Starting phenix.real_space_refine
on Thu Mar 13 07:42:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyv_60580/03_2025/8zyv_60580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyv_60580/03_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_60580/03_2025/8zyv_60580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyv_60580/03_2025/8zyv_60580.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyv_60580/03_2025/8zyv_60580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyv_60580/03_2025/8zyv_60580.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.35, per 1000 atoms: 0.60
  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: 2.23
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.69
  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: 2.58

  Time building geometry restraints manager: 2.65 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:             0.230
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.320
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.410
-------------------------------------------------------------------------------
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= 0.166
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.007   0.001   TRP A  18 
 HIS   0.002   0.000   HIS E 136 
 PHE   0.019   0.001   PHE A  32 
 TYR   0.014   0.001   TYR F 241 
 ARG   0.005   0.000   ARG G 215 

*********************** 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  : 0.983 
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: 0.2225
  time to fit residues: 46.9571
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  : 0.879 
-------------------------------------------------------------------------------
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 97 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3922 r_free = 0.3922 target = 0.178421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.112544 restraints weight = 8812.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.63
r_work: 0.2949 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9029  Z= 0.268
  Angle     :  0.501   7.121  12160  Z= 0.263
  Chirality :  0.038   0.129   1446
  Planarity :  0.004   0.047   1543
  Dihedral  :  3.814  40.018   1224
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 25.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.25), residues: 1148
  helix:  2.59 (0.16), residues: 1011
  sheet:  None (None), residues: 0
  loop : -0.57 (0.51), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B  18 
 HIS   0.005   0.001   HIS G 136 
 PHE   0.022   0.002   PHE A  32 
 TYR   0.011   0.001   TYR F 241 
 ARG   0.003   0.000   ARG G 215 

*********************** 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
  175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.940 
Fit side-chains
REVERT: F   67 MET cc_start: 0.8488 (mtm) cc_final: 0.8225 (mtm)
  outliers start: 21
  outliers final: 13
  residues processed: 166
  average time/residue: 0.2382
  time to fit residues: 54.8895
Evaluate side-chains
  165 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  212 THR
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  105 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  185 THR
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue  185 THR
Chi-restraints excluded: chain G residue   61 ILE
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 69 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.182175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.118231 restraints weight = 8936.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.91
r_work: 0.2967 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2785
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2785 r_free = 0.2785    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2785
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.0961

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= 0.156
  Angle     :  0.433   7.298  12160  Z= 0.228
  Chirality :  0.035   0.113   1446
  Planarity :  0.004   0.045   1543
  Dihedral  :  3.329  13.361   1221
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 26.38 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.85 (0.25), residues: 1148
  helix:  2.95 (0.16), residues: 1004
  sheet:  None (None), residues: 0
  loop : -0.73 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  18 
 HIS   0.002   0.000   HIS G 136 
 PHE   0.023   0.001   PHE A  32 
 TYR   0.006   0.001   TYR F 241 
 ARG   0.002   0.000   ARG G 215 

*********************** 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
  166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 1.093 
Fit side-chains
REVERT: D  128 ASP cc_start: 0.6506 (t0) cc_final: 0.6251 (t0)
REVERT: F   67 MET cc_start: 0.8457 (mtm) cc_final: 0.8203 (mtm)
REVERT: F   83 MET cc_start: 0.7538 (mtt) cc_final: 0.7184 (mtp)
  outliers start: 9
  outliers final: 4
  residues processed: 159
  average time/residue: 0.2122
  time to fit residues: 46.5435
Evaluate side-chains
  154 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 150
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain D residue  105 MET
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 18 optimal weight:    4.9990
   chunk 52 optimal weight:    0.4980
   chunk 93 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0370
   chunk 47 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    0.8460

-------------------------------------------------------------------------------
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 = 0.181755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.118923 restraints weight = 8791.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 1.67
r_work: 0.2970 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1054

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= 0.159
  Angle     :  0.435   7.194  12160  Z= 0.228
  Chirality :  0.035   0.115   1446
  Planarity :  0.004   0.044   1543
  Dihedral  :  3.279  13.102   1221
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 26.28 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.98 (0.25), residues: 1148
  helix:  3.03 (0.16), residues: 1004
  sheet:  None (None), residues: 0
  loop : -0.69 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  18 
 HIS   0.002   0.001   HIS E 136 
 PHE   0.029   0.001   PHE A  32 
 TYR   0.006   0.001   TYR F 241 
 ARG   0.002   0.000   ARG G 215 

*********************** 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
  174 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 1.021 
Fit side-chains
REVERT: D   64 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7512 (ttmt)
REVERT: D  112 LEU cc_start: 0.5375 (OUTLIER) cc_final: 0.4988 (mm)
REVERT: E   85 ASP cc_start: 0.6595 (t70) cc_final: 0.6354 (t0)
REVERT: F   83 MET cc_start: 0.7550 (mtt) cc_final: 0.7183 (mtp)
REVERT: F  165 MET cc_start: 0.9206 (ttp) cc_final: 0.8922 (tmm)
  outliers start: 19
  outliers final: 12
  residues processed: 165
  average time/residue: 0.2189
  time to fit residues: 49.6646
Evaluate side-chains
  165 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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   64 LYS
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  251 ILE
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain F residue   51 THR
Chi-restraints excluded: chain F residue  155 MET
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 77 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 114 optimal weight:    0.8980
   chunk 112 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.179285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.115180 restraints weight = 8867.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.81
r_work: 0.2943 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9029  Z= 0.227
  Angle     :  0.471   8.310  12160  Z= 0.246
  Chirality :  0.036   0.124   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.389  13.699   1221
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 26.06 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.76 (0.25), residues: 1148
  helix:  2.88 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.69 (0.48), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B  18 
 HIS   0.004   0.001   HIS G 136 
 PHE   0.031   0.002   PHE A  32 
 TYR   0.008   0.001   TYR F 241 
 ARG   0.002   0.000   ARG F 215 

*********************** 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
  173 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.935 
Fit side-chains
REVERT: C  179 MET cc_start: 0.7864 (mpp) cc_final: 0.7082 (mpp)
REVERT: D  100 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5517 (pt)
REVERT: D  112 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.5110 (mm)
REVERT: E   85 ASP cc_start: 0.6560 (t70) cc_final: 0.6312 (t0)
REVERT: E  218 ILE cc_start: 0.6917 (mp) cc_final: 0.6689 (mp)
REVERT: F   67 MET cc_start: 0.8508 (mtm) cc_final: 0.8265 (mtp)
REVERT: F   83 MET cc_start: 0.7441 (mtt) cc_final: 0.7128 (mtm)
REVERT: F  165 MET cc_start: 0.9234 (ttp) cc_final: 0.8930 (tmm)
REVERT: F  239 LYS cc_start: 0.7251 (mmtm) cc_final: 0.7030 (mmtm)
  outliers start: 20
  outliers final: 13
  residues processed: 163
  average time/residue: 0.2193
  time to fit residues: 49.0206
Evaluate side-chains
  166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
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  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  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 F residue   51 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 47 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.180486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.114394 restraints weight = 8803.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.69
r_work: 0.2975 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2794
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2794
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1148

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= 0.187
  Angle     :  0.452   8.276  12160  Z= 0.237
  Chirality :  0.036   0.128   1446
  Planarity :  0.004   0.047   1543
  Dihedral  :  3.346  13.527   1221
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 25.85 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.88 (0.25), residues: 1148
  helix:  2.97 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.75 (0.47), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A  18 
 HIS   0.003   0.001   HIS G 136 
 PHE   0.017   0.001   PHE A  32 
 TYR   0.006   0.001   TYR F 241 
 ARG   0.001   0.000   ARG D 207 

*********************** 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
  177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.923 
Fit side-chains
REVERT: D  100 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5484 (pt)
REVERT: D  112 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.5061 (mm)
REVERT: E   85 ASP cc_start: 0.6537 (t70) cc_final: 0.6285 (t0)
REVERT: E  218 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6567 (mp)
REVERT: F   67 MET cc_start: 0.8459 (mtm) cc_final: 0.8197 (mtp)
REVERT: F   83 MET cc_start: 0.7437 (mtt) cc_final: 0.7117 (mtm)
REVERT: F  165 MET cc_start: 0.9215 (ttp) cc_final: 0.8854 (tmm)
  outliers start: 26
  outliers final: 18
  residues processed: 165
  average time/residue: 0.2109
  time to fit residues: 47.9502
Evaluate side-chains
  168 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  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  233 VAL
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  185 THR
Chi-restraints excluded: chain E residue  218 ILE
Chi-restraints excluded: chain F residue   51 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0050
   chunk 32 optimal weight:    0.0050
   chunk 3 optimal weight:    0.8980
   chunk 100 optimal weight:    7.9990
   overall best weight:    0.5208

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.183793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.122278 restraints weight = 8863.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.84
r_work: 0.3008 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1266

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= 0.133
  Angle     :  0.420   6.796  12160  Z= 0.220
  Chirality :  0.034   0.130   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.213  12.615   1221
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 26.38 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.16 (0.25), residues: 1148
  helix:  3.14 (0.16), residues: 1009
  sheet:  None (None), residues: 0
  loop : -0.63 (0.49), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  18 
 HIS   0.001   0.000   HIS E 136 
 PHE   0.019   0.001   PHE A  32 
 TYR   0.004   0.001   TYR D 188 
 ARG   0.002   0.000   ARG G 215 

*********************** 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
  177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.984 
Fit side-chains
REVERT: C  149 VAL cc_start: 0.8550 (p) cc_final: 0.8323 (t)
REVERT: C  168 ASN cc_start: 0.7573 (m110) cc_final: 0.7040 (m-40)
REVERT: D  100 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5568 (pt)
REVERT: D  112 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.4916 (mm)
REVERT: D  165 MET cc_start: 0.8564 (ttt) cc_final: 0.8241 (tmm)
REVERT: E   85 ASP cc_start: 0.6555 (t70) cc_final: 0.6290 (t0)
REVERT: E  106 GLN cc_start: 0.6989 (tp-100) cc_final: 0.6730 (tp40)
REVERT: E  218 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6613 (mp)
REVERT: F   67 MET cc_start: 0.8443 (mtm) cc_final: 0.8189 (mtp)
REVERT: F   83 MET cc_start: 0.7441 (mtt) cc_final: 0.7092 (mtp)
REVERT: F  165 MET cc_start: 0.9174 (ttp) cc_final: 0.8811 (tmm)
REVERT: G   75 ASP cc_start: 0.7221 (t0) cc_final: 0.6839 (t0)
REVERT: G  173 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8355 (mmtt)
  outliers start: 21
  outliers final: 14
  residues processed: 168
  average time/residue: 0.2437
  time to fit residues: 55.7019
Evaluate side-chains
  171 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 MET
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   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  233 VAL
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  218 ILE
Chi-restraints excluded: chain F residue  155 MET
Chi-restraints excluded: chain F residue  251 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.180591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.118736 restraints weight = 8995.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.67
r_work: 0.2994 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1258

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= 0.186
  Angle     :  0.449   6.950  12160  Z= 0.234
  Chirality :  0.036   0.123   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.277  13.277   1221
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.70 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.07 (0.24), residues: 1148
  helix:  3.08 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.46 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP B  18 
 HIS   0.003   0.001   HIS G 136 
 PHE   0.017   0.001   PHE A  32 
 TYR   0.006   0.001   TYR F 241 
 ARG   0.001   0.000   ARG D 207 

*********************** 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
  177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 1.755 
Fit side-chains
REVERT: B   30 MET cc_start: 0.8839 (ttp) cc_final: 0.8329 (tmm)
REVERT: C  168 ASN cc_start: 0.7748 (m110) cc_final: 0.7220 (m-40)
REVERT: D  100 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5420 (pt)
REVERT: D  112 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4890 (mm)
REVERT: D  165 MET cc_start: 0.8598 (ttt) cc_final: 0.8394 (tmm)
REVERT: E  106 GLN cc_start: 0.7127 (tp-100) cc_final: 0.6836 (tp40)
REVERT: E  217 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5857 (tt)
REVERT: E  218 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6598 (mp)
REVERT: F   67 MET cc_start: 0.8465 (mtm) cc_final: 0.8196 (mtp)
REVERT: F   83 MET cc_start: 0.7489 (mtt) cc_final: 0.7097 (mtp)
REVERT: F  216 ARG cc_start: 0.7519 (mtp180) cc_final: 0.7274 (mtp180)
  outliers start: 23
  outliers final: 18
  residues processed: 166
  average time/residue: 0.2716
  time to fit residues: 62.0595
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  : 1.216 
-------------------------------------------------------------------------------
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  181 VAL
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  233 VAL
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  217 LEU
Chi-restraints excluded: chain E residue  218 ILE
Chi-restraints excluded: chain F residue   51 THR
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 84 optimal weight:    2.9990
   chunk 90 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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**
C 136 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.177351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.115898 restraints weight = 8970.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.66
r_work: 0.2928 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9029  Z= 0.287
  Angle     :  0.507   7.031  12160  Z= 0.263
  Chirality :  0.038   0.133   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.486  14.025   1221
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.60 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.60 (0.24), residues: 1148
  helix:  2.77 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -0.54 (0.47), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  18 
 HIS   0.005   0.001   HIS G 136 
 PHE   0.022   0.002   PHE A  32 
 TYR   0.009   0.001   TYR F 241 
 ARG   0.003   0.000   ARG F 207 

*********************** 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
  183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.948 
Fit side-chains
REVERT: C  179 MET cc_start: 0.7874 (mmm) cc_final: 0.7475 (mmm)
REVERT: D  100 ILE cc_start: 0.5800 (OUTLIER) cc_final: 0.5465 (pt)
REVERT: D  112 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.5000 (mm)
REVERT: E  218 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6665 (mp)
REVERT: F   67 MET cc_start: 0.8508 (mtm) cc_final: 0.8252 (mtp)
REVERT: F   83 MET cc_start: 0.7549 (mtt) cc_final: 0.7283 (mtp)
REVERT: G   75 ASP cc_start: 0.7364 (t0) cc_final: 0.7004 (t0)
  outliers start: 27
  outliers final: 21
  residues processed: 169
  average time/residue: 0.2198
  time to fit residues: 50.7372
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  : 0.904 
-------------------------------------------------------------------------------
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  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  112 LEU
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  233 VAL
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  218 ILE
Chi-restraints excluded: chain E residue  222 VAL
Chi-restraints excluded: chain F residue   51 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 85 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3950 r_free = 0.3950 target = 0.181366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.114290 restraints weight = 8846.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.89
r_work: 0.2958 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2775
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2775 r_free = 0.2775    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2775
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1285

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= 0.184
  Angle     :  0.463   7.129  12160  Z= 0.242
  Chirality :  0.036   0.154   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.372  13.405   1221
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 27.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.84 (0.24), residues: 1148
  helix:  2.93 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.54 (0.47), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A  18 
 HIS   0.003   0.001   HIS G 136 
 PHE   0.012   0.001   PHE A  39 
 TYR   0.007   0.001   TYR F 241 
 ARG   0.002   0.000   ARG E 144 

********************** 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
  172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.924 
Fit side-chains
REVERT: D  100 ILE cc_start: 0.5749 (OUTLIER) cc_final: 0.5339 (pt)
REVERT: D  112 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.4940 (mm)
REVERT: E  217 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.6023 (tt)
REVERT: E  218 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6619 (mp)
REVERT: F   67 MET cc_start: 0.8424 (mtm) cc_final: 0.8178 (mtp)
REVERT: F   83 MET cc_start: 0.7524 (mtt) cc_final: 0.7193 (mtm)
REVERT: G   75 ASP cc_start: 0.7312 (t0) cc_final: 0.6930 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 163
  average time/residue: 0.2155
  time to fit residues: 48.5399
Evaluate side-chains
  172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
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  181 VAL
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  233 VAL
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  217 LEU
Chi-restraints excluded: chain E residue  218 ILE
Chi-restraints excluded: chain F residue   51 THR
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 84 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.178352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.113630 restraints weight = 8868.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.81
r_work: 0.2939 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2752 r_free = 0.2752    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9029  Z= 0.248
  Angle     :  0.500   8.527  12160  Z= 0.260
  Chirality :  0.037   0.148   1446
  Planarity :  0.004   0.046   1543
  Dihedral  :  3.459  13.944   1221
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 26.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.61 (0.24), residues: 1148
  helix:  2.76 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop : -0.48 (0.47), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B  18 
 HIS   0.004   0.001   HIS G 136 
 PHE   0.015   0.002   PHE D 143 
 TYR   0.009   0.001   TYR F 241 
 ARG   0.002   0.000   ARG D 207 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5966.42 seconds
wall clock time: 104 minutes 54.52 seconds (6294.52 seconds total)