     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  LEU B 188 "
           pdb=" C   LEU B 188 "
           pdb=" N   LYS B 189 "
           pdb=" CA  LYS B 189 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.58   22.42     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  ILE E 125 "
           pdb=" C   ILE E 125 "
           pdb=" N   ILE E 126 "
           pdb=" CA  ILE E 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.13   21.87     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 4535 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 879
       0.043 -    0.087: 213
       0.087 -    0.130: 78
       0.130 -    0.173: 3
       0.173 -    0.216: 3
  Chirality restraints: 1176
  Sorted by residual:
  chirality pdb=" CG  LEU B  56 "
            pdb=" CB  LEU B  56 "
            pdb=" CD1 LEU B  56 "
            pdb=" CD2 LEU B  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE A 536 "
            pdb=" CA  ILE A 536 "
            pdb=" CG1 ILE A 536 "
            pdb=" CG2 ILE A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  VAL C 251 "
            pdb=" CA  VAL C 251 "
            pdb=" CG1 VAL C 251 "
            pdb=" CG2 VAL C 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.66e-01
  ... (remaining 1173 not shown)

  Planarity restraints: 1290
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 102 "    0.023 2.00e-02 2.50e+03   4.49e-02 2.02e+01
        pdb=" C   ASP B 102 "   -0.078 2.00e-02 2.50e+03
        pdb=" O   ASP B 102 "    0.030 2.00e-02 2.50e+03
        pdb=" N   THR B 103 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 234 "   -0.049 5.00e-02 4.00e+02   7.32e-02 8.58e+00
        pdb=" N   PRO C 235 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO C 235 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 235 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D 116 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.98e+00
        pdb=" C   ASP D 116 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ASP D 116 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LYS D 117 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1287 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 124
        2.66 -     3.22: 7181
        3.22 -     3.78: 11179
        3.78 -     4.34: 14252
        4.34 -     4.90: 23009
  Nonbonded interactions: 55745
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 273 "
            pdb=" O   MET D  58 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   ILE B  97 "
            pdb=" OG1 THR B 100 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" NZ  LYS E  76 "
            pdb=" O   MET F  58 "
     model   vdw
     2.170 3.120
  nonbonded pdb=" O   GLY B 106 "
            pdb=" OG1 THR B 109 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OH  TYR C 179 "
            pdb=" OG  SER C 182 "
     model   vdw
     2.220 3.040
  ... (remaining 55740 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 'D' and resid 57 through 135)
  selection = (chain 'E' and resid 57 through 135)
  selection = (chain 'F' and resid 57 through 135)
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.170
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.980
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
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      :  0.003   0.047   7290  Z= 0.153
  Angle     :  0.722  12.213   9865  Z= 0.375
  Chirality :  0.043   0.216   1176
  Planarity :  0.005   0.073   1290
  Dihedral  : 16.777  89.258   2822
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.89 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 26.69 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.54 (0.29), residues: 899
  helix:  1.56 (0.26), residues: 435
  sheet:  0.15 (0.52), residues: 97
  loop : -1.05 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 169 
 HIS   0.004   0.001   HIS C 295 
 PHE   0.018   0.002   PHE C  70 
 TYR   0.009   0.001   TYR D 118 
 ARG   0.010   0.001   ARG F 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15535 (  392)
  hydrogen bonds       : angle       6.85495 ( 1152)
  covalent geometry    : bond        0.00329 ( 7290)
  covalent geometry    : angle       0.72181 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.8573 (ttt) cc_final: 0.7989 (tpt)
REVERT: B  270 LEU cc_start: 0.8772 (tp) cc_final: 0.8524 (mm)
REVERT: C   67 MET cc_start: 0.9235 (mmt) cc_final: 0.8907 (mmm)
REVERT: C   69 LEU cc_start: 0.9503 (mt) cc_final: 0.9272 (mt)
REVERT: E   70 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7546 (ptp90)
  outliers start: 4
  outliers final: 2
  residues processed: 96
  average time/residue: 0.2175
  time to fit residues: 27.4769
Evaluate side-chains
  64 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain E residue   74 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 70 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.045983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.034948 restraints weight = 58929.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.035723 restraints weight = 35765.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.036274 restraints weight = 25391.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7290  Z= 0.130
  Angle     :  0.682  12.028   9865  Z= 0.344
  Chirality :  0.044   0.172   1176
  Planarity :  0.005   0.062   1290
  Dihedral  :  4.611  25.777   1003
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.34 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 24.19 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.62 (0.29), residues: 899
  helix:  1.63 (0.25), residues: 437
  sheet:  0.02 (0.54), residues: 92
  loop : -0.97 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 169 
 HIS   0.002   0.001   HIS B 126 
 PHE   0.011   0.001   PHE C 215 
 TYR   0.006   0.001   TYR E 118 
 ARG   0.006   0.000   ARG E 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  392)
  hydrogen bonds       : angle       5.08229 ( 1152)
  covalent geometry    : bond        0.00277 ( 7290)
  covalent geometry    : angle       0.68185 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9296 (ttt) cc_final: 0.8471 (tpt)
REVERT: B  270 LEU cc_start: 0.9050 (tp) cc_final: 0.8766 (mm)
REVERT: B  278 MET cc_start: 0.3554 (mmt) cc_final: 0.2296 (mmt)
REVERT: C   67 MET cc_start: 0.8949 (mmt) cc_final: 0.8571 (mmm)
REVERT: C  170 LYS cc_start: 0.9686 (tppp) cc_final: 0.9381 (tppp)
REVERT: E   67 GLU cc_start: 0.9138 (mt-10) cc_final: 0.7880 (tt0)
REVERT: E   70 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.7298 (ptp90)
REVERT: E   71 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8408 (p)
REVERT: E   77 GLU cc_start: 0.9100 (mp0) cc_final: 0.8841 (mp0)
REVERT: F  116 ASP cc_start: 0.7637 (t0) cc_final: 0.7347 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 94
  average time/residue: 0.2008
  time to fit residues: 25.7454
Evaluate side-chains
  77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  135 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0050
   chunk 38 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 59 optimal weight:    9.9990
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 238 ASN
C 106 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.045208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.034313 restraints weight = 59737.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.035080 restraints weight = 36156.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.035629 restraints weight = 25475.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7290  Z= 0.128
  Angle     :  0.626   8.904   9865  Z= 0.320
  Chirality :  0.043   0.176   1176
  Planarity :  0.004   0.060   1290
  Dihedral  :  4.385  22.869   1000
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.01 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.93 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.72 (0.29), residues: 899
  helix:  1.71 (0.26), residues: 436
  sheet:  0.17 (0.56), residues: 91
  loop : -0.94 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 554 
 HIS   0.003   0.001   HIS B 126 
 PHE   0.012   0.001   PHE C  65 
 TYR   0.006   0.001   TYR C  38 
 ARG   0.005   0.000   ARG E 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  392)
  hydrogen bonds       : angle       4.77166 ( 1152)
  covalent geometry    : bond        0.00277 ( 7290)
  covalent geometry    : angle       0.62576 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 62
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9178 (ttt) cc_final: 0.8917 (ttt)
REVERT: B  270 LEU cc_start: 0.8972 (tp) cc_final: 0.8706 (mm)
REVERT: B  278 MET cc_start: 0.3974 (mmt) cc_final: 0.2955 (mmt)
REVERT: C   67 MET cc_start: 0.8932 (mmt) cc_final: 0.8548 (mmm)
REVERT: C  170 LYS cc_start: 0.9681 (tppp) cc_final: 0.9405 (tppp)
REVERT: D   73 MET cc_start: 0.8065 (tmm) cc_final: 0.7810 (tmm)
REVERT: E   67 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8629 (tt0)
REVERT: E   77 GLU cc_start: 0.9129 (mp0) cc_final: 0.8827 (mp0)
  outliers start: 30
  outliers final: 20
  residues processed: 88
  average time/residue: 0.1916
  time to fit residues: 23.2331
Evaluate side-chains
  75 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  135 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.044864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.033880 restraints weight = 61045.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.034661 restraints weight = 36955.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.035225 restraints weight = 25946.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7290  Z= 0.130
  Angle     :  0.607   9.740   9865  Z= 0.312
  Chirality :  0.042   0.163   1176
  Planarity :  0.004   0.059   1290
  Dihedral  :  4.304  23.025   1000
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.56 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 22.93 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.87 (0.30), residues: 899
  helix:  1.81 (0.26), residues: 434
  sheet: -0.05 (0.55), residues: 93
  loop : -0.71 (0.35), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 554 
 HIS   0.003   0.001   HIS B 126 
 PHE   0.011   0.001   PHE B 234 
 TYR   0.007   0.001   TYR C  38 
 ARG   0.004   0.000   ARG E 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  392)
  hydrogen bonds       : angle       4.60929 ( 1152)
  covalent geometry    : bond        0.00286 ( 7290)
  covalent geometry    : angle       0.60715 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9200 (ttt) cc_final: 0.8915 (ttt)
REVERT: B  270 LEU cc_start: 0.9017 (tp) cc_final: 0.8746 (mm)
REVERT: B  278 MET cc_start: 0.4758 (mmt) cc_final: 0.3982 (mmt)
REVERT: C   67 MET cc_start: 0.8907 (mmt) cc_final: 0.8526 (mmm)
REVERT: C  170 LYS cc_start: 0.9680 (tppp) cc_final: 0.9385 (tppp)
REVERT: E   77 GLU cc_start: 0.9107 (mp0) cc_final: 0.8826 (mp0)
REVERT: F   73 MET cc_start: 0.8731 (ppp) cc_final: 0.8191 (ppp)
REVERT: F  116 ASP cc_start: 0.7760 (t0) cc_final: 0.7549 (t0)
  outliers start: 32
  outliers final: 19
  residues processed: 88
  average time/residue: 0.2082
  time to fit residues: 24.6020
Evaluate side-chains
  77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 81 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0050
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.045041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.034061 restraints weight = 60108.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.034865 restraints weight = 36217.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.035432 restraints weight = 25525.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7290  Z= 0.119
  Angle     :  0.609   8.700   9865  Z= 0.311
  Chirality :  0.042   0.138   1176
  Planarity :  0.004   0.058   1290
  Dihedral  :  4.243  22.814   1000
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.34 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.56 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.77 (0.30), residues: 899
  helix:  1.73 (0.26), residues: 438
  sheet: -0.20 (0.60), residues: 78
  loop : -0.76 (0.34), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 554 
 HIS   0.003   0.001   HIS B 126 
 PHE   0.014   0.001   PHE C 131 
 TYR   0.006   0.001   TYR F 104 
 ARG   0.002   0.000   ARG E 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  392)
  hydrogen bonds       : angle       4.50667 ( 1152)
  covalent geometry    : bond        0.00265 ( 7290)
  covalent geometry    : angle       0.60943 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 61
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9238 (ttt) cc_final: 0.8929 (ttt)
REVERT: B  270 LEU cc_start: 0.9060 (tp) cc_final: 0.8785 (mm)
REVERT: B  278 MET cc_start: 0.5135 (mmt) cc_final: 0.4387 (mmt)
REVERT: C   67 MET cc_start: 0.9095 (mmt) cc_final: 0.8659 (mmm)
REVERT: C  170 LYS cc_start: 0.9762 (tppp) cc_final: 0.9469 (tppp)
REVERT: D   73 MET cc_start: 0.8313 (tmm) cc_final: 0.7928 (tmm)
REVERT: E   67 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8240 (tt0)
REVERT: E   77 GLU cc_start: 0.9177 (mp0) cc_final: 0.8818 (mp0)
REVERT: F   73 MET cc_start: 0.9089 (ppp) cc_final: 0.8756 (ppp)
REVERT: F   97 LEU cc_start: 0.9356 (mt) cc_final: 0.8852 (mt)
REVERT: F  110 GLU cc_start: 0.7625 (mp0) cc_final: 0.7286 (mm-30)
REVERT: F  123 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8872 (p)
  outliers start: 32
  outliers final: 24
  residues processed: 89
  average time/residue: 0.1812
  time to fit residues: 22.3926
Evaluate side-chains
  80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 55
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  189 LYS
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  123 THR
Chi-restraints excluded: chain F residue  135 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 69 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0370
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.045376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.034273 restraints weight = 60932.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.035083 restraints weight = 36618.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.035640 restraints weight = 25718.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   7290  Z= 0.109
  Angle     :  0.615   9.791   9865  Z= 0.309
  Chirality :  0.042   0.213   1176
  Planarity :  0.004   0.058   1290
  Dihedral  :  4.154  22.557   1000
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.23 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 25.31 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.79 (0.30), residues: 899
  helix:  1.77 (0.26), residues: 438
  sheet: -0.21 (0.60), residues: 78
  loop : -0.77 (0.34), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 554 
 HIS   0.003   0.000   HIS B 126 
 PHE   0.013   0.001   PHE B 234 
 TYR   0.006   0.001   TYR D 118 
 ARG   0.002   0.000   ARG F 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 (  392)
  hydrogen bonds       : angle       4.41300 ( 1152)
  covalent geometry    : bond        0.00242 ( 7290)
  covalent geometry    : angle       0.61452 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 58
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  113 MET cc_start: 0.8554 (tmm) cc_final: 0.8075 (tmm)
REVERT: B  233 MET cc_start: 0.9177 (ttt) cc_final: 0.8870 (ttt)
REVERT: B  270 LEU cc_start: 0.9019 (tp) cc_final: 0.8761 (mm)
REVERT: B  278 MET cc_start: 0.4703 (mmt) cc_final: 0.3967 (mmt)
REVERT: C   67 MET cc_start: 0.8886 (mmt) cc_final: 0.8525 (mmm)
REVERT: C  108 LYS cc_start: 0.9427 (mmtt) cc_final: 0.9177 (mmtt)
REVERT: D   73 MET cc_start: 0.8335 (tmm) cc_final: 0.8117 (tmm)
REVERT: E   67 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8402 (tt0)
REVERT: E   77 GLU cc_start: 0.9031 (mp0) cc_final: 0.8738 (mp0)
  outliers start: 27
  outliers final: 23
  residues processed: 83
  average time/residue: 0.1909
  time to fit residues: 21.8994
Evaluate side-chains
  80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  189 LYS
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 14 optimal weight:    0.2980
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 HIS
C 103 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.044249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.033585 restraints weight = 60051.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.034368 restraints weight = 34760.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.034922 restraints weight = 23968.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7290  Z= 0.217
  Angle     :  0.673  11.317   9865  Z= 0.344
  Chirality :  0.043   0.189   1176
  Planarity :  0.004   0.058   1290
  Dihedral  :  4.342  24.411   1000
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.34 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.31 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.78 (0.30), residues: 899
  helix:  1.61 (0.25), residues: 441
  sheet:  0.00 (0.56), residues: 93
  loop : -0.67 (0.36), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 554 
 HIS   0.004   0.001   HIS B 136 
 PHE   0.017   0.002   PHE C 131 
 TYR   0.017   0.002   TYR C  38 
 ARG   0.008   0.000   ARG A 537 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  392)
  hydrogen bonds       : angle       4.65838 ( 1152)
  covalent geometry    : bond        0.00457 ( 7290)
  covalent geometry    : angle       0.67309 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 54
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 MET cc_start: 0.9250 (ttt) cc_final: 0.8967 (ttt)
REVERT: B  270 LEU cc_start: 0.9121 (tp) cc_final: 0.8842 (mm)
REVERT: B  278 MET cc_start: 0.5631 (mmt) cc_final: 0.4792 (mmt)
REVERT: C   67 MET cc_start: 0.9125 (mmt) cc_final: 0.8670 (mmm)
REVERT: D   73 MET cc_start: 0.8629 (tmm) cc_final: 0.8313 (tmm)
REVERT: E   67 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8286 (tt0)
REVERT: E   77 GLU cc_start: 0.9090 (mp0) cc_final: 0.8869 (mp0)
  outliers start: 38
  outliers final: 27
  residues processed: 91
  average time/residue: 0.1760
  time to fit residues: 22.3204
Evaluate side-chains
  78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 51
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  189 LYS
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain D residue   67 GLU
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain D residue  118 TYR
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 8 optimal weight:    7.9990
   chunk 88 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0060
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0030
   chunk 32 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.3606

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN
C 106 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.045316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.034404 restraints weight = 60558.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.035267 restraints weight = 34739.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.035860 restraints weight = 23756.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   7290  Z= 0.113
  Angle     :  0.667  11.206   9865  Z= 0.330
  Chirality :  0.043   0.208   1176
  Planarity :  0.004   0.056   1290
  Dihedral  :  4.190  24.435   1000
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.12 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 26.32 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.69 (0.30), residues: 899
  helix:  1.64 (0.26), residues: 439
  sheet: -0.21 (0.62), residues: 73
  loop : -0.77 (0.34), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 246 
 HIS   0.003   0.001   HIS B 126 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.008   0.001   TYR D 118 
 ARG   0.003   0.000   ARG F 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  392)
  hydrogen bonds       : angle       4.46996 ( 1152)
  covalent geometry    : bond        0.00248 ( 7290)
  covalent geometry    : angle       0.66733 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 58
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  113 MET cc_start: 0.8611 (tmm) cc_final: 0.8037 (ppp)
REVERT: B  233 MET cc_start: 0.9213 (ttt) cc_final: 0.8934 (ttt)
REVERT: B  270 LEU cc_start: 0.9145 (tp) cc_final: 0.8858 (mm)
REVERT: B  278 MET cc_start: 0.5135 (mmt) cc_final: 0.4277 (mmt)
REVERT: B  321 MET cc_start: 0.7290 (pmm) cc_final: 0.6611 (pmm)
REVERT: D   73 MET cc_start: 0.8482 (tmm) cc_final: 0.8225 (tmm)
REVERT: E   67 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8373 (tt0)
REVERT: E   77 GLU cc_start: 0.9024 (mp0) cc_final: 0.8741 (mp0)
REVERT: F  123 THR cc_start: 0.9268 (t) cc_final: 0.8949 (p)
  outliers start: 26
  outliers final: 24
  residues processed: 81
  average time/residue: 0.1942
  time to fit residues: 21.5607
Evaluate side-chains
  80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  189 LYS
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue  101 ILE
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 66 optimal weight:    0.4980
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0030
   chunk 48 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.2994

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.044769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.034002 restraints weight = 60480.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.034774 restraints weight = 35866.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.035339 restraints weight = 25099.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7290  Z= 0.135
  Angle     :  0.657  11.136   9865  Z= 0.332
  Chirality :  0.042   0.177   1176
  Planarity :  0.004   0.056   1290
  Dihedral  :  4.156  23.606   1000
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.12 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 26.07 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.69 (0.30), residues: 899
  helix:  1.62 (0.26), residues: 440
  sheet: -0.31 (0.63), residues: 73
  loop : -0.74 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 554 
 HIS   0.003   0.001   HIS C 106 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.009   0.001   TYR D 118 
 ARG   0.002   0.000   ARG E 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03297 (  392)
  hydrogen bonds       : angle       4.50534 ( 1152)
  covalent geometry    : bond        0.00298 ( 7290)
  covalent geometry    : angle       0.65718 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 55
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  113 MET cc_start: 0.8312 (tmm) cc_final: 0.7917 (ppp)
REVERT: B  233 MET cc_start: 0.9187 (ttt) cc_final: 0.8875 (ttt)
REVERT: B  270 LEU cc_start: 0.9129 (tp) cc_final: 0.8844 (mm)
REVERT: B  278 MET cc_start: 0.4983 (mmt) cc_final: 0.4162 (mmt)
REVERT: D   73 MET cc_start: 0.8504 (tmm) cc_final: 0.8235 (tmm)
REVERT: E   67 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8342 (tt0)
  outliers start: 29
  outliers final: 25
  residues processed: 82
  average time/residue: 0.1984
  time to fit residues: 22.5669
Evaluate side-chains
  78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 53
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  189 LYS
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0870
   chunk 89 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.045139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.034297 restraints weight = 61598.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.035138 restraints weight = 35265.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.035720 restraints weight = 24131.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7290  Z= 0.123
  Angle     :  0.667  11.150   9865  Z= 0.336
  Chirality :  0.043   0.176   1176
  Planarity :  0.004   0.057   1290
  Dihedral  :  4.169  23.939   1000
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.34 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 26.57 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.59 (0.30), residues: 899
  helix:  1.50 (0.26), residues: 440
  sheet: -0.32 (0.61), residues: 74
  loop : -0.74 (0.34), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 246 
 HIS   0.002   0.000   HIS B 126 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.008   0.001   TYR D 118 
 ARG   0.002   0.000   ARG F 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03346 (  392)
  hydrogen bonds       : angle       4.57110 ( 1152)
  covalent geometry    : bond        0.00273 ( 7290)
  covalent geometry    : angle       0.66727 ( 9865)

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

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

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1798 Ramachandran restraints generated.
    899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  113 MET cc_start: 0.8377 (tmm) cc_final: 0.8060 (ppp)
REVERT: B  233 MET cc_start: 0.9224 (ttt) cc_final: 0.8907 (ttt)
REVERT: B  270 LEU cc_start: 0.9157 (tp) cc_final: 0.8871 (mm)
REVERT: B  278 MET cc_start: 0.5278 (mmt) cc_final: 0.4416 (mmt)
REVERT: B  321 MET cc_start: 0.7380 (pmm) cc_final: 0.6669 (pmm)
REVERT: D   73 MET cc_start: 0.8529 (tmm) cc_final: 0.8239 (tmm)
REVERT: E   67 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8370 (tt0)
  outliers start: 24
  outliers final: 23
  residues processed: 76
  average time/residue: 0.1866
  time to fit residues: 19.6589
Evaluate side-chains
  77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain B residue   26 PHE
Chi-restraints excluded: chain B residue  189 LYS
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  267 GLU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  112 VAL
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain E residue  127 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 24 optimal weight:    0.2980
   chunk 35 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.045321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.034432 restraints weight = 60665.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.035267 restraints weight = 35676.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.035836 restraints weight = 24769.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7290  Z= 0.118
  Angle     :  0.671  11.079   9865  Z= 0.338
  Chirality :  0.043   0.174   1176
  Planarity :  0.004   0.056   1290
  Dihedral  :  4.115  23.440   1000
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.89 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 26.32 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.30), residues: 899
  helix:  1.52 (0.26), residues: 438
  sheet:  0.15 (0.65), residues: 64
  loop : -0.71 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 554 
 HIS   0.002   0.000   HIS B 126 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.007   0.001   TYR D 118 
 ARG   0.002   0.000   ARG F 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03288 (  392)
  hydrogen bonds       : angle       4.54660 ( 1152)
  covalent geometry    : bond        0.00264 ( 7290)
  covalent geometry    : angle       0.67094 ( 9865)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2997.75 seconds
wall clock time: 53 minutes 28.25 seconds (3208.25 seconds total)