Starting phenix.real_space_refine
on Wed Sep 17 12:44:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyv_60580/09_2025/8zyv_60580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyv_60580/09_2025/8zyv_60580.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyv_60580/09_2025/8zyv_60580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyv_60580/09_2025/8zyv_60580.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyv_60580/09_2025/8zyv_60580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyv_60580/09_2025/8zyv_60580.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      77      5.16       5
     Na      2      4.78       5
     C    5741      2.51       5
     N    1469      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8913
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 361
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 368
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "C"
      Number of atoms: 1601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1621
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 6, 'TRANS': 207}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' NA': 2}
          Classifications: {'undetermined': 2, 'water': 2}
          Link IDs: {None: 3}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb="NA    NA A 502 " occ=0.97
    residue:
      pdb=" O   HOH A 601 " occ=0.65
    residue:
      pdb=" O   HOH E 602 " occ=0.97
    residue:
      pdb=" O   HOH G 301 " occ=0.42
  Time building chain proxies: 2.43, per 1000 atoms: 0.27
  Number of scatterers: 8913
  At special positions: 0
  Unit cell: (102.6, 98.55, 105.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      77     16.00
     Na      2     11.00
     O    1624      8.00
     N    1469      7.00
     C    5741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 377.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 1 sheets defined
      91.3% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.877A  pdb=" N   GLY A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 59
    Processing helix  chain 'B' and resid 18 through 39
      removed outlier: 3.956A  pdb=" N   PHE B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 58
    Processing helix  chain 'C' and resid 31 through 50
    Processing helix  chain 'C' and resid 51 through 68
    Processing helix  chain 'C' and resid 72 through 87
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.974A  pdb=" N   ASP C 114 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 167
      removed outlier: 3.639A  pdb=" N   VAL C 121 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
      Proline residue:  C 151  - end of helix
    Processing helix  chain 'C' and resid 171 through 173
      No H-bonds generated for 'chain 'C' and resid 171 through 173'
    Processing helix  chain 'C' and resid 174 through 195
      removed outlier: 3.939A  pdb=" N   MET C 179 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ALA C 180 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL C 181 " --> pdb=" O   PRO C 177 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR C 185 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   THR C 186 " --> pdb=" O   ALA C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 228
    Processing helix  chain 'C' and resid 230 through 240
    Processing helix  chain 'D' and resid 31 through 47
    Processing helix  chain 'D' and resid 51 through 68
    Processing helix  chain 'D' and resid 72 through 87
      removed outlier: 3.964A  pdb=" N   ASP D  85 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ALA D  86 " --> pdb=" O   GLU D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 115
    Processing helix  chain 'D' and resid 117 through 167
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 175 through 196
      removed outlier: 3.734A  pdb=" N   VAL D 181 " --> pdb=" O   PRO D 177 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ALA D 182 " --> pdb=" O   ALA D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 228
    Processing helix  chain 'D' and resid 230 through 239
      removed outlier: 4.293A  pdb=" N   ILE D 234 " --> pdb=" O   ASN D 230 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ASP D 235 " --> pdb=" O   PRO D 231 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER D 236 " --> pdb=" O   ARG D 232 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   TYR D 237 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LYS D 239 " --> pdb=" O   ASP D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 250
      removed outlier: 3.556A  pdb=" N   ARG D 247 " --> pdb=" O   GLU D 244 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU D 249 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 48
      removed outlier: 3.565A  pdb=" N   ASP E  31 " --> pdb=" O   GLY E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 68
    Processing helix  chain 'E' and resid 72 through 87
    Processing helix  chain 'E' and resid 102 through 114
    Processing helix  chain 'E' and resid 117 through 168
      Proline residue:  E 151  - end of helix
    Processing helix  chain 'E' and resid 171 through 196
      removed outlier: 3.807A  pdb=" N   GLY E 176 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      Proline residue:  E 177  - end of helix
    Processing helix  chain 'E' and resid 196 through 228
    Processing helix  chain 'E' and resid 230 through 240
    Processing helix  chain 'E' and resid 241 through 248
      removed outlier: 6.723A  pdb=" N   GLY E 245 " --> pdb=" O   LEU E 242 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   LYS E 246 " --> pdb=" O   ASN E 243 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA E 248 " --> pdb=" O   GLY E 245 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 23
    Processing helix  chain 'F' and resid 32 through 47
      removed outlier: 3.564A  pdb=" N   VAL F  38 " --> pdb=" O   SER F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 68
    Processing helix  chain 'F' and resid 72 through 87
    Processing helix  chain 'F' and resid 102 through 115
      removed outlier: 3.866A  pdb=" N   GLY F 115 " --> pdb=" O   LEU F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 117 through 168
      Proline residue:  F 151  - end of helix
    Processing helix  chain 'F' and resid 171 through 173
      No H-bonds generated for 'chain 'F' and resid 171 through 173'
    Processing helix  chain 'F' and resid 174 through 196
      removed outlier: 3.686A  pdb=" N   THR F 185 " --> pdb=" O   VAL F 181 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   THR F 186 " --> pdb=" O   ALA F 182 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   MET F 195 " --> pdb=" O   ILE F 191 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 228
    Processing helix  chain 'F' and resid 230 through 243
    Processing helix  chain 'F' and resid 244 through 251
      removed outlier: 3.546A  pdb=" N   ARG F 247 " --> pdb=" O   GLU F 244 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 50
    Processing helix  chain 'G' and resid 51 through 67
    Processing helix  chain 'G' and resid 72 through 87
    Processing helix  chain 'G' and resid 102 through 113
    Processing helix  chain 'G' and resid 117 through 169
      removed outlier: 4.142A  pdb=" N   VAL G 121 " --> pdb=" O   ASP G 117 " (cutoff:3.500A)
      Proline residue:  G 151  - end of helix
    Processing helix  chain 'G' and resid 171 through 196
      removed outlier: 3.564A  pdb=" N   GLY G 176 " --> pdb=" O   PRO G 172 " (cutoff:3.500A)
      Proline residue:  G 177  - end of helix
    Processing helix  chain 'G' and resid 196 through 228
    Processing helix  chain 'G' and resid 230 through 238
    Processing helix  chain 'G' and resid 238 through 243
      removed outlier: 3.611A  pdb=" N   ASN G 243 " --> pdb=" O   LYS G 239 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 244 through 250
      removed outlier: 3.659A  pdb=" N   ARG G 247 " --> pdb=" O   GLU G 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42

    815 hydrogen bonds defined for protein.
    2412 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2896
        1.35 -     1.46: 1873
        1.46 -     1.58: 4108
        1.58 -     1.70: 0
        1.70 -     1.82: 152
  Bond restraints: 9029
  Sorted by residual:
  bond pdb=" CB  MET C 179 "
       pdb=" CG  MET C 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.484  0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" CG  MET C 179 "
       pdb=" SD  MET C 179 "
    ideal  model  delta    sigma   weight residual
    1.803  1.773  0.030 2.50e-02 1.60e+03 1.46e+00
  bond pdb=" CB  ASP G  75 "
       pdb=" CG  ASP G  75 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.93e-01
  bond pdb=" CB  ILE D  61 "
       pdb=" CG1 ILE D  61 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 2.00e-02 2.50e+03 6.64e-01
  bond pdb=" CA  PRO D 172 "
       pdb=" CB  PRO D 172 "
    ideal  model  delta    sigma   weight residual
    1.532  1.537 -0.006 7.10e-03 1.98e+04 6.59e-01
  ... (remaining 9024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 11943
        1.47 -     2.94: 158
        2.94 -     4.41: 45
        4.41 -     5.88: 12
        5.88 -     7.35: 2
  Bond angle restraints: 12160
  Sorted by residual:
  angle pdb=" CG  MET C 179 "
        pdb=" SD  MET C 179 "
        pdb=" CE  MET C 179 "
      ideal   model   delta    sigma   weight residual
     100.90   94.42    6.48 2.20e+00 2.07e-01 8.68e+00
  angle pdb=" N   MET F  67 "
        pdb=" CA  MET F  67 "
        pdb=" C   MET F  67 "
      ideal   model   delta    sigma   weight residual
     111.03  113.90   -2.87 1.11e+00 8.12e-01 6.70e+00
  angle pdb=" N   GLY E 245 "
        pdb=" CA  GLY E 245 "
        pdb=" C   GLY E 245 "
      ideal   model   delta    sigma   weight residual
     110.86  115.21   -4.35 1.84e+00 2.95e-01 5.58e+00
  angle pdb=" CA  MET D 105 "
        pdb=" CB  MET D 105 "
        pdb=" CG  MET D 105 "
      ideal   model   delta    sigma   weight residual
     114.10  118.38   -4.28 2.00e+00 2.50e-01 4.58e+00
  angle pdb=" CA  LEU D 213 "
        pdb=" CB  LEU D 213 "
        pdb=" CG  LEU D 213 "
      ideal   model   delta    sigma   weight residual
     116.30  123.65   -7.35 3.50e+00 8.16e-02 4.41e+00
  ... (remaining 12155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 4572
       17.50 -    35.00: 636
       35.00 -    52.50: 194
       52.50 -    70.00: 31
       70.00 -    87.50: 10
  Dihedral angle restraints: 5443
    sinusoidal: 2129
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  ASP F 220 "
           pdb=" CB  ASP F 220 "
           pdb=" CG  ASP F 220 "
           pdb=" OD1 ASP F 220 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.57   57.57     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ASP D 133 "
           pdb=" CB  ASP D 133 "
           pdb=" CG  ASP D 133 "
           pdb=" OD1 ASP D 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.01   57.01     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  ASP E  85 "
           pdb=" CB  ASP E  85 "
           pdb=" CG  ASP E  85 "
           pdb=" OD1 ASP E  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.26   55.26     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 5440 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 931
       0.027 -    0.054: 317
       0.054 -    0.081: 150
       0.081 -    0.108: 39
       0.108 -    0.135: 9
  Chirality restraints: 1446
  Sorted by residual:
  chirality pdb=" CA  ASP C 148 "
            pdb=" N   ASP C 148 "
            pdb=" C   ASP C 148 "
            pdb=" CB  ASP C 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" CA  ASP E 148 "
            pdb=" N   ASP E 148 "
            pdb=" C   ASP E 148 "
            pdb=" CB  ASP E 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CG  LEU D 166 "
            pdb=" CB  LEU D 166 "
            pdb=" CD1 LEU D 166 "
            pdb=" CD2 LEU D 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.47   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 1443 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 180 "   -0.009 2.00e-02 2.50e+03   1.84e-02 3.37e+00
        pdb=" C   ALA C 180 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ALA C 180 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL C 181 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  15 "   -0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO B  16 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE G  37 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.73e+00
        pdb=" C   ILE G  37 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE G  37 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL G  38 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 210
        2.72 -     3.26: 9197
        3.26 -     3.81: 15322
        3.81 -     4.35: 17308
        4.35 -     4.90: 30752
  Nonbonded interactions: 72789
  Sorted by model distance:
  nonbonded pdb=" O   PHE D  29 "
            pdb=" OH  TYR D 188 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OG1 THR E 158 "
            pdb=" OG1 THR E 186 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   LEU A  35 "
            pdb=" OG  SER A  38 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OD1 ASP E  31 "
            pdb=" OH  TYR E 188 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   VAL F  38 "
            pdb=" OG  SER F  42 "
     model   vdw
     2.318 3.040
  ... (remaining 72784 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 14 through 59)
  selection = (chain 'B' and resid 14 through 59)
}
ncs_group {
  reference = (chain 'C' and resid 29 through 250)
  selection = (chain 'D' and resid 29 through 250)
  selection = (chain 'E' and resid 29 through 250)
  selection = (chain 'F' and (resid 15 through 16 or resid 31 through 250))
  selection = (chain 'G' and resid 29 through 250)
}

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=0.42 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:             0.220
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.690
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9029  Z= 0.121
  Angle     :  0.488   7.347  12160  Z= 0.259
  Chirality :  0.035   0.135   1446
  Planarity :  0.004   0.045   1543
  Dihedral  : 17.749  87.504   3305
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 27.98 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.33 (0.25), residues: 1148
  helix:  2.57 (0.16), residues: 998
  sheet:  None (None), residues: 0
  loop : -0.47 (0.51), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G 215 
 TYR   0.014   0.001   TYR F 241 
 PHE   0.019   0.001   PHE A  32 
 TRP   0.007   0.001   TRP A  18 
 HIS   0.002   0.000   HIS E 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9029)
  covalent geometry    : angle       0.48802 (12160)
  hydrogen bonds       : bond        0.12792 (  815)
  hydrogen bonds       : angle       5.07470 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.276 
Fit side-chains
REVERT: C  149 VAL cc_start: 0.8627 (p) cc_final: 0.8422 (t)
REVERT: D   75 ASP cc_start: 0.7664 (m-30) cc_final: 0.7139 (t70)
REVERT: F   67 MET cc_start: 0.8345 (mtm) cc_final: 0.8119 (mtm)
REVERT: G   75 ASP cc_start: 0.7105 (t0) cc_final: 0.6798 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 154
  average time/residue: 0.1004
  time to fit residues: 21.2403
Evaluate side-chains
  152 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain F residue   51 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3957 r_free = 0.3957 target = 0.182166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.114914 restraints weight = 8889.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.82
r_work: 0.2972 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.0733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9029  Z= 0.128
  Angle     :  0.456   5.831  12160  Z= 0.241
  Chirality :  0.036   0.118   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.649  39.147   1224
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 26.17 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.79 (0.25), residues: 1148
  helix:  2.89 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -0.50 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 215 
 TYR   0.009   0.001   TYR F 241 
 PHE   0.023   0.001   PHE A  32 
 TRP   0.005   0.002   TRP A  18 
 HIS   0.003   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9029)
  covalent geometry    : angle       0.45567 (12160)
  hydrogen bonds       : bond        0.04223 (  815)
  hydrogen bonds       : angle       3.82431 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.360 
Fit side-chains
REVERT: D   64 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7630 (ttmt)
REVERT: F   83 MET cc_start: 0.7509 (mtt) cc_final: 0.7043 (mtp)
REVERT: G  135 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7297 (mtp85)
  outliers start: 14
  outliers final: 7
  residues processed: 159
  average time/residue: 0.1037
  time to fit residues: 22.3512
Evaluate side-chains
  160 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   64 LYS
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.181716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.118024 restraints weight = 8838.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.78
r_work: 0.3003 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9029  Z= 0.113
  Angle     :  0.428   6.624  12160  Z= 0.226
  Chirality :  0.035   0.114   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.279  13.088   1221
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 26.28 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.01 (0.25), residues: 1148
  helix:  3.05 (0.16), residues: 998
  sheet:  None (None), residues: 0
  loop : -0.50 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 215 
 TYR   0.007   0.001   TYR F 241 
 PHE   0.021   0.001   PHE A  32 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9029)
  covalent geometry    : angle       0.42840 (12160)
  hydrogen bonds       : bond        0.03834 (  815)
  hydrogen bonds       : angle       3.64935 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.289 
Fit side-chains
REVERT: F   67 MET cc_start: 0.8608 (mtm) cc_final: 0.8363 (mtp)
REVERT: F   83 MET cc_start: 0.7514 (mtt) cc_final: 0.7167 (mtp)
REVERT: F  148 ASP cc_start: 0.8566 (m-30) cc_final: 0.8313 (m-30)
REVERT: G   75 ASP cc_start: 0.7262 (t0) cc_final: 0.6813 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 162
  average time/residue: 0.0900
  time to fit residues: 20.0171
Evaluate side-chains
  156 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 150
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain F residue  251 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 99 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3955 r_free = 0.3955 target = 0.181522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.117444 restraints weight = 8998.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.59
r_work: 0.2997 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9029  Z= 0.115
  Angle     :  0.432   7.000  12160  Z= 0.226
  Chirality :  0.035   0.115   1446
  Planarity :  0.004   0.044   1543
  Dihedral  :  3.255  13.088   1221
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 25.64 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.06 (0.25), residues: 1148
  helix:  3.07 (0.16), residues: 1006
  sheet:  None (None), residues: 0
  loop : -0.54 (0.49), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 215 
 TYR   0.007   0.001   TYR F 241 
 PHE   0.030   0.001   PHE A  32 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9029)
  covalent geometry    : angle       0.43180 (12160)
  hydrogen bonds       : bond        0.03791 (  815)
  hydrogen bonds       : angle       3.62574 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.359 
Fit side-chains
REVERT: D  112 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.4996 (mm)
REVERT: E   85 ASP cc_start: 0.6520 (t70) cc_final: 0.6261 (t0)
REVERT: F   67 MET cc_start: 0.8636 (mtm) cc_final: 0.8420 (mtp)
REVERT: F   83 MET cc_start: 0.7551 (mtt) cc_final: 0.7183 (mtp)
REVERT: F  165 MET cc_start: 0.9242 (ttp) cc_final: 0.8988 (tmm)
REVERT: G   75 ASP cc_start: 0.7448 (t0) cc_final: 0.7094 (t0)
  outliers start: 20
  outliers final: 15
  residues processed: 165
  average time/residue: 0.0921
  time to fit residues: 21.0480
Evaluate side-chains
  166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3958 r_free = 0.3958 target = 0.181906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.117894 restraints weight = 8856.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.76
r_work: 0.2986 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9029  Z= 0.111
  Angle     :  0.424   6.393  12160  Z= 0.222
  Chirality :  0.035   0.120   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.235  12.937   1221
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 25.43 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.09 (0.25), residues: 1148
  helix:  3.09 (0.16), residues: 1008
  sheet:  None (None), residues: 0
  loop : -0.57 (0.49), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 215 
 TYR   0.006   0.001   TYR F 241 
 PHE   0.011   0.001   PHE C 143 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9029)
  covalent geometry    : angle       0.42392 (12160)
  hydrogen bonds       : bond        0.03686 (  815)
  hydrogen bonds       : angle       3.58928 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.252 
Fit side-chains
REVERT: C  179 MET cc_start: 0.7813 (mmm) cc_final: 0.7437 (mmm)
REVERT: D  100 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5347 (pt)
REVERT: D  112 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4922 (mm)
REVERT: F   67 MET cc_start: 0.8430 (mtm) cc_final: 0.8212 (mtp)
REVERT: F   83 MET cc_start: 0.7424 (mtt) cc_final: 0.7066 (mtp)
REVERT: F  148 ASP cc_start: 0.8619 (m-30) cc_final: 0.8260 (m-30)
REVERT: F  165 MET cc_start: 0.9244 (ttp) cc_final: 0.8928 (tmm)
REVERT: F  239 LYS cc_start: 0.7172 (mmtm) cc_final: 0.6929 (mmtm)
REVERT: G   75 ASP cc_start: 0.7503 (t0) cc_final: 0.7106 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 164
  average time/residue: 0.0910
  time to fit residues: 20.6573
Evaluate side-chains
  168 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 MET
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0270
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.1442

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.182014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.114583 restraints weight = 8911.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.82
r_work: 0.2958 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9029  Z= 0.123
  Angle     :  0.437   6.593  12160  Z= 0.229
  Chirality :  0.035   0.131   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.277  13.259   1221
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 25.32 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.07 (0.24), residues: 1148
  helix:  3.07 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.39 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 215 
 TYR   0.007   0.001   TYR F 241 
 PHE   0.013   0.001   PHE A  39 
 TRP   0.004   0.002   TRP A  18 
 HIS   0.003   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9029)
  covalent geometry    : angle       0.43668 (12160)
  hydrogen bonds       : bond        0.03821 (  815)
  hydrogen bonds       : angle       3.62235 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.320 
Fit side-chains
REVERT: C  179 MET cc_start: 0.7947 (mmm) cc_final: 0.7428 (mmm)
REVERT: D  100 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5499 (pt)
REVERT: D  112 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5045 (mm)
REVERT: F   83 MET cc_start: 0.7400 (mtt) cc_final: 0.7047 (mtp)
REVERT: G   75 ASP cc_start: 0.7497 (t0) cc_final: 0.7249 (t0)
  outliers start: 28
  outliers final: 22
  residues processed: 168
  average time/residue: 0.0958
  time to fit residues: 22.0960
Evaluate side-chains
  172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  220 ASP
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3963 r_free = 0.3963 target = 0.182683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.118669 restraints weight = 8898.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.85
r_work: 0.2987 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9029  Z= 0.115
  Angle     :  0.431   6.745  12160  Z= 0.226
  Chirality :  0.035   0.133   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.250  12.904   1221
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 25.64 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.13 (0.24), residues: 1148
  helix:  3.11 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.39 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 215 
 TYR   0.007   0.001   TYR F 241 
 PHE   0.018   0.001   PHE A  32 
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9029)
  covalent geometry    : angle       0.43108 (12160)
  hydrogen bonds       : bond        0.03721 (  815)
  hydrogen bonds       : angle       3.60406 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.372 
Fit side-chains
REVERT: C  179 MET cc_start: 0.7994 (mmm) cc_final: 0.7646 (mmm)
REVERT: D  100 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5572 (pt)
REVERT: D  112 LEU cc_start: 0.5358 (OUTLIER) cc_final: 0.5059 (mm)
REVERT: F   67 MET cc_start: 0.8363 (mtm) cc_final: 0.8101 (mtp)
REVERT: F   83 MET cc_start: 0.7447 (mtt) cc_final: 0.7087 (mtp)
REVERT: F  239 LYS cc_start: 0.7248 (mmtm) cc_final: 0.7045 (mmtm)
REVERT: G   75 ASP cc_start: 0.7535 (t0) cc_final: 0.7294 (t0)
  outliers start: 23
  outliers final: 19
  residues processed: 165
  average time/residue: 0.1023
  time to fit residues: 23.2321
Evaluate side-chains
  173 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  220 ASP
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 99 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3916 r_free = 0.3916 target = 0.177700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.112336 restraints weight = 8906.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.88
r_work: 0.2922 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9029  Z= 0.182
  Angle     :  0.506   6.947  12160  Z= 0.264
  Chirality :  0.038   0.136   1446
  Planarity :  0.004   0.047   1543
  Dihedral  :  3.479  13.870   1221
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 25.85 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.63 (0.24), residues: 1148
  helix:  2.78 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -0.48 (0.47), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 207 
 TYR   0.011   0.001   TYR F 241 
 PHE   0.022   0.002   PHE A  32 
 TRP   0.006   0.002   TRP B  18 
 HIS   0.006   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 9029)
  covalent geometry    : angle       0.50582 (12160)
  hydrogen bonds       : bond        0.04425 (  815)
  hydrogen bonds       : angle       3.81639 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.364 
Fit side-chains
REVERT: C  179 MET cc_start: 0.8014 (mmm) cc_final: 0.7686 (mmm)
REVERT: D  100 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5447 (pt)
REVERT: D  112 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.5007 (mm)
REVERT: F   67 MET cc_start: 0.8508 (mtm) cc_final: 0.8200 (mtp)
REVERT: F   83 MET cc_start: 0.7525 (mtt) cc_final: 0.7264 (mtp)
REVERT: F  134 GLU cc_start: 0.8350 (tp30) cc_final: 0.7975 (mm-30)
REVERT: G   75 ASP cc_start: 0.7612 (t0) cc_final: 0.7385 (t0)
  outliers start: 24
  outliers final: 20
  residues processed: 170
  average time/residue: 0.1001
  time to fit residues: 23.5711
Evaluate side-chains
  175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  220 ASP
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 113 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.177078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.110505 restraints weight = 8882.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.65
r_work: 0.2930 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9029  Z= 0.192
  Angle     :  0.514   7.006  12160  Z= 0.270
  Chirality :  0.038   0.146   1446
  Planarity :  0.004   0.047   1543
  Dihedral  :  3.557  14.126   1221
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 25.96 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.35 (0.24), residues: 1148
  helix:  2.60 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -0.61 (0.46), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 207 
 TYR   0.010   0.001   TYR F 241 
 PHE   0.018   0.002   PHE D 143 
 TRP   0.007   0.002   TRP B  18 
 HIS   0.006   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9029)
  covalent geometry    : angle       0.51394 (12160)
  hydrogen bonds       : bond        0.04518 (  815)
  hydrogen bonds       : angle       3.88414 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.348 
Fit side-chains
REVERT: C  179 MET cc_start: 0.8068 (mmm) cc_final: 0.7681 (mmm)
REVERT: D  100 ILE cc_start: 0.5702 (OUTLIER) cc_final: 0.5200 (pt)
REVERT: D  112 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5083 (mm)
REVERT: F   83 MET cc_start: 0.7545 (mtt) cc_final: 0.7266 (mtp)
REVERT: F  134 GLU cc_start: 0.8211 (tp30) cc_final: 0.7839 (mm-30)
REVERT: G   75 ASP cc_start: 0.7627 (t0) cc_final: 0.7407 (t0)
  outliers start: 26
  outliers final: 22
  residues processed: 164
  average time/residue: 0.1062
  time to fit residues: 24.0296
Evaluate side-chains
  173 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  212 THR
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 95 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.180814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.113020 restraints weight = 8876.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.74
r_work: 0.2968 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9029  Z= 0.128
  Angle     :  0.457   7.089  12160  Z= 0.241
  Chirality :  0.036   0.137   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.404  13.360   1221
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 26.70 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.71 (0.24), residues: 1148
  helix:  2.83 (0.16), residues: 1003
  sheet:  None (None), residues: 0
  loop : -0.50 (0.47), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 207 
 TYR   0.009   0.001   TYR F 241 
 PHE   0.012   0.001   PHE A  39 
 TRP   0.006   0.002   TRP A  18 
 HIS   0.003   0.001   HIS G 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9029)
  covalent geometry    : angle       0.45652 (12160)
  hydrogen bonds       : bond        0.03931 (  815)
  hydrogen bonds       : angle       3.75217 ( 2412)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.347 
Fit side-chains
REVERT: C  179 MET cc_start: 0.7875 (mmm) cc_final: 0.7489 (mmm)
REVERT: D  100 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.5182 (pt)
REVERT: D  112 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.5027 (mm)
REVERT: F   67 MET cc_start: 0.8472 (mtm) cc_final: 0.8124 (mtp)
REVERT: F   83 MET cc_start: 0.7565 (mtt) cc_final: 0.7324 (mtp)
REVERT: G   75 ASP cc_start: 0.7652 (t0) cc_final: 0.7330 (t0)
  outliers start: 20
  outliers final: 17
  residues processed: 160
  average time/residue: 0.0970
  time to fit residues: 21.5236
Evaluate side-chains
  166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  212 THR
Chi-restraints excluded: chain D residue  251 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  185 THR
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain F residue  220 ASP
Chi-restraints excluded: chain F residue  251 ILE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 110 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0770
   chunk 38 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0000
   chunk 24 optimal weight:    5.9990
   chunk 76 optimal weight:    0.6980
   chunk 107 optimal weight:    4.9990
   overall best weight:    0.4942

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** 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 = 0.3979 r_free = 0.3979 target = 0.184367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.122553 restraints weight = 8731.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.82
r_work: 0.3036 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9029  Z= 0.101
  Angle     :  0.427   7.203  12160  Z= 0.225
  Chirality :  0.035   0.144   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.218  12.264   1221
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.45 %
    Favored  : 70.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.08 (0.24), residues: 1148
  helix:  3.09 (0.16), residues: 1003
  sheet:  None (None), residues: 0
  loop : -0.53 (0.48), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 215 
 TYR   0.008   0.001   TYR F 241 
 PHE   0.013   0.001   PHE A  39 
 TRP   0.009   0.001   TRP A  18 
 HIS   0.001   0.000   HIS E 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9029)
  covalent geometry    : angle       0.42690 (12160)
  hydrogen bonds       : bond        0.03463 (  815)
  hydrogen bonds       : angle       3.59079 ( 2412)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2771.55 seconds
wall clock time: 47 minutes 57.65 seconds (2877.65 seconds total)