Starting phenix.real_space_refine
on Sat Oct 11 21:12:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g02_29642/10_2025/8g02_29642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g02_29642/10_2025/8g02_29642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g02_29642/10_2025/8g02_29642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g02_29642/10_2025/8g02_29642.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g02_29642/10_2025/8g02_29642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g02_29642/10_2025/8g02_29642.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
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: 5
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5906      2.51       5
     N    1480      2.21       5
     O    1536      1.98       5
     H    9228      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18194
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 360, 5758
          Classifications: {'peptide': 360}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 345}
    Chain: "E"
      Number of atoms: 5758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 360, 5758
          Classifications: {'peptide': 360}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 345}
    Chain: "B"
      Number of atoms: 1109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1109
          Classifications: {'peptide': 65}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 59}
    Chain: "G"
      Number of atoms: 1109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1109
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "F"
      Number of atoms: 2230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 2230
          Classifications: {'peptide': 149}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 143}
    Chain: "H"
      Number of atoms: 2230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 2230
          Classifications: {'peptide': 149}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 143}
  Time building chain proxies: 3.19, per 1000 atoms: 0.18
  Number of scatterers: 18194
  At special positions: 0
  Unit cell: (89.024, 103.168, 119.808, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     O    1536      8.00
     N    1480      7.00
     C    5906      6.00
     H    9228      1.00
    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: 1.73
  Conformation dependent library (CDL) restraints added in 773.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2096

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      62.3% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 11
      removed outlier: 4.434A  pdb=" N   LYS A  11 " --> pdb=" O   GLU A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 20
    Processing helix  chain 'A' and resid 21 through 53
      Proline residue:  A  42  - end of helix
    Processing helix  chain 'A' and resid 75 through 91
      removed outlier: 4.195A  pdb=" N   ILE A  79 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 121
      removed outlier: 3.665A  pdb=" N   TRP A  99 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 153
    Processing helix  chain 'A' and resid 155 through 159
    Processing helix  chain 'A' and resid 174 through 195
      removed outlier: 3.881A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASN A 192 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU A 193 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASP A 195 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 201 through 220
      removed outlier: 3.653A  pdb=" N   THR A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   PHE A 207 " --> pdb=" O   MET A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 229
    Processing helix  chain 'A' and resid 235 through 257
      removed outlier: 3.629A  pdb=" N   LEU A 239 " --> pdb=" O   HIS A 235 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 240 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   ILE A 241 " --> pdb=" O   GLY A 237 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE A 256 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 284
      removed outlier: 3.706A  pdb=" N   GLY A 269 " --> pdb=" O   MET A 265 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 294
    Processing helix  chain 'A' and resid 294 through 314
    Processing helix  chain 'A' and resid 323 through 332
    Processing helix  chain 'A' and resid 334 through 360
      removed outlier: 3.764A  pdb=" N   VAL A 340 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 10
    Processing helix  chain 'E' and resid 13 through 20
    Processing helix  chain 'E' and resid 21 through 41
    Processing helix  chain 'E' and resid 42 through 53
      removed outlier: 3.566A  pdb=" N   LEU E  51 " --> pdb=" O   HIS E  47 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 91
      removed outlier: 4.047A  pdb=" N   ILE E  79 " --> pdb=" O   GLY E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 122
      removed outlier: 3.737A  pdb=" N   TRP E  99 " --> pdb=" O   ASN E  95 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP E 115 " --> pdb=" O   ILE E 111 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG E 118 " --> pdb=" O   VAL E 114 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 124 through 128
      removed outlier: 3.738A  pdb=" N   GLY E 127 " --> pdb=" O   ASP E 124 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   LEU E 128 " --> pdb=" O   THR E 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 124 through 128'
    Processing helix  chain 'E' and resid 129 through 152
      removed outlier: 3.864A  pdb=" N   LYS E 133 " --> pdb=" O   ILE E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 155 through 159
    Processing helix  chain 'E' and resid 174 through 195
      removed outlier: 3.798A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 220
    Processing helix  chain 'E' and resid 221 through 229
    Processing helix  chain 'E' and resid 233 through 237
    Processing helix  chain 'E' and resid 238 through 258
      removed outlier: 3.776A  pdb=" N   PHE E 256 " --> pdb=" O   GLY E 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 265 through 284
      removed outlier: 3.731A  pdb=" N   GLY E 269 " --> pdb=" O   MET E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 286 through 294
    Processing helix  chain 'E' and resid 294 through 314
    Processing helix  chain 'E' and resid 323 through 332
      removed outlier: 3.534A  pdb=" N   HIS E 327 " --> pdb=" O   PRO E 323 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY E 332 " --> pdb=" O   TYR E 328 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 334 through 357
      removed outlier: 3.812A  pdb=" N   LEU E 357 " --> pdb=" O   GLY E 353 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 358 through 360
      No H-bonds generated for 'chain 'E' and resid 358 through 360'
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.511A  pdb=" N   THR B   9 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      Proline residue:  B  21  - end of helix
      removed outlier: 3.842A  pdb=" N   ILE B  25 " --> pdb=" O   PRO B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 4.056A  pdb=" N   ARG B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 52
      removed outlier: 3.541A  pdb=" N   ALA B  41 " --> pdb=" O   SER B  37 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 5 through 25
      Proline residue:  G  21  - end of helix
    Processing helix  chain 'G' and resid 26 through 28
      No H-bonds generated for 'chain 'G' and resid 26 through 28'
    Processing helix  chain 'G' and resid 29 through 34
    Processing helix  chain 'G' and resid 35 through 51
    Processing helix  chain 'F' and resid 42 through 50
    Processing helix  chain 'F' and resid 63 through 68
    Processing helix  chain 'F' and resid 143 through 149
    Processing helix  chain 'H' and resid 42 through 50
    Processing helix  chain 'H' and resid 72 through 74
      No H-bonds generated for 'chain 'H' and resid 72 through 74'
    Processing helix  chain 'H' and resid 143 through 149
    Processing sheet with id=AA1, first strand: chain 'B' and resid 57 through 58
      removed outlier: 3.756A  pdb=" N   THR F 110 " --> pdb=" O   VAL F 118 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   VAL F 118 " --> pdb=" O   THR F 110 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   VAL F 112 " --> pdb=" O   HIS F 116 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   HIS F 116 " --> pdb=" O   VAL F 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58
      removed outlier: 3.825A  pdb=" N   LYS G  57 " --> pdb=" O   LEU H  97 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   VAL H 118 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   VAL H 112 " --> pdb=" O   HIS H 116 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   HIS H 116 " --> pdb=" O   VAL H 112 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 22 through 25
      removed outlier: 7.747A  pdb=" N   VAL F  15 " --> pdb=" O   VAL F  23 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   GLU F  25 " --> pdb=" O   TYR F  13 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TYR F  13 " --> pdb=" O   GLU F  25 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 22 through 25
      removed outlier: 7.747A  pdb=" N   VAL F  15 " --> pdb=" O   VAL F  23 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   GLU F  25 " --> pdb=" O   TYR F  13 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TYR F  13 " --> pdb=" O   GLU F  25 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ALA F 138 " --> pdb=" O   SER F  10 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ALA F  12 " --> pdb=" O   VAL F 136 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   VAL F 136 " --> pdb=" O   ALA F  12 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   GLN F  14 " --> pdb=" O   VAL F 134 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   VAL F 134 " --> pdb=" O   GLN F  14 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   ARG F  16 " --> pdb=" O   PHE F 132 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   PHE F 132 " --> pdb=" O   ARG F  16 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25
      removed outlier: 6.918A  pdb=" N   LEU H  22 " --> pdb=" O   THR H  17 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR H  17 " --> pdb=" O   LEU H  22 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ASP H  24 " --> pdb=" O   VAL H  15 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL H  15 " --> pdb=" O   ASP H  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 25
      removed outlier: 6.918A  pdb=" N   LEU H  22 " --> pdb=" O   THR H  17 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR H  17 " --> pdb=" O   LEU H  22 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ASP H  24 " --> pdb=" O   VAL H  15 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL H  15 " --> pdb=" O   ASP H  24 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL H   8 " --> pdb=" O   ILE H 139 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ILE H 139 " --> pdb=" O   VAL H   8 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   SER H  10 " --> pdb=" O   VAL H 137 " (cutoff:3.500A)

    538 hydrogen bonds defined for protein.
    1545 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: 3.81

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 9222
        1.04 -     1.24: 1121
        1.24 -     1.44: 2771
        1.44 -     1.64: 5220
        1.64 -     1.84: 82
  Bond restraints: 18416
  Sorted by residual:
  bond pdb=" CB  MET H  85 "
       pdb=" CG  MET H  85 "
    ideal  model  delta    sigma   weight residual
    1.520  1.594 -0.074 3.00e-02 1.11e+03 6.15e+00
  bond pdb=" N   GLY G   1 "
       pdb=" CA  GLY G   1 "
    ideal  model  delta    sigma   weight residual
    1.451  1.490 -0.039 1.60e-02 3.91e+03 6.05e+00
  bond pdb=" N   GLY B   1 "
       pdb=" CA  GLY B   1 "
    ideal  model  delta    sigma   weight residual
    1.451  1.490 -0.039 1.60e-02 3.91e+03 6.03e+00
  bond pdb=" CG  MET H  85 "
       pdb=" SD  MET H  85 "
    ideal  model  delta    sigma   weight residual
    1.803  1.842 -0.039 2.50e-02 1.60e+03 2.43e+00
  bond pdb=" N   GLY G   1 "
       pdb=" H   GLY G   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.35e+00
  ... (remaining 18411 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 33274
        2.52 -     5.05: 125
        5.05 -     7.57: 12
        7.57 -    10.09: 2
       10.09 -    12.61: 1
  Bond angle restraints: 33414
  Sorted by residual:
  angle pdb=" CG  MET H  85 "
        pdb=" SD  MET H  85 "
        pdb=" CE  MET H  85 "
      ideal   model   delta    sigma   weight residual
     100.90  110.19   -9.29 2.20e+00 2.07e-01 1.78e+01
  angle pdb=" CB  MET H  85 "
        pdb=" CG  MET H  85 "
        pdb=" SD  MET H  85 "
      ideal   model   delta    sigma   weight residual
     112.70  125.31  -12.61 3.00e+00 1.11e-01 1.77e+01
  angle pdb=" N   MET H  85 "
        pdb=" CA  MET H  85 "
        pdb=" CB  MET H  85 "
      ideal   model   delta    sigma   weight residual
     111.56  117.41   -5.85 1.58e+00 4.01e-01 1.37e+01
  angle pdb=" C   MET A 203 "
        pdb=" N   PRO A 204 "
        pdb=" CD  PRO A 204 "
      ideal   model   delta    sigma   weight residual
     120.60  113.40    7.20 2.20e+00 2.07e-01 1.07e+01
  angle pdb=" C   MET A 203 "
        pdb=" N   PRO A 204 "
        pdb=" CA  PRO A 204 "
      ideal   model   delta    sigma   weight residual
     127.00  134.65   -7.65 2.40e+00 1.74e-01 1.02e+01
  ... (remaining 33409 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 7447
       17.10 -    34.19: 762
       34.19 -    51.29: 266
       51.29 -    68.39: 98
       68.39 -    85.48: 7
  Dihedral angle restraints: 8580
    sinusoidal: 4602
      harmonic: 3978
  Sorted by residual:
  dihedral pdb=" CA  LEU B  24 "
           pdb=" C   LEU B  24 "
           pdb=" N   ILE B  25 "
           pdb=" CA  ILE B  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.29   17.71     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ILE A 202 "
           pdb=" C   ILE A 202 "
           pdb=" N   MET A 203 "
           pdb=" CA  MET A 203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.56   17.44     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  LEU A 197 "
           pdb=" C   LEU A 197 "
           pdb=" N   ASP A 198 "
           pdb=" CA  ASP A 198 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.21   16.79     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 8577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1040
       0.035 -    0.071: 288
       0.071 -    0.106: 99
       0.106 -    0.142: 32
       0.142 -    0.177: 3
  Chirality restraints: 1462
  Sorted by residual:
  chirality pdb=" CB  VAL A 308 "
            pdb=" CA  VAL A 308 "
            pdb=" CG1 VAL A 308 "
            pdb=" CG2 VAL A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  ILE A 230 "
            pdb=" N   ILE A 230 "
            pdb=" C   ILE A 230 "
            pdb=" CB  ILE A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.96e-01
  chirality pdb=" CA  ARG G  55 "
            pdb=" N   ARG G  55 "
            pdb=" C   ARG G  55 "
            pdb=" CB  ARG G  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1459 not shown)

  Planarity restraints: 2640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 255 "    0.025 2.00e-02 2.50e+03   1.79e-02 1.29e+01
        pdb=" CG  TRP A 255 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 255 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 255 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 255 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 255 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 255 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 255 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 255 "    0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 255 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 255 "    0.014 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 255 "    0.004 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 255 "   -0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 255 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 255 "    0.002 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 255 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  55 "    0.295 9.50e-02 1.11e+02   9.88e-02 1.10e+01
        pdb=" NE  ARG G  55 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  55 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  55 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  55 "    0.010 2.00e-02 2.50e+03
        pdb="HH11 ARG G  55 "   -0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG G  55 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG G  55 "   -0.012 2.00e-02 2.50e+03
        pdb="HH22 ARG G  55 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 335 "    0.049 5.00e-02 4.00e+02   7.37e-02 8.68e+00
        pdb=" N   PRO A 336 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 336 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 336 "    0.041 5.00e-02 4.00e+02
  ... (remaining 2637 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 1308
        2.20 -     2.80: 38234
        2.80 -     3.40: 52285
        3.40 -     4.00: 65943
        4.00 -     4.60: 102050
  Nonbonded interactions: 259820
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 287 "
            pdb=" H   GLU A 287 "
     model   vdw
     1.605 2.450
  nonbonded pdb=" O   MET E  40 "
            pdb=" H   MET E  44 "
     model   vdw
     1.641 2.450
  nonbonded pdb=" O   LEU B  19 "
            pdb=" HG  SER B  22 "
     model   vdw
     1.654 2.450
  nonbonded pdb="HE22 GLN E 307 "
            pdb=" O   PHE E 319 "
     model   vdw
     1.680 2.450
  nonbonded pdb="HH12 ARG E 314 "
            pdb=" OE1 GLN E 316 "
     model   vdw
     1.681 2.450
  ... (remaining 259815 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  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:             0.080
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     18.050
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
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   0.074   9188  Z= 0.130
  Angle     :  0.614  12.613  12508  Z= 0.312
  Chirality :  0.040   0.177   1462
  Planarity :  0.007   0.128   1546
  Dihedral  : 15.732  84.149   3236
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 19.52 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1136
  helix:  1.11 (0.21), residues: 630
  sheet:  0.53 (0.57), residues: 92
  loop : -0.10 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  43 
 TYR   0.018   0.001   TYR E 176 
 PHE   0.023   0.001   PHE A 319 
 TRP   0.058   0.002   TRP A 255 
 HIS   0.004   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9188)
  covalent geometry    : angle       0.61363 (12508)
  hydrogen bonds       : bond        0.15933 (  537)
  hydrogen bonds       : angle       5.95133 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 296
  time to evaluate  : 0.417 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.7369 (tp40) cc_final: 0.7154 (tp40)
REVERT: A  329 GLU cc_start: 0.7078 (tp30) cc_final: 0.6797 (tp30)
  outliers start: 1
  outliers final: 1
  residues processed: 296
  average time/residue: 0.2192
  time to fit residues: 87.8331
Evaluate side-chains
  293 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 292
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   85 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
H  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.155490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121542 restraints weight = 41514.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.126748 restraints weight = 14439.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.129680 restraints weight = 7444.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.131308 restraints weight = 5167.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.131952 restraints weight = 4295.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9188  Z= 0.224
  Angle     :  0.615   6.649  12508  Z= 0.324
  Chirality :  0.041   0.188   1462
  Planarity :  0.006   0.117   1546
  Dihedral  :  4.838  40.125   1235
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.95 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.24), residues: 1136
  helix:  0.86 (0.20), residues: 660
  sheet:  0.33 (0.55), residues: 90
  loop : -0.38 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  42 
 TYR   0.012   0.002   TYR E 328 
 PHE   0.020   0.002   PHE F  96 
 TRP   0.023   0.002   TRP A 255 
 HIS   0.005   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 9188)
  covalent geometry    : angle       0.61502 (12508)
  hydrogen bonds       : bond        0.04826 (  537)
  hydrogen bonds       : angle       4.77469 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 326
  time to evaluate  : 0.459 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 GLN cc_start: 0.7575 (tp40) cc_final: 0.7296 (tp40)
REVERT: A  329 GLU cc_start: 0.7031 (tp30) cc_final: 0.6740 (tp30)
REVERT: E  119 LYS cc_start: 0.8048 (tptt) cc_final: 0.7773 (tptt)
REVERT: G   24 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7939 (mp)
REVERT: F  102 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: H   96 PHE cc_start: 0.6811 (m-80) cc_final: 0.6572 (m-80)
  outliers start: 19
  outliers final: 15
  residues processed: 330
  average time/residue: 0.2185
  time to fit residues: 98.5479
Evaluate side-chains
  336 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 320
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  193 LEU
Chi-restraints excluded: chain E residue  359 VAL
Chi-restraints excluded: chain G residue   20 LEU
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   79 VAL
Chi-restraints excluded: chain H residue  107 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 9 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.151873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.117845 restraints weight = 41473.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.122997 restraints weight = 14386.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.125926 restraints weight = 7355.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.127544 restraints weight = 5071.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.128197 restraints weight = 4210.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9188  Z= 0.301
  Angle     :  0.639   6.906  12508  Z= 0.346
  Chirality :  0.043   0.201   1462
  Planarity :  0.006   0.096   1546
  Dihedral  :  4.969  29.154   1232
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.10 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.24), residues: 1136
  helix:  0.49 (0.19), residues: 662
  sheet:  0.19 (0.54), residues: 90
  loop : -0.54 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  42 
 TYR   0.017   0.002   TYR F  71 
 PHE   0.020   0.002   PHE F  96 
 TRP   0.024   0.002   TRP B  39 
 HIS   0.009   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 9188)
  covalent geometry    : angle       0.63856 (12508)
  hydrogen bonds       : bond        0.05225 (  537)
  hydrogen bonds       : angle       4.87098 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 335
  time to evaluate  : 0.459 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.6775 (m-80) cc_final: 0.6551 (m-80)
REVERT: A  244 THR cc_start: 0.8116 (p) cc_final: 0.7895 (p)
REVERT: E  138 SER cc_start: 0.8109 (p) cc_final: 0.7869 (p)
REVERT: E  321 MET cc_start: 0.7045 (mtp) cc_final: 0.6739 (mtp)
REVERT: B   50 MET cc_start: 0.6934 (tpp) cc_final: 0.6734 (tpp)
REVERT: G   55 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6000 (mtp85)
REVERT: F   14 GLN cc_start: 0.3562 (mp10) cc_final: 0.3314 (mp10)
REVERT: H   96 PHE cc_start: 0.6868 (m-80) cc_final: 0.6533 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 339
  average time/residue: 0.2310
  time to fit residues: 106.3417
Evaluate side-chains
  344 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 327
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  106 VAL
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  193 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain G residue   20 LEU
Chi-restraints excluded: chain G residue   55 ARG
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue  107 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 104 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0060
   chunk 82 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.155366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.122167 restraints weight = 41336.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.127355 restraints weight = 14165.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.130200 restraints weight = 7154.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131817 restraints weight = 4933.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132563 restraints weight = 4083.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9188  Z= 0.149
  Angle     :  0.557   6.878  12508  Z= 0.287
  Chirality :  0.040   0.181   1462
  Planarity :  0.005   0.098   1546
  Dihedral  :  4.604  33.224   1232
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.19 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.24), residues: 1136
  helix:  0.80 (0.20), residues: 668
  sheet:  0.10 (0.51), residues: 94
  loop : -0.61 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B   3 
 TYR   0.011   0.001   TYR A  92 
 PHE   0.015   0.001   PHE F  96 
 TRP   0.018   0.001   TRP B  39 
 HIS   0.003   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9188)
  covalent geometry    : angle       0.55680 (12508)
  hydrogen bonds       : bond        0.04337 (  537)
  hydrogen bonds       : angle       4.49839 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 318
  time to evaluate  : 0.462 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LEU cc_start: 0.8205 (mt) cc_final: 0.7981 (mp)
REVERT: A   35 PHE cc_start: 0.6751 (m-80) cc_final: 0.6520 (m-80)
REVERT: A  179 LEU cc_start: 0.8176 (tp) cc_final: 0.7976 (tp)
REVERT: A  197 LEU cc_start: 0.7741 (mt) cc_final: 0.7540 (mt)
REVERT: E  138 SER cc_start: 0.8072 (p) cc_final: 0.7864 (p)
REVERT: E  321 MET cc_start: 0.7110 (mtp) cc_final: 0.6334 (mtp)
REVERT: G   24 LEU cc_start: 0.8484 (mp) cc_final: 0.8178 (mp)
REVERT: H   96 PHE cc_start: 0.6772 (m-80) cc_final: 0.6510 (m-80)
  outliers start: 17
  outliers final: 15
  residues processed: 322
  average time/residue: 0.2307
  time to fit residues: 100.3196
Evaluate side-chains
  331 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 316
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  193 LEU
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  133 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.0060
   chunk 110 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 92 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.0600

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

Flipped N/Q/H residues before XYZ refinement:
F 102 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.153609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120463 restraints weight = 40971.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.125603 restraints weight = 14009.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.128476 restraints weight = 7099.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.130025 restraints weight = 4888.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.130656 restraints weight = 4063.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9188  Z= 0.169
  Angle     :  0.550   6.791  12508  Z= 0.286
  Chirality :  0.040   0.171   1462
  Planarity :  0.005   0.093   1546
  Dihedral  :  4.563  33.451   1232
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.67 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.24), residues: 1136
  helix:  0.90 (0.20), residues: 668
  sheet:  0.02 (0.50), residues: 94
  loop : -0.55 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   3 
 TYR   0.013   0.001   TYR A 232 
 PHE   0.013   0.001   PHE F  96 
 TRP   0.015   0.001   TRP B  39 
 HIS   0.006   0.001   HIS E 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9188)
  covalent geometry    : angle       0.55039 (12508)
  hydrogen bonds       : bond        0.04294 (  537)
  hydrogen bonds       : angle       4.44797 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 322
  time to evaluate  : 0.318 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LEU cc_start: 0.8213 (mt) cc_final: 0.7999 (mp)
REVERT: E  138 SER cc_start: 0.8077 (p) cc_final: 0.7866 (p)
REVERT: E  321 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6585 (mtp)
REVERT: E  341 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7261 (mmt-90)
REVERT: H   96 PHE cc_start: 0.6785 (m-80) cc_final: 0.6542 (m-80)
  outliers start: 30
  outliers final: 20
  residues processed: 332
  average time/residue: 0.2237
  time to fit residues: 100.7610
Evaluate side-chains
  340 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 318
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  193 LEU
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain E residue  321 MET
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain G residue   55 ARG
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  133 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 86 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
F 102 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.154443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.121446 restraints weight = 40725.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.126586 restraints weight = 13915.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.129471 restraints weight = 7020.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.131017 restraints weight = 4824.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.131653 restraints weight = 4005.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9188  Z= 0.133
  Angle     :  0.536   6.827  12508  Z= 0.274
  Chirality :  0.039   0.168   1462
  Planarity :  0.005   0.063   1546
  Dihedral  :  4.425  34.482   1232
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.35 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1136
  helix:  1.08 (0.20), residues: 668
  sheet:  0.12 (0.52), residues: 90
  loop : -0.48 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   3 
 TYR   0.011   0.001   TYR A 232 
 PHE   0.016   0.001   PHE E 165 
 TRP   0.013   0.001   TRP B  39 
 HIS   0.004   0.001   HIS E 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9188)
  covalent geometry    : angle       0.53605 (12508)
  hydrogen bonds       : bond        0.04035 (  537)
  hydrogen bonds       : angle       4.30972 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 319
  time to evaluate  : 0.462 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LEU cc_start: 0.8187 (mt) cc_final: 0.7971 (mp)
REVERT: A   35 PHE cc_start: 0.6773 (m-80) cc_final: 0.6530 (m-80)
REVERT: A  321 MET cc_start: 0.7873 (ttm) cc_final: 0.7646 (ttm)
REVERT: E  321 MET cc_start: 0.6927 (mtp) cc_final: 0.6670 (mtp)
REVERT: E  341 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7091 (mmt-90)
REVERT: H   96 PHE cc_start: 0.6747 (m-80) cc_final: 0.6493 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 329
  average time/residue: 0.2265
  time to fit residues: 101.1187
Evaluate side-chains
  336 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 314
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   39 TRP
Chi-restraints excluded: chain G residue   55 ARG
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  133 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 76 optimal weight:    7.9990
   chunk 99 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
F  74 ASN
F 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.153799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.120428 restraints weight = 41152.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.125583 restraints weight = 14054.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128467 restraints weight = 7118.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.130021 restraints weight = 4893.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.130656 restraints weight = 4070.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9188  Z= 0.156
  Angle     :  0.545   6.733  12508  Z= 0.281
  Chirality :  0.040   0.171   1462
  Planarity :  0.005   0.074   1546
  Dihedral  :  4.453  37.497   1232
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.50 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.25), residues: 1136
  helix:  1.11 (0.20), residues: 668
  sheet:  0.02 (0.52), residues: 90
  loop : -0.43 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   3 
 TYR   0.017   0.001   TYR A 232 
 PHE   0.012   0.001   PHE E 165 
 TRP   0.012   0.001   TRP B  39 
 HIS   0.004   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9188)
  covalent geometry    : angle       0.54512 (12508)
  hydrogen bonds       : bond        0.04091 (  537)
  hydrogen bonds       : angle       4.31810 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 318
  time to evaluate  : 0.469 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LEU cc_start: 0.8198 (mt) cc_final: 0.7989 (mp)
REVERT: A  321 MET cc_start: 0.7896 (ttm) cc_final: 0.7695 (ttm)
REVERT: E  181 TYR cc_start: 0.8571 (t80) cc_final: 0.7997 (t80)
REVERT: E  321 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6682 (mtp)
REVERT: E  330 LEU cc_start: 0.8302 (mt) cc_final: 0.8059 (mm)
REVERT: G   23 LEU cc_start: 0.8392 (tp) cc_final: 0.8150 (tt)
REVERT: H   96 PHE cc_start: 0.6793 (m-80) cc_final: 0.6491 (m-80)
  outliers start: 25
  outliers final: 22
  residues processed: 327
  average time/residue: 0.2282
  time to fit residues: 101.4320
Evaluate side-chains
  339 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 316
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain E residue  321 MET
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  359 VAL
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain B residue   39 TRP
Chi-restraints excluded: chain G residue   55 ARG
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   73 GLU
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  133 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 87 optimal weight:    7.9990
   chunk 103 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   chunk 26 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
F 102 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.154028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.121163 restraints weight = 40993.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.126308 restraints weight = 13966.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129098 restraints weight = 7015.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.130698 restraints weight = 4831.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.131400 restraints weight = 3982.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9188  Z= 0.138
  Angle     :  0.534   6.755  12508  Z= 0.273
  Chirality :  0.040   0.176   1462
  Planarity :  0.005   0.068   1546
  Dihedral  :  4.379  38.952   1232
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.92 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.25), residues: 1136
  helix:  1.19 (0.20), residues: 668
  sheet:  0.01 (0.52), residues: 90
  loop : -0.38 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B   3 
 TYR   0.018   0.001   TYR A 232 
 PHE   0.015   0.001   PHE E 165 
 TRP   0.011   0.001   TRP B  39 
 HIS   0.004   0.001   HIS E 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9188)
  covalent geometry    : angle       0.53411 (12508)
  hydrogen bonds       : bond        0.03974 (  537)
  hydrogen bonds       : angle       4.24306 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 315
  time to evaluate  : 0.499 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.6764 (m-80) cc_final: 0.6517 (m-80)
REVERT: A  321 MET cc_start: 0.7893 (ttm) cc_final: 0.7686 (ttm)
REVERT: E  181 TYR cc_start: 0.8571 (t80) cc_final: 0.7870 (t80)
REVERT: E  321 MET cc_start: 0.6947 (mtp) cc_final: 0.6731 (mtp)
REVERT: G   23 LEU cc_start: 0.8370 (tp) cc_final: 0.8144 (tt)
REVERT: H   96 PHE cc_start: 0.6768 (m-80) cc_final: 0.6480 (m-80)
  outliers start: 24
  outliers final: 23
  residues processed: 325
  average time/residue: 0.2520
  time to fit residues: 111.2261
Evaluate side-chains
  335 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 312
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  359 VAL
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   39 TRP
Chi-restraints excluded: chain G residue   20 LEU
Chi-restraints excluded: chain G residue   55 ARG
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   90 LEU
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  133 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 84 optimal weight:   30.0000
   chunk 18 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   chunk 93 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
F 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.152526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119435 restraints weight = 40912.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.124514 restraints weight = 14053.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.127345 restraints weight = 7152.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.128820 restraints weight = 4922.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.129377 restraints weight = 4116.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9188  Z= 0.259
  Angle     :  0.598   6.738  12508  Z= 0.320
  Chirality :  0.042   0.218   1462
  Planarity :  0.005   0.069   1546
  Dihedral  :  4.689  40.046   1232
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.50 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.25), residues: 1136
  helix:  0.86 (0.20), residues: 672
  sheet: -0.30 (0.51), residues: 94
  loop : -0.60 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 285 
 TYR   0.020   0.002   TYR A 232 
 PHE   0.017   0.002   PHE E 165 
 TRP   0.012   0.001   TRP E 217 
 HIS   0.007   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 9188)
  covalent geometry    : angle       0.59849 (12508)
  hydrogen bonds       : bond        0.04535 (  537)
  hydrogen bonds       : angle       4.51516 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 326
  time to evaluate  : 0.493 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.6797 (m-80) cc_final: 0.6566 (m-80)
REVERT: A  317 ARG cc_start: 0.6560 (mtm180) cc_final: 0.6289 (mtt180)
REVERT: E  138 SER cc_start: 0.8165 (t) cc_final: 0.7582 (p)
REVERT: E  341 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7528 (mmt-90)
REVERT: G   23 LEU cc_start: 0.8375 (tp) cc_final: 0.8154 (tt)
REVERT: H   96 PHE cc_start: 0.6895 (m-80) cc_final: 0.6591 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 337
  average time/residue: 0.2460
  time to fit residues: 112.3646
Evaluate side-chains
  346 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 324
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue    6 LEU
Chi-restraints excluded: chain B residue   39 TRP
Chi-restraints excluded: chain G residue   55 ARG
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue   90 LEU
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  133 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0870
   chunk 67 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 109 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0370
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 95 optimal weight:    0.0670
   overall best weight:    0.5576

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

Flipped N/Q/H residues before XYZ refinement:
** E 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.155199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122646 restraints weight = 40966.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.127661 restraints weight = 13933.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.130507 restraints weight = 7035.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.132049 restraints weight = 4805.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132650 restraints weight = 3983.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9188  Z= 0.124
  Angle     :  0.543   6.943  12508  Z= 0.277
  Chirality :  0.040   0.168   1462
  Planarity :  0.005   0.069   1546
  Dihedral  :  4.436  40.051   1232
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 23.70 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.25), residues: 1136
  helix:  1.32 (0.20), residues: 652
  sheet: -0.18 (0.53), residues: 90
  loop : -0.49 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B   3 
 TYR   0.022   0.001   TYR A 232 
 PHE   0.015   0.001   PHE A 253 
 TRP   0.011   0.001   TRP B  39 
 HIS   0.004   0.001   HIS E 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9188)
  covalent geometry    : angle       0.54316 (12508)
  hydrogen bonds       : bond        0.03987 (  537)
  hydrogen bonds       : angle       4.24083 ( 1545)

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 319
  time to evaluate  : 0.324 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 LEU cc_start: 0.8111 (mp) cc_final: 0.7879 (mp)
REVERT: A   35 PHE cc_start: 0.6783 (m-80) cc_final: 0.6524 (m-80)
REVERT: A  283 LEU cc_start: 0.8356 (mt) cc_final: 0.8004 (mp)
REVERT: A  329 GLU cc_start: 0.6919 (tp30) cc_final: 0.6601 (tp30)
REVERT: G   23 LEU cc_start: 0.8381 (tp) cc_final: 0.8138 (tt)
REVERT: H   96 PHE cc_start: 0.6746 (m-80) cc_final: 0.6446 (m-80)
REVERT: H  102 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6896 (tm-30)
  outliers start: 20
  outliers final: 18
  residues processed: 326
  average time/residue: 0.2276
  time to fit residues: 99.9553
Evaluate side-chains
  335 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 317
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain E residue   40 MET
Chi-restraints excluded: chain E residue  122 ARG
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain E residue  321 MET
Chi-restraints excluded: chain E residue  341 ARG
Chi-restraints excluded: chain E residue  344 ILE
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain B residue   39 TRP
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain F residue   77 GLN
Chi-restraints excluded: chain F residue  117 VAL
Chi-restraints excluded: chain H residue  107 VAL
Chi-restraints excluded: chain H residue  125 LEU
Chi-restraints excluded: chain H residue  133 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 99 optimal weight:    9.9990
   chunk 40 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0040
   chunk 82 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0870
   overall best weight:    0.4770

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.155774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.122980 restraints weight = 41091.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.127967 restraints weight = 13939.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.130806 restraints weight = 7081.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132297 restraints weight = 4868.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.133119 restraints weight = 4059.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9188  Z= 0.119
  Angle     :  0.539   7.454  12508  Z= 0.274
  Chirality :  0.039   0.171   1462
  Planarity :  0.004   0.046   1546
  Dihedral  :  4.320  39.366   1232
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 24.11 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.25), residues: 1136
  helix:  1.42 (0.20), residues: 652
  sheet: -0.08 (0.53), residues: 90
  loop : -0.42 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B   3 
 TYR   0.019   0.001   TYR A 232 
 PHE   0.016   0.001   PHE E 165 
 TRP   0.012   0.001   TRP A  39 
 HIS   0.004   0.001   HIS E 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9188)
  covalent geometry    : angle       0.53887 (12508)
  hydrogen bonds       : bond        0.03849 (  537)
  hydrogen bonds       : angle       4.16915 ( 1545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3786.85 seconds
wall clock time: 64 minutes 58.66 seconds (3898.66 seconds total)