Starting phenix.real_space_refine
on Thu Mar 13 04:31:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yh3_39280/03_2025/8yh3_39280.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yh3_39280/03_2025/8yh3_39280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yh3_39280/03_2025/8yh3_39280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yh3_39280/03_2025/8yh3_39280.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yh3_39280/03_2025/8yh3_39280.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yh3_39280/03_2025/8yh3_39280.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 sd=   1.094
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    5560      2.51       5
     N    1462      2.21       5
     O    1603      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8691
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "R"
      Number of atoms: 2198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2198
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1700
          Classifications: {'peptide': 211}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 208}
          Chain breaks: 2
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'6MD%rna2p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 4.86, per 1000 atoms: 0.56
  Number of scatterers: 8691
  At special positions: 0
  Unit cell: (85.47, 123.21, 124.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1603      8.00
     N    1462      7.00
     C    5560      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  83 " - pdb=" SG  CYS R 165 " distance=2.02
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.01
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  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: 2.98
  Conformation dependent library (CDL) restraints added in 996.1 milliseconds
  

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2066

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      38.3% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.705A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 34'
    Processing helix  chain 'R' and resid 10 through 40
    Processing helix  chain 'R' and resid 41 through 44
    Processing helix  chain 'R' and resid 45 through 64
    Processing helix  chain 'R' and resid 64 through 75
    Processing helix  chain 'R' and resid 79 through 115
      removed outlier: 3.735A  pdb=" N   THR R 115 " --> pdb=" O   ARG R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 117 through 122
    Processing helix  chain 'R' and resid 123 through 144
    Processing helix  chain 'R' and resid 145 through 148
    Processing helix  chain 'R' and resid 150 through 154
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.501A  pdb=" N   VAL R 170 " --> pdb=" O   ARG R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 179
      removed outlier: 3.553A  pdb=" N   MET R 176 " --> pdb=" O   ARG R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 179 through 185
    Processing helix  chain 'R' and resid 185 through 207
    Processing helix  chain 'R' and resid 225 through 254
      Proline residue:  R 244  - end of helix
    Processing helix  chain 'R' and resid 259 through 282
      removed outlier: 3.862A  pdb=" N   MET R 275 " --> pdb=" O   HIS R 271 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 285 through 295
    Processing helix  chain 'A' and resid 8 through 31
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.502A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.548A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.690A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 349
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 62 through 65
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.915A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.955A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.847A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.635A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.137A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.757A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.028A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.409A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.472A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.391A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.597A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.278A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLY S  44 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130
      removed outlier: 3.555A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.190A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.49

  Time building geometry restraints manager: 3.33 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1487
        1.31 -     1.44: 2371
        1.44 -     1.57: 4918
        1.57 -     1.69: 0
        1.69 -     1.82: 98
  Bond restraints: 8874
  Sorted by residual:
  bond pdb=" C   ASP A 200 "
       pdb=" O   ASP A 200 "
    ideal  model  delta    sigma   weight residual
    1.236  1.297 -0.061 1.22e-02 6.72e+03 2.49e+01
  bond pdb=" CA  SER R 100 "
       pdb=" CB  SER R 100 "
    ideal  model  delta    sigma   weight residual
    1.528  1.456  0.073 1.56e-02 4.11e+03 2.18e+01
  bond pdb=" C   PHE R 167 "
       pdb=" O   PHE R 167 "
    ideal  model  delta    sigma   weight residual
    1.237  1.290 -0.053 1.17e-02 7.31e+03 2.05e+01
  bond pdb=" C   TYR R 118 "
       pdb=" O   TYR R 118 "
    ideal  model  delta    sigma   weight residual
    1.236  1.287 -0.051 1.15e-02 7.56e+03 1.93e+01
  bond pdb=" C   ILE R 267 "
       pdb=" O   ILE R 267 "
    ideal  model  delta    sigma   weight residual
    1.237  1.289 -0.051 1.17e-02 7.31e+03 1.93e+01
  ... (remaining 8869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 10759
        2.05 -     4.10: 1146
        4.10 -     6.15: 99
        6.15 -     8.20: 8
        8.20 -    10.25: 6
  Bond angle restraints: 12018
  Sorted by residual:
  angle pdb=" N   PRO G  53 "
        pdb=" CA  PRO G  53 "
        pdb=" C   PRO G  53 "
      ideal   model   delta    sigma   weight residual
     111.14  121.39  -10.25 1.56e+00 4.11e-01 4.32e+01
  angle pdb=" N   GLY B 162 "
        pdb=" CA  GLY B 162 "
        pdb=" C   GLY B 162 "
      ideal   model   delta    sigma   weight residual
     114.67  108.01    6.66 1.10e+00 8.26e-01 3.66e+01
  angle pdb=" N   LEU R  84 "
        pdb=" CA  LEU R  84 "
        pdb=" C   LEU R  84 "
      ideal   model   delta    sigma   weight residual
     111.82  105.46    6.36 1.16e+00 7.43e-01 3.01e+01
  angle pdb=" C   HIS S  35 "
        pdb=" CA  HIS S  35 "
        pdb=" CB  HIS S  35 "
      ideal   model   delta    sigma   weight residual
     109.80  101.52    8.28 1.65e+00 3.67e-01 2.52e+01
  angle pdb=" N   VAL R 121 "
        pdb=" CA  VAL R 121 "
        pdb=" C   VAL R 121 "
      ideal   model   delta    sigma   weight residual
     113.42  107.70    5.72 1.17e+00 7.31e-01 2.39e+01
  ... (remaining 12013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 4648
       15.91 -    31.82: 490
       31.82 -    47.73: 105
       47.73 -    63.63: 23
       63.63 -    79.54: 5
  Dihedral angle restraints: 5271
    sinusoidal: 2069
      harmonic: 3202
  Sorted by residual:
  dihedral pdb=" CD  ARG S  67 "
           pdb=" NE  ARG S  67 "
           pdb=" CZ  ARG S  67 "
           pdb=" NH1 ARG S  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.41  -75.41     1      1.00e+01 1.00e-02 7.18e+01
  dihedral pdb=" CD  ARG R 172 "
           pdb=" NE  ARG R 172 "
           pdb=" CZ  ARG R 172 "
           pdb=" NH1 ARG R 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -52.92   52.92     1      1.00e+01 1.00e-02 3.81e+01
  dihedral pdb=" C1' 6MD R 801 "
           pdb=" C2' 6MD R 801 "
           pdb=" C3' 6MD R 801 "
           pdb=" C4' 6MD R 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00    2.40  -37.40     1      8.00e+00 1.56e-02 3.08e+01
  ... (remaining 5268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1070
       0.098 -    0.196: 275
       0.196 -    0.294: 27
       0.294 -    0.392: 2
       0.392 -    0.489: 2
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CA  PRO G  53 "
            pdb=" N   PRO G  53 "
            pdb=" C   PRO G  53 "
            pdb=" CB  PRO G  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.23    0.49 2.00e-01 2.50e+01 5.99e+00
  chirality pdb=" CB  VAL R 112 "
            pdb=" CA  VAL R 112 "
            pdb=" CG1 VAL R 112 "
            pdb=" CG2 VAL R 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.20   -0.43 2.00e-01 2.50e+01 4.58e+00
  chirality pdb=" CB  VAL A 332 "
            pdb=" CA  VAL A 332 "
            pdb=" CG1 VAL A 332 "
            pdb=" CG2 VAL A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.13e+00
  ... (remaining 1373 not shown)

  Planarity restraints: 1498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' 6MD R 801 "   -0.174 2.00e-02 2.50e+03   7.31e-02 1.47e+02
        pdb=" C2  6MD R 801 "    0.008 2.00e-02 2.50e+03
        pdb=" C4  6MD R 801 "    0.060 2.00e-02 2.50e+03
        pdb=" C5  6MD R 801 "    0.044 2.00e-02 2.50e+03
        pdb=" C6  6MD R 801 "   -0.002 2.00e-02 2.50e+03
        pdb=" C8  6MD R 801 "    0.048 2.00e-02 2.50e+03
        pdb=" N1  6MD R 801 "   -0.016 2.00e-02 2.50e+03
        pdb=" N3  6MD R 801 "    0.049 2.00e-02 2.50e+03
        pdb=" N6  6MD R 801 "   -0.115 2.00e-02 2.50e+03
        pdb=" N7  6MD R 801 "    0.039 2.00e-02 2.50e+03
        pdb=" N9  6MD R 801 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG S  67 "   -1.060 9.50e-02 1.11e+02   4.75e-01 1.36e+02
        pdb=" NE  ARG S  67 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG S  67 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG S  67 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG S  67 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 172 "    0.861 9.50e-02 1.11e+02   3.86e-01 9.04e+01
        pdb=" NE  ARG R 172 "   -0.053 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 172 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 172 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 172 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1495 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 232
        2.68 -     3.23: 8682
        3.23 -     3.79: 13582
        3.79 -     4.34: 19393
        4.34 -     4.90: 31082
  Nonbonded interactions: 72971
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN S 130 "
            pdb=" OG1 THR S 231 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER S  99 "
            pdb=" O   PRO S 107 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   LEU A 249 "
            pdb=" OG  SER A 252 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OH  TYR A 287 "
            pdb=" OE1 GLN A 306 "
     model   vdw
     2.211 3.040
  ... (remaining 72966 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.330
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5706
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      :  0.010   0.073   8874  Z= 0.654
  Angle     :  1.218  10.252  12018  Z= 0.865
  Chirality :  0.081   0.489   1376
  Planarity :  0.022   0.475   1498
  Dihedral  : 13.857  79.543   3196
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.52 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  3.36 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.25), residues: 1085
  helix:  0.37 (0.26), residues: 362
  sheet: -0.95 (0.30), residues: 269
  loop : -0.72 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.004   TRP A 211 
 HIS   0.019   0.004   HIS A 322 
 PHE   0.041   0.005   PHE A 334 
 TYR   0.029   0.004   TYR R 292 
 ARG   0.013   0.001   ARG R 168 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 323
  time to evaluate  : 0.885 
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: R   99 MET cc_start: 0.6520 (mmp) cc_final: 0.6261 (mmp)
REVERT: A  337 ASP cc_start: 0.5559 (m-30) cc_final: 0.5110 (m-30)
REVERT: A  354 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5566 (m-80)
  outliers start: 11
  outliers final: 0
  residues processed: 331
  average time/residue: 0.2397
  time to fit residues: 103.3038
Evaluate side-chains
  184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  79 HIS
R 249 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 213 HIS
A 244 HIS
A 255 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.133026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.108484 restraints weight = 22272.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 4.37
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8874  Z= 0.236
  Angle     :  0.691  10.863  12018  Z= 0.365
  Chirality :  0.045   0.225   1376
  Planarity :  0.005   0.049   1498
  Dihedral  :  5.072  57.493   1216
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.59 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 14.48 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.26), residues: 1085
  helix:  1.04 (0.27), residues: 365
  sheet: -0.85 (0.29), residues: 287
  loop : -0.63 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.021   0.002   PHE S 108 
 TYR   0.022   0.002   TYR S 178 
 ARG   0.007   0.001   ARG R 206 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 222
  time to evaluate  : 0.886 
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: B   82 TRP cc_start: 0.8431 (m100) cc_final: 0.8086 (m100)
REVERT: B  258 ASP cc_start: 0.6497 (m-30) cc_final: 0.6101 (t0)
REVERT: B  262 MET cc_start: 0.7634 (tpt) cc_final: 0.6630 (tpt)
REVERT: R   17 THR cc_start: 0.8297 (p) cc_final: 0.8038 (t)
REVERT: R  171 MET cc_start: 0.8132 (tpp) cc_final: 0.7557 (tpp)
REVERT: R  206 ARG cc_start: 0.8387 (ttt90) cc_final: 0.8097 (tpt-90)
REVERT: A   21 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8467 (ttm110)
REVERT: A   28 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: A   53 MET cc_start: 0.6120 (tpp) cc_final: 0.5601 (tpp)
REVERT: A  204 GLN cc_start: 0.9329 (tp-100) cc_final: 0.9078 (tp-100)
REVERT: A  287 TYR cc_start: 0.7433 (t80) cc_final: 0.7228 (t80)
REVERT: A  293 SER cc_start: 0.9061 (t) cc_final: 0.8802 (p)
REVERT: A  333 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8243 (tm-30)
REVERT: A  337 ASP cc_start: 0.8466 (m-30) cc_final: 0.8131 (m-30)
REVERT: A  354 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.5618 (m-80)
REVERT: S   93 MET cc_start: 0.7825 (mmm) cc_final: 0.7580 (tmm)
  outliers start: 23
  outliers final: 12
  residues processed: 240
  average time/residue: 0.2254
  time to fit residues: 72.5433
Evaluate side-chains
  186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  286 LYS
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  202 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0570
   chunk 89 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.4900

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
R  95 HIS
R 249 ASN
A 304 GLN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.126526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.102775 restraints weight = 22675.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 4.31
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.5481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8874  Z= 0.247
  Angle     :  0.683   9.695  12018  Z= 0.362
  Chirality :  0.045   0.194   1376
  Planarity :  0.005   0.050   1498
  Dihedral  :  4.782  54.872   1216
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.06 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.42 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.26), residues: 1085
  helix:  1.37 (0.28), residues: 364
  sheet: -0.78 (0.30), residues: 276
  loop : -0.52 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 184 
 HIS   0.007   0.001   HIS R  95 
 PHE   0.020   0.002   PHE R  93 
 TYR   0.016   0.002   TYR S  60 
 ARG   0.009   0.001   ARG A 205 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 203
  time to evaluate  : 0.985 
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: B   82 TRP cc_start: 0.8546 (m100) cc_final: 0.8161 (m100)
REVERT: B  176 GLN cc_start: 0.8906 (pt0) cc_final: 0.8640 (pt0)
REVERT: B  233 CYS cc_start: 0.7223 (t) cc_final: 0.7015 (t)
REVERT: B  258 ASP cc_start: 0.7151 (m-30) cc_final: 0.6647 (t70)
REVERT: B  292 PHE cc_start: 0.8340 (m-80) cc_final: 0.8074 (m-80)
REVERT: A   53 MET cc_start: 0.5532 (tpp) cc_final: 0.4904 (tpp)
REVERT: A  267 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8524 (m-80)
REVERT: A  354 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6068 (m-80)
REVERT: S   19 LYS cc_start: 0.8898 (mttm) cc_final: 0.8071 (mmtm)
REVERT: S   34 MET cc_start: 0.6910 (mmp) cc_final: 0.5823 (mmp)
REVERT: S   93 MET cc_start: 0.7906 (mmm) cc_final: 0.7703 (tmm)
  outliers start: 22
  outliers final: 9
  residues processed: 216
  average time/residue: 0.2393
  time to fit residues: 68.3826
Evaluate side-chains
  170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  185 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 96 optimal weight:    0.2980
   chunk 27 optimal weight:    0.1980
   chunk 61 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 85 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B  91 HIS
R  44 GLN
A 244 HIS
A 256 ASN
S 130 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.128954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.103784 restraints weight = 21835.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 4.40
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.6050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8874  Z= 0.192
  Angle     :  0.656   9.978  12018  Z= 0.339
  Chirality :  0.043   0.155   1376
  Planarity :  0.004   0.042   1498
  Dihedral  :  4.516  54.317   1216
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.59 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 21.20 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1085
  helix:  1.52 (0.28), residues: 373
  sheet: -0.58 (0.30), residues: 279
  loop : -0.42 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP R 184 
 HIS   0.003   0.001   HIS R 271 
 PHE   0.035   0.002   PHE R  50 
 TYR   0.014   0.001   TYR R 283 
 ARG   0.006   0.001   ARG R 206 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 0.815 
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: B    7 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6395 (tp)
REVERT: B   82 TRP cc_start: 0.8545 (m100) cc_final: 0.8133 (m100)
REVERT: B  124 TYR cc_start: 0.7864 (m-80) cc_final: 0.7617 (m-80)
REVERT: B  176 GLN cc_start: 0.8870 (pt0) cc_final: 0.8670 (pt0)
REVERT: B  226 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7403 (mp0)
REVERT: B  258 ASP cc_start: 0.6967 (m-30) cc_final: 0.6527 (t0)
REVERT: B  292 PHE cc_start: 0.8136 (m-80) cc_final: 0.7800 (m-80)
REVERT: R  284 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7705 (mmmt)
REVERT: A   53 MET cc_start: 0.5539 (tpp) cc_final: 0.4917 (tpp)
REVERT: A  205 ARG cc_start: 0.8623 (mmm160) cc_final: 0.7956 (mmm160)
REVERT: A  354 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.5793 (m-80)
REVERT: S   19 LYS cc_start: 0.8738 (mttm) cc_final: 0.8028 (mmtm)
REVERT: S   34 MET cc_start: 0.7115 (mmp) cc_final: 0.6129 (mmp)
REVERT: S   43 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8645 (mmmm)
REVERT: S   93 MET cc_start: 0.8174 (mmm) cc_final: 0.7944 (tmm)
REVERT: S   94 TYR cc_start: 0.8290 (m-80) cc_final: 0.7908 (m-10)
REVERT: S  103 TYR cc_start: 0.7555 (t80) cc_final: 0.7111 (t80)
REVERT: S  234 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7865 (mp0)
REVERT: G   47 GLU cc_start: 0.7891 (tp30) cc_final: 0.7680 (tp30)
  outliers start: 29
  outliers final: 16
  residues processed: 203
  average time/residue: 0.2307
  time to fit residues: 62.7086
Evaluate side-chains
  178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   34 ILE
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  134 CYS
Chi-restraints excluded: chain R residue  233 LEU
Chi-restraints excluded: chain R residue  286 LYS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  163 TYR
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 102 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.7562

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.127065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.103385 restraints weight = 22511.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 4.31
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.6465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8874  Z= 0.187
  Angle     :  0.641  10.252  12018  Z= 0.330
  Chirality :  0.043   0.251   1376
  Planarity :  0.004   0.040   1498
  Dihedral  :  4.460  52.978   1216
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.42 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.25 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1085
  helix:  1.47 (0.27), residues: 379
  sheet: -0.56 (0.30), residues: 273
  loop : -0.45 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 184 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.022   0.001   PHE B 253 
 TYR   0.022   0.001   TYR S 178 
 ARG   0.009   0.001   ARG A 208 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 181
  time to evaluate  : 0.914 
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: B    7 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6407 (tp)
REVERT: B  124 TYR cc_start: 0.7969 (m-80) cc_final: 0.7651 (m-80)
REVERT: B  226 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7554 (mp0)
REVERT: B  233 CYS cc_start: 0.7106 (t) cc_final: 0.6899 (t)
REVERT: B  258 ASP cc_start: 0.7039 (m-30) cc_final: 0.6611 (t0)
REVERT: B  262 MET cc_start: 0.7284 (mmm) cc_final: 0.6800 (mmt)
REVERT: B  292 PHE cc_start: 0.8195 (m-80) cc_final: 0.7727 (m-10)
REVERT: R   30 ASN cc_start: 0.7070 (m-40) cc_final: 0.6732 (m-40)
REVERT: R   58 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7764 (t70)
REVERT: R   99 MET cc_start: 0.8702 (mmm) cc_final: 0.8381 (mmp)
REVERT: R  206 ARG cc_start: 0.8514 (tpt-90) cc_final: 0.8246 (ttt90)
REVERT: R  284 LYS cc_start: 0.8466 (mmmt) cc_final: 0.7916 (mmmt)
REVERT: A   53 MET cc_start: 0.5704 (tpp) cc_final: 0.5112 (tpp)
REVERT: A  354 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.5926 (m-80)
REVERT: S   19 LYS cc_start: 0.8710 (mttm) cc_final: 0.8262 (mmtm)
REVERT: S   82 GLN cc_start: 0.7568 (tp-100) cc_final: 0.6723 (tp-100)
REVERT: S   94 TYR cc_start: 0.8277 (m-80) cc_final: 0.7807 (m-10)
REVERT: S  103 TYR cc_start: 0.7539 (t80) cc_final: 0.7188 (t80)
REVERT: S  148 ARG cc_start: 0.8819 (ptm-80) cc_final: 0.8545 (ptm-80)
REVERT: G   48 ASP cc_start: 0.7673 (t0) cc_final: 0.7373 (t70)
  outliers start: 28
  outliers final: 18
  residues processed: 198
  average time/residue: 0.2266
  time to fit residues: 60.1776
Evaluate side-chains
  186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   20 ILE
Chi-restraints excluded: chain R residue   58 ASP
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  134 CYS
Chi-restraints excluded: chain R residue  144 THR
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  286 LYS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  207 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 102 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 106 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
A 256 ASN
A 304 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.124858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.101213 restraints weight = 22565.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 4.29
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.6883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8874  Z= 0.216
  Angle     :  0.663   9.929  12018  Z= 0.343
  Chirality :  0.044   0.178   1376
  Planarity :  0.004   0.038   1498
  Dihedral  :  4.438  52.800   1216
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.15 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.56 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1085
  helix:  1.52 (0.28), residues: 379
  sheet: -0.51 (0.30), residues: 272
  loop : -0.52 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 184 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.031   0.002   PHE R  50 
 TYR   0.016   0.001   TYR R 109 
 ARG   0.009   0.001   ARG A 208 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.907 
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: B    7 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6410 (tp)
REVERT: B  124 TYR cc_start: 0.8036 (m-80) cc_final: 0.7729 (m-80)
REVERT: B  226 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7867 (mp0)
REVERT: B  258 ASP cc_start: 0.6972 (m-30) cc_final: 0.6511 (t0)
REVERT: B  280 LYS cc_start: 0.8690 (tttt) cc_final: 0.8313 (tttm)
REVERT: B  292 PHE cc_start: 0.8226 (m-80) cc_final: 0.7706 (m-10)
REVERT: R   58 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7796 (t70)
REVERT: R   99 MET cc_start: 0.8559 (mmm) cc_final: 0.8225 (mmp)
REVERT: R  173 MET cc_start: 0.7390 (mmm) cc_final: 0.7171 (mpp)
REVERT: R  184 TRP cc_start: 0.7601 (m-90) cc_final: 0.7175 (m-90)
REVERT: R  284 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8173 (mmmt)
REVERT: A   35 LYS cc_start: 0.8466 (mtmm) cc_final: 0.8249 (mtmt)
REVERT: A   53 MET cc_start: 0.5562 (tpp) cc_final: 0.4944 (tpp)
REVERT: A  256 ASN cc_start: 0.8007 (m110) cc_final: 0.7740 (m110)
REVERT: A  354 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.5960 (m-80)
REVERT: S   34 MET cc_start: 0.6634 (mmm) cc_final: 0.5256 (mmp)
REVERT: S  148 ARG cc_start: 0.8724 (ptm-80) cc_final: 0.8459 (ptm-80)
REVERT: G   42 GLU cc_start: 0.7751 (pp20) cc_final: 0.7382 (pt0)
  outliers start: 30
  outliers final: 18
  residues processed: 198
  average time/residue: 0.2202
  time to fit residues: 58.5656
Evaluate side-chains
  182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   20 ILE
Chi-restraints excluded: chain R residue   58 ASP
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  134 CYS
Chi-restraints excluded: chain R residue  144 THR
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  207 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 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 = 0.3980 r_free = 0.3980 target = 0.121434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.096763 restraints weight = 22807.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 4.45
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.7469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8874  Z= 0.279
  Angle     :  0.721   9.929  12018  Z= 0.375
  Chirality :  0.045   0.210   1376
  Planarity :  0.004   0.035   1498
  Dihedral  :  4.731  54.403   1216
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.70 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 24.45 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1085
  helix:  1.45 (0.27), residues: 376
  sheet: -0.59 (0.30), residues: 272
  loop : -0.55 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 211 
 HIS   0.007   0.002   HIS B 225 
 PHE   0.016   0.002   PHE S 200 
 TYR   0.020   0.002   TYR S 103 
 ARG   0.008   0.001   ARG R 206 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 170
  time to evaluate  : 0.912 
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: B    7 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6410 (tp)
REVERT: B  226 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8002 (mp0)
REVERT: B  267 ASP cc_start: 0.8748 (t0) cc_final: 0.8457 (p0)
REVERT: B  292 PHE cc_start: 0.8402 (m-80) cc_final: 0.7684 (m-10)
REVERT: R   58 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8235 (t70)
REVERT: R   99 MET cc_start: 0.8595 (mmm) cc_final: 0.8371 (mmp)
REVERT: R  119 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8235 (mmm-85)
REVERT: R  173 MET cc_start: 0.7493 (mmm) cc_final: 0.7273 (mpp)
REVERT: R  284 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8086 (mmmt)
REVERT: A  205 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.7235 (tmm160)
REVERT: A  354 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6341 (m-80)
REVERT: S   19 LYS cc_start: 0.8825 (mttm) cc_final: 0.8373 (mmtp)
REVERT: G   47 GLU cc_start: 0.7731 (tp30) cc_final: 0.7508 (tp30)
  outliers start: 35
  outliers final: 20
  residues processed: 193
  average time/residue: 0.2228
  time to fit residues: 57.6302
Evaluate side-chains
  175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   20 ILE
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   47 THR
Chi-restraints excluded: chain R residue   58 ASP
Chi-restraints excluded: chain R residue   83 CYS
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  134 CYS
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  207 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 103 optimal weight:   20.0000
   chunk 55 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 0 optimal weight:   50.0000
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
R 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.122955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.098078 restraints weight = 22517.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 4.49
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.7722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8874  Z= 0.218
  Angle     :  0.702  10.421  12018  Z= 0.360
  Chirality :  0.043   0.206   1376
  Planarity :  0.004   0.035   1498
  Dihedral  :  4.680  54.089   1216
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.15 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.55 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.26), residues: 1085
  helix:  1.47 (0.27), residues: 379
  sheet: -0.48 (0.31), residues: 269
  loop : -0.55 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.029   0.002   PHE R  50 
 TYR   0.021   0.001   TYR S 103 
 ARG   0.006   0.001   ARG R 206 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6449 (tp)
REVERT: B   82 TRP cc_start: 0.8584 (m100) cc_final: 0.8223 (m100)
REVERT: B  226 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8043 (mp0)
REVERT: B  292 PHE cc_start: 0.8326 (m-80) cc_final: 0.7582 (m-10)
REVERT: R   15 TYR cc_start: 0.7196 (t80) cc_final: 0.6887 (t80)
REVERT: R   47 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8316 (t)
REVERT: R   58 ASP cc_start: 0.8443 (t0) cc_final: 0.8236 (t70)
REVERT: R   86 MET cc_start: 0.3661 (mtt) cc_final: 0.3415 (mtt)
REVERT: R  113 LYS cc_start: 0.7886 (tmtt) cc_final: 0.7394 (tptp)
REVERT: R  119 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8294 (mmm-85)
REVERT: R  173 MET cc_start: 0.7530 (mmm) cc_final: 0.7304 (mpp)
REVERT: R  183 LEU cc_start: 0.8417 (tp) cc_final: 0.7981 (tp)
REVERT: R  184 TRP cc_start: 0.7475 (m-90) cc_final: 0.6966 (m-90)
REVERT: R  275 MET cc_start: 0.7937 (tmm) cc_final: 0.7223 (tpt)
REVERT: R  284 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8077 (mmmt)
REVERT: A   33 GLU cc_start: 0.6782 (pp20) cc_final: 0.6181 (pp20)
REVERT: A  354 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6221 (m-80)
REVERT: S   19 LYS cc_start: 0.8811 (mttm) cc_final: 0.8374 (mmtp)
REVERT: S   42 GLU cc_start: 0.9127 (pm20) cc_final: 0.8892 (pm20)
REVERT: S   43 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8573 (mmmm)
  outliers start: 30
  outliers final: 18
  residues processed: 188
  average time/residue: 0.2201
  time to fit residues: 55.7851
Evaluate side-chains
  175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   20 ILE
Chi-restraints excluded: chain R residue   47 THR
Chi-restraints excluded: chain R residue   83 CYS
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  134 CYS
Chi-restraints excluded: chain R residue  144 THR
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue  159 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    8.9990
   chunk 87 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 92 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0770
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.2144

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.123672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.098706 restraints weight = 22596.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 4.46
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.7989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8874  Z= 0.227
  Angle     :  0.736  10.542  12018  Z= 0.373
  Chirality :  0.045   0.218   1376
  Planarity :  0.004   0.035   1498
  Dihedral  :  4.776  53.718   1216
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 25.18 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1085
  helix:  1.48 (0.27), residues: 381
  sheet: -0.51 (0.31), residues: 269
  loop : -0.52 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 211 
 HIS   0.005   0.001   HIS A 322 
 PHE   0.016   0.002   PHE A 250 
 TYR   0.025   0.002   TYR R 264 
 ARG   0.009   0.001   ARG R 206 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6462 (tp)
REVERT: B   45 MET cc_start: 0.7746 (ppp) cc_final: 0.7049 (ppp)
REVERT: B   82 TRP cc_start: 0.8589 (m100) cc_final: 0.8366 (m100)
REVERT: B  226 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7892 (mp0)
REVERT: B  292 PHE cc_start: 0.8366 (m-80) cc_final: 0.7677 (m-10)
REVERT: R   15 TYR cc_start: 0.7150 (t80) cc_final: 0.6819 (t80)
REVERT: R   58 ASP cc_start: 0.8407 (t0) cc_final: 0.8179 (t70)
REVERT: R  113 LYS cc_start: 0.7943 (tmtt) cc_final: 0.7494 (tptp)
REVERT: R  119 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8499 (mmm-85)
REVERT: R  173 MET cc_start: 0.7528 (mmm) cc_final: 0.7281 (mpp)
REVERT: R  275 MET cc_start: 0.7932 (tmm) cc_final: 0.7159 (tpt)
REVERT: R  284 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8057 (mmmt)
REVERT: R  290 GLU cc_start: 0.8621 (mp0) cc_final: 0.8167 (mp0)
REVERT: A   33 GLU cc_start: 0.6767 (pp20) cc_final: 0.6445 (pp20)
REVERT: A  195 HIS cc_start: 0.8160 (t-90) cc_final: 0.7841 (t-90)
REVERT: A  354 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6377 (m-80)
REVERT: S   19 LYS cc_start: 0.8831 (mttm) cc_final: 0.8267 (mmtp)
REVERT: S   34 MET cc_start: 0.6496 (mmm) cc_final: 0.5757 (mmm)
REVERT: G   42 GLU cc_start: 0.7646 (pp20) cc_final: 0.7140 (pt0)
  outliers start: 28
  outliers final: 23
  residues processed: 185
  average time/residue: 0.2099
  time to fit residues: 52.9253
Evaluate side-chains
  181 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   20 ILE
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   83 CYS
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  134 CYS
Chi-restraints excluded: chain R residue  144 THR
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  286 LYS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 48 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.125082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.100219 restraints weight = 22428.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 4.45
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.8147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8874  Z= 0.203
  Angle     :  0.736  11.020  12018  Z= 0.373
  Chirality :  0.044   0.205   1376
  Planarity :  0.004   0.035   1498
  Dihedral  :  4.742  52.885   1216
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.92 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1085
  helix:  1.55 (0.27), residues: 380
  sheet: -0.50 (0.30), residues: 274
  loop : -0.53 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP R 184 
 HIS   0.003   0.001   HIS A 322 
 PHE   0.021   0.002   PHE R  50 
 TYR   0.036   0.002   TYR R 264 
 ARG   0.011   0.001   ARG B 314 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.998 
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: B    7 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6453 (tp)
REVERT: B   45 MET cc_start: 0.7570 (ppp) cc_final: 0.6886 (ppp)
REVERT: B  226 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7972 (mp0)
REVERT: B  289 TYR cc_start: 0.7235 (m-80) cc_final: 0.6535 (m-80)
REVERT: B  292 PHE cc_start: 0.8357 (m-80) cc_final: 0.7896 (m-10)
REVERT: R  113 LYS cc_start: 0.7890 (tmtt) cc_final: 0.7438 (tptp)
REVERT: R  119 ARG cc_start: 0.8899 (mmm-85) cc_final: 0.8503 (mmm-85)
REVERT: R  275 MET cc_start: 0.7868 (tmm) cc_final: 0.7163 (tpt)
REVERT: R  284 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8087 (mmmt)
REVERT: R  290 GLU cc_start: 0.8569 (mp0) cc_final: 0.8099 (mp0)
REVERT: A   33 GLU cc_start: 0.6636 (pp20) cc_final: 0.6330 (pp20)
REVERT: A  195 HIS cc_start: 0.8121 (t-90) cc_final: 0.7719 (t-90)
REVERT: A  354 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6410 (m-80)
REVERT: S   19 LYS cc_start: 0.8795 (mttm) cc_final: 0.8137 (mmtp)
REVERT: S   34 MET cc_start: 0.6437 (mmm) cc_final: 0.5700 (mmm)
REVERT: G   42 GLU cc_start: 0.7658 (pp20) cc_final: 0.7218 (pt0)
  outliers start: 26
  outliers final: 21
  residues processed: 183
  average time/residue: 0.2181
  time to fit residues: 54.5058
Evaluate side-chains
  178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   20 ILE
Chi-restraints excluded: chain R residue   83 CYS
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  134 CYS
Chi-restraints excluded: chain R residue  144 THR
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  286 LYS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  159 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 94 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
R 150 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.123293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.098501 restraints weight = 22582.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 4.49
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.8353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8874  Z= 0.244
  Angle     :  0.771  13.194  12018  Z= 0.386
  Chirality :  0.045   0.219   1376
  Planarity :  0.004   0.034   1498
  Dihedral  :  4.847  53.186   1216
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 27.07 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1085
  helix:  1.52 (0.27), residues: 379
  sheet: -0.60 (0.30), residues: 278
  loop : -0.57 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP R 184 
 HIS   0.004   0.001   HIS A 322 
 PHE   0.038   0.002   PHE R  93 
 TYR   0.030   0.002   TYR R 264 
 ARG   0.008   0.001   ARG R 206 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4146.23 seconds
wall clock time: 72 minutes 8.59 seconds (4328.59 seconds total)