Starting phenix.real_space_refine
on Wed Mar 12 03:41:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d85_27247/03_2025/8d85_27247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d85_27247/03_2025/8d85_27247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2025/8d85_27247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2025/8d85_27247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2025/8d85_27247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d85_27247/03_2025/8d85_27247.cif"
  }
  resolution = 3.81
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4527      2.51       5
     N    1197      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 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: 7093
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 178}
    Chain: "D"
      Number of atoms: 1452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1452
          Classifications: {'peptide': 177}
          Link IDs: {'PTRANS': 9, 'TRANS': 167}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1524
          Classifications: {'peptide': 191}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 172}
    Chain: "B"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2373
          Classifications: {'peptide': 296}
          Link IDs: {'PTRANS': 16, 'TRANS': 279}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.47, per 1000 atoms: 0.77
  Number of scatterers: 7093
  At special positions: 0
  Unit cell: (107.5, 104.06, 139.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1338      8.00
     N    1197      7.00
     C    4527      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  35 " - pdb=" SG  CYS C  46 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  79 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B  54 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  48 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 182 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A  76 "
      " NAG B 701 " - " ASN B 227 "
      " NAG B 702 " - " ASN B 157 "
      " NAG B 703 " - " ASN B 131 "
      " NAG C 301 " - " ASN C 105 "
      " NAG E   1 " - " ASN A  51 "
      " NAG F   1 " - " ASN B  83 "
      " NAG G   1 " - " ASN B  43 "
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 928.8 milliseconds
  

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1646

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 18 sheets defined
      17.8% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'D' and resid 42 through 73
    Processing helix  chain 'D' and resid 93 through 100
    Processing helix  chain 'D' and resid 103 through 124
      Proline residue:  D 115  - end of helix
    Processing helix  chain 'D' and resid 130 through 158
    Processing helix  chain 'D' and resid 166 through 179
    Processing helix  chain 'D' and resid 196 through 225
    Processing helix  chain 'B' and resid 51 through 58
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 4.305A  pdb=" N   SER B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.643A  pdb=" N   ALA B 278 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46
      removed outlier: 4.160A  pdb=" N   CYS C  46 " --> pdb=" O   CYS C  89 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   CYS C  89 " --> pdb=" O   CYS C  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.649A  pdb=" N   ILE C  63 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL C 103 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE C 121 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138
      removed outlier: 3.686A  pdb=" N   LEU C 145 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 183
      removed outlier: 6.205A  pdb=" N   TYR C 165 " --> pdb=" O   PRO C 182 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66
      removed outlier: 3.674A  pdb=" N   GLU A  65 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR A 108 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 105
      removed outlier: 3.526A  pdb=" N   VAL A 105 " --> pdb=" O   VAL A 118 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL A 118 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 139
      removed outlier: 3.829A  pdb=" N   ARG A 132 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   HIS A 150 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ASP A 136 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   THR A 148 " --> pdb=" O   ASP A 136 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 178
      removed outlier: 3.869A  pdb=" N   LEU A 183 " --> pdb=" O   CYS A 164 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 178
    Processing sheet with id=AB1, first strand: chain 'A' and resid 202 through 204
      removed outlier: 3.561A  pdb=" N   LEU A 224 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38
      removed outlier: 3.957A  pdb=" N   VAL B  38 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47
    Processing sheet with id=AB4, first strand: chain 'B' and resid 73 through 74
      removed outlier: 4.735A  pdb=" N   TRP B  67 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL B  66 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ASN B 104 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN B 113 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183
      removed outlier: 4.364A  pdb=" N   CYS B 182 " --> pdb=" O   CYS B 144 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   CYS B 144 " --> pdb=" O   CYS B 182 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B 143 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASP B 147 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASN B 131 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
      removed outlier: 8.563A  pdb=" N   LYS B 221 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   VAL B 136 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 172 through 173
      removed outlier: 3.864A  pdb=" N   LYS B 161 " --> pdb=" O   TRP B 197 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 197 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 195 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173
      removed outlier: 3.864A  pdb=" N   LYS B 161 " --> pdb=" O   TRP B 197 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TRP B 197 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 195 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE B 194 " --> pdb=" O   PHE B 214 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   PHE B 214 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   VAL B 196 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE B 212 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 231
      removed outlier: 3.622A  pdb=" N   THR B 243 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS B 241 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 270 through 271
      removed outlier: 3.987A  pdb=" N   TYR B 295 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY B 319 " --> pdb=" O   TYR B 295 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B 317 " --> pdb=" O   PHE B 297 " (cutoff:3.500A)

    205 hydrogen bonds defined for protein.
    549 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: 2.13

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2263
        1.34 -     1.46: 1724
        1.46 -     1.58: 3259
        1.58 -     1.70: 0
        1.70 -     1.82: 43
  Bond restraints: 7289
  Sorted by residual:
  bond pdb=" C   ASP D 102 "
       pdb=" N   PRO D 103 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.08e-02 8.57e+03 3.24e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.05e+00
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.83e+00
  ... (remaining 7284 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 9795
        2.03 -     4.05: 129
        4.05 -     6.08: 14
        6.08 -     8.10: 2
        8.10 -    10.13: 1
  Bond angle restraints: 9941
  Sorted by residual:
  angle pdb=" CA  LEU A  68 "
        pdb=" CB  LEU A  68 "
        pdb=" CG  LEU A  68 "
      ideal   model   delta    sigma   weight residual
     116.30  126.43  -10.13 3.50e+00 8.16e-02 8.37e+00
  angle pdb=" N   SER B  32 "
        pdb=" CA  SER B  32 "
        pdb=" C   SER B  32 "
      ideal   model   delta    sigma   weight residual
     109.81  115.62   -5.81 2.21e+00 2.05e-01 6.92e+00
  angle pdb=" C   VAL C 109 "
        pdb=" N   HIS C 110 "
        pdb=" CA  HIS C 110 "
      ideal   model   delta    sigma   weight residual
     121.80  116.20    5.60 2.44e+00 1.68e-01 5.28e+00
  angle pdb=" C   LEU A 198 "
        pdb=" N   ALA A 199 "
        pdb=" CA  ALA A 199 "
      ideal   model   delta    sigma   weight residual
     122.08  125.21   -3.13 1.47e+00 4.63e-01 4.53e+00
  angle pdb=" C   ILE B  31 "
        pdb=" N   SER B  32 "
        pdb=" CA  SER B  32 "
      ideal   model   delta    sigma   weight residual
     121.80  116.99    4.81 2.44e+00 1.68e-01 3.89e+00
  ... (remaining 9936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.69: 4205
       21.69 -    43.38: 204
       43.38 -    65.07: 46
       65.07 -    86.76: 21
       86.76 -   108.45: 52
  Dihedral angle restraints: 4528
    sinusoidal: 1995
      harmonic: 2533
  Sorted by residual:
  dihedral pdb=" CB  CYS C  35 "
           pdb=" SG  CYS C  35 "
           pdb=" SG  CYS C  46 "
           pdb=" CB  CYS C  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -43.34  -42.66     1      1.00e+01 1.00e-02 2.54e+01
  dihedral pdb=" CA  SER B  32 "
           pdb=" C   SER B  32 "
           pdb=" N   PRO B  33 "
           pdb=" CA  PRO B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" C1  NAG G   1 "
           pdb=" C2  NAG G   1 "
           pdb=" C3  NAG G   1 "
           pdb=" O3  NAG G   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -66.64 -108.45     1      3.00e+01 1.11e-03 1.40e+01
  ... (remaining 4525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 891
       0.041 -    0.082: 136
       0.082 -    0.122: 92
       0.122 -    0.163: 7
       0.163 -    0.204: 2
  Chirality restraints: 1128
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A  51 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C1  NAG C 301 "
            pdb=" ND2 ASN C 105 "
            pdb=" C2  NAG C 301 "
            pdb=" O5  NAG C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" C1  NAG B 701 "
            pdb=" ND2 ASN B 227 "
            pdb=" C2  NAG B 701 "
            pdb=" O5  NAG B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.44e-01
  ... (remaining 1125 not shown)

  Planarity restraints: 1264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 102 "   -0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO D 103 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C  40 "    0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO C  41 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO C  41 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  41 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 272 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO B 273 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 273 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 273 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1261 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2379
        2.87 -     3.37: 6114
        3.37 -     3.88: 10679
        3.88 -     4.39: 10827
        4.39 -     4.90: 19504
  Nonbonded interactions: 49503
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN C  81 "
            pdb=" O   SER C  86 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" NH2 ARG C 168 "
            pdb=" OE1 GLN C 202 "
     model   vdw
     2.367 3.120
  nonbonded pdb=" NE1 TRP C 166 "
            pdb=" OE1 GLN C 206 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" OE1 GLU B  34 "
            pdb=" OG  SER B  35 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" ND2 ASN B 246 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.381 3.120
  ... (remaining 49498 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 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.790
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     20.300
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6271
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   0.041   7289  Z= 0.167
  Angle     :  0.531  10.127   9941  Z= 0.261
  Chirality :  0.040   0.204   1128
  Planarity :  0.003   0.039   1256
  Dihedral  : 19.549 108.448   2858
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.09 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    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: -2.45 (0.25), residues: 855
  helix:  0.17 (0.39), residues: 154
  sheet: -0.72 (0.39), residues: 174
  loop : -2.67 (0.22), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP A 115 
 HIS   0.001   0.000   HIS D 117 
 PHE   0.005   0.000   PHE D 116 
 TYR   0.005   0.000   TYR B  79 
 ARG   0.001   0.000   ARG D 152 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   30 LEU cc_start: 0.8169 (pt) cc_final: 0.7776 (mt)
REVERT: C  110 HIS cc_start: 0.2159 (m170) cc_final: 0.1914 (m90)
REVERT: D  144 LEU cc_start: 0.8883 (tp) cc_final: 0.8462 (tt)
REVERT: B  146 TRP cc_start: 0.8176 (p90) cc_final: 0.7824 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2574
  time to fit residues: 61.4592
Evaluate side-chains
  109 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
C  75 HIS
D 126 GLN
D 150 HIS
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN
A 159 HIS
** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 ASN
B 211 HIS
B 258 ASN
B 260 GLN
B 271 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.170532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.148433 restraints weight = 14836.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.151650 restraints weight = 9021.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.153951 restraints weight = 6369.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4123 r_free = 0.4123    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       91 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4120 r_free = 0.4120    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7289  Z= 0.312
  Angle     :  0.794  13.837   9941  Z= 0.373
  Chirality :  0.051   0.419   1128
  Planarity :  0.006   0.099   1256
  Dihedral  : 17.411  88.399   1167
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.79 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -1.61 (0.27), residues: 855
  helix:  1.66 (0.41), residues: 148
  sheet: -0.90 (0.32), residues: 223
  loop : -2.12 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 217 
 HIS   0.006   0.001   HIS B 211 
 PHE   0.020   0.002   PHE C 188 
 TYR   0.018   0.002   TYR B  79 
 ARG   0.009   0.001   ARG D 105 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6622 (mtm-85)
REVERT: D  144 LEU cc_start: 0.8936 (tp) cc_final: 0.8652 (tt)
REVERT: B  146 TRP cc_start: 0.8771 (p90) cc_final: 0.8387 (p90)
REVERT: B  239 ILE cc_start: 0.7230 (mm) cc_final: 0.6920 (pt)
  outliers start: 14
  outliers final: 8
  residues processed: 133
  average time/residue: 0.2344
  time to fit residues: 40.2681
Evaluate side-chains
  105 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain A residue   99 MET
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  223 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0070
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
D  64 GLN
A  71 GLN
A  79 GLN
A 167 HIS
B 114 ASN
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.168030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.146224 restraints weight = 14861.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.149463 restraints weight = 8953.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.151693 restraints weight = 6309.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4078 r_free = 0.4078    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4078 r_free = 0.4078    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       92 |
|-----------------------------------------------------------------------------|
r_final: 0.4078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7289  Z= 0.220
  Angle     :  0.681   9.341   9941  Z= 0.311
  Chirality :  0.048   0.470   1128
  Planarity :  0.005   0.093   1256
  Dihedral  : 13.420  78.669   1167
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.15 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.12 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -1.30 (0.28), residues: 855
  helix:  2.22 (0.42), residues: 148
  sheet: -0.85 (0.31), residues: 233
  loop : -1.97 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 310 
 HIS   0.003   0.001   HIS A  67 
 PHE   0.016   0.001   PHE C 188 
 TYR   0.017   0.001   TYR B 295 
 ARG   0.005   0.000   ARG D 141 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6650 (mtm-85)
REVERT: D  144 LEU cc_start: 0.8923 (tp) cc_final: 0.8605 (tt)
REVERT: A  160 LYS cc_start: 0.5707 (pttm) cc_final: 0.5463 (pttm)
REVERT: B   76 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6787 (tttp)
REVERT: B  146 TRP cc_start: 0.8793 (p90) cc_final: 0.8380 (p90)
  outliers start: 21
  outliers final: 11
  residues processed: 124
  average time/residue: 0.1952
  time to fit residues: 32.2834
Evaluate side-chains
  110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  230 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
D 154 GLN
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.167493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.146054 restraints weight = 14815.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.149334 restraints weight = 8923.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.151645 restraints weight = 6201.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7289  Z= 0.215
  Angle     :  0.674  13.367   9941  Z= 0.305
  Chirality :  0.047   0.399   1128
  Planarity :  0.005   0.089   1256
  Dihedral  : 11.012  65.962   1167
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.43 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.29 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -1.10 (0.28), residues: 855
  helix:  2.41 (0.42), residues: 148
  sheet: -0.77 (0.31), residues: 241
  loop : -1.82 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 310 
 HIS   0.003   0.001   HIS D  52 
 PHE   0.018   0.001   PHE B  72 
 TYR   0.015   0.001   TYR B  79 
 ARG   0.005   0.001   ARG D 105 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7058 (mtm-85) cc_final: 0.6668 (mtm-85)
REVERT: D  132 MET cc_start: 0.7491 (ppp) cc_final: 0.7184 (ppp)
REVERT: D  140 MET cc_start: 0.8446 (tmm) cc_final: 0.8183 (tmm)
REVERT: A  160 LYS cc_start: 0.5726 (pttm) cc_final: 0.5469 (pttm)
REVERT: B   76 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6958 (tttp)
REVERT: B  146 TRP cc_start: 0.8776 (p90) cc_final: 0.8327 (p90)
  outliers start: 26
  outliers final: 18
  residues processed: 122
  average time/residue: 0.2050
  time to fit residues: 33.5659
Evaluate side-chains
  104 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0010
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
D  77 ASN
D 154 GLN
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.166935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.146025 restraints weight = 15425.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.149355 restraints weight = 9228.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.151575 restraints weight = 6383.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7289  Z= 0.191
  Angle     :  0.657  11.090   9941  Z= 0.299
  Chirality :  0.046   0.391   1128
  Planarity :  0.005   0.091   1256
  Dihedral  :  9.541  55.102   1167
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.62 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.28), residues: 855
  helix:  2.51 (0.42), residues: 146
  sheet: -0.68 (0.31), residues: 241
  loop : -1.71 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  89 
 HIS   0.003   0.001   HIS D 117 
 PHE   0.018   0.001   PHE B  72 
 TYR   0.014   0.001   TYR B 261 
 ARG   0.004   0.000   ARG B 298 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7081 (mtm-85) cc_final: 0.6718 (mtm-85)
REVERT: D  134 ARG cc_start: 0.8339 (mtt-85) cc_final: 0.8043 (mtt-85)
REVERT: D  140 MET cc_start: 0.8524 (tmm) cc_final: 0.8240 (tmm)
REVERT: B   76 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6935 (tttp)
REVERT: B  146 TRP cc_start: 0.8785 (p90) cc_final: 0.8380 (p90)
REVERT: B  302 MET cc_start: 0.6116 (ptt) cc_final: 0.5426 (mtm)
  outliers start: 23
  outliers final: 15
  residues processed: 111
  average time/residue: 0.2095
  time to fit residues: 30.9698
Evaluate side-chains
  104 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  230 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 20 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0770
   chunk 81 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.0342

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

Flipped N/Q/H residues before XYZ refinement:
** B 258 ASN ** 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 = 0.4259 r_free = 0.4259 target = 0.164396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.143660 restraints weight = 15352.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.146667 restraints weight = 9498.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.148691 restraints weight = 6790.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.5126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7289  Z= 0.227
  Angle     :  0.675  10.246   9941  Z= 0.315
  Chirality :  0.048   0.525   1128
  Planarity :  0.005   0.091   1256
  Dihedral  :  8.074  57.445   1167
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.25 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.10 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.28), residues: 855
  helix:  2.52 (0.42), residues: 146
  sheet: -0.64 (0.32), residues: 233
  loop : -1.66 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 115 
 HIS   0.003   0.001   HIS D  52 
 PHE   0.019   0.002   PHE B  72 
 TYR   0.016   0.002   TYR B  79 
 ARG   0.004   0.001   ARG D 105 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  150 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7601 (mm-30)
REVERT: C  198 ARG cc_start: 0.7093 (mtm-85) cc_final: 0.6727 (mtm-85)
REVERT: D  132 MET cc_start: 0.7562 (ppp) cc_final: 0.6871 (ppp)
REVERT: D  134 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7720 (mtt90)
REVERT: D  140 MET cc_start: 0.8461 (tmm) cc_final: 0.8113 (tmm)
REVERT: A  217 TRP cc_start: 0.7968 (m100) cc_final: 0.6926 (m100)
REVERT: B   76 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7102 (tttp)
REVERT: B  146 TRP cc_start: 0.8770 (p90) cc_final: 0.8354 (p90)
  outliers start: 27
  outliers final: 20
  residues processed: 122
  average time/residue: 0.2078
  time to fit residues: 33.3070
Evaluate side-chains
  116 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  180 VAL
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0470
   chunk 64 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** B 271 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 = 0.4283 r_free = 0.4283 target = 0.166336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.145492 restraints weight = 15281.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.148592 restraints weight = 9280.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.150718 restraints weight = 6544.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7289  Z= 0.176
  Angle     :  0.645  10.140   9941  Z= 0.303
  Chirality :  0.046   0.421   1128
  Planarity :  0.006   0.091   1256
  Dihedral  :  7.590  56.331   1167
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.15 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.79 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.28), residues: 855
  helix:  2.50 (0.42), residues: 148
  sheet: -0.60 (0.31), residues: 243
  loop : -1.65 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  89 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.020   0.001   PHE B  72 
 TYR   0.014   0.001   TYR B 261 
 ARG   0.004   0.000   ARG D  67 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  150 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7620 (mm-30)
REVERT: C  198 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6740 (mtm-85)
REVERT: D  132 MET cc_start: 0.7566 (ppp) cc_final: 0.7212 (ppp)
REVERT: D  134 ARG cc_start: 0.8358 (mtt-85) cc_final: 0.8110 (mtt-85)
REVERT: D  135 MET cc_start: 0.7961 (ptp) cc_final: 0.7596 (pmm)
REVERT: D  140 MET cc_start: 0.8488 (tmm) cc_final: 0.8161 (tmm)
REVERT: A  217 TRP cc_start: 0.7929 (m100) cc_final: 0.6939 (m100)
REVERT: B   76 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7190 (tttp)
REVERT: B  146 TRP cc_start: 0.8752 (p90) cc_final: 0.8362 (p90)
REVERT: B  302 MET cc_start: 0.5925 (ptt) cc_final: 0.5327 (mtm)
  outliers start: 26
  outliers final: 20
  residues processed: 118
  average time/residue: 0.1966
  time to fit residues: 31.2750
Evaluate side-chains
  116 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
D 126 GLN
D 154 GLN
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 258 ASN
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.162019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.141811 restraints weight = 15007.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.144568 restraints weight = 9353.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.146471 restraints weight = 6760.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.5953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7289  Z= 0.308
  Angle     :  0.763   9.369   9941  Z= 0.372
  Chirality :  0.050   0.413   1128
  Planarity :  0.006   0.100   1256
  Dihedral  :  7.777  59.742   1167
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.90 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.18 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    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: -1.16 (0.28), residues: 855
  helix:  2.16 (0.42), residues: 148
  sheet: -0.80 (0.31), residues: 240
  loop : -1.79 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 310 
 HIS   0.005   0.001   HIS A 159 
 PHE   0.023   0.002   PHE B  72 
 TYR   0.020   0.002   TYR B  79 
 ARG   0.005   0.001   ARG D 105 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  198 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6753 (mtm-85)
REVERT: D  132 MET cc_start: 0.7876 (ppp) cc_final: 0.6908 (ppp)
REVERT: D  135 MET cc_start: 0.7893 (ptp) cc_final: 0.7402 (pmm)
REVERT: D  140 MET cc_start: 0.8459 (tmm) cc_final: 0.8176 (tmm)
REVERT: A   53 SER cc_start: 0.4687 (OUTLIER) cc_final: 0.4455 (m)
REVERT: A  194 GLN cc_start: 0.7855 (mp10) cc_final: 0.7607 (mp10)
REVERT: A  217 TRP cc_start: 0.8149 (m100) cc_final: 0.6611 (m100)
REVERT: B   74 ILE cc_start: 0.9094 (mm) cc_final: 0.8885 (mt)
REVERT: B   76 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7092 (tttp)
REVERT: B  146 TRP cc_start: 0.8788 (p90) cc_final: 0.8360 (p90)
REVERT: B  244 TRP cc_start: 0.7243 (p90) cc_final: 0.6968 (p90)
  outliers start: 28
  outliers final: 22
  residues processed: 117
  average time/residue: 0.1762
  time to fit residues: 28.0729
Evaluate side-chains
  117 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0370
   chunk 75 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
D 126 GLN
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.175018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.153196 restraints weight = 15426.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.155405 restraints weight = 9796.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.156827 restraints weight = 7427.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.5883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7289  Z= 0.189
  Angle     :  0.679   9.700   9941  Z= 0.323
  Chirality :  0.046   0.391   1128
  Planarity :  0.005   0.094   1256
  Dihedral  :  7.686  58.246   1167
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.96 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.18 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.28), residues: 855
  helix:  2.39 (0.42), residues: 148
  sheet: -0.65 (0.32), residues: 243
  loop : -1.69 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 115 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.020   0.001   PHE B  72 
 TYR   0.028   0.001   TYR B 295 
 ARG   0.003   0.000   ARG A 209 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  132 MET cc_start: 0.7690 (ppp) cc_final: 0.6657 (ppp)
REVERT: D  135 MET cc_start: 0.7655 (ptp) cc_final: 0.7342 (pmm)
REVERT: D  140 MET cc_start: 0.8409 (tmm) cc_final: 0.8094 (tmm)
REVERT: A   53 SER cc_start: 0.4369 (OUTLIER) cc_final: 0.4166 (m)
REVERT: A  194 GLN cc_start: 0.7513 (mp10) cc_final: 0.6716 (mt0)
REVERT: A  210 MET cc_start: 0.6173 (mmp) cc_final: 0.5939 (mmm)
REVERT: A  217 TRP cc_start: 0.8031 (m100) cc_final: 0.6702 (m100)
REVERT: B   76 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7172 (tttp)
REVERT: B  146 TRP cc_start: 0.8686 (p90) cc_final: 0.8307 (p90)
  outliers start: 29
  outliers final: 25
  residues processed: 116
  average time/residue: 0.2132
  time to fit residues: 33.6542
Evaluate side-chains
  115 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0980
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0270
   chunk 67 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0050
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.2256

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 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 = 0.4284 r_free = 0.4284 target = 0.164516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.144663 restraints weight = 15475.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.147575 restraints weight = 9423.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.149552 restraints weight = 6648.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.6038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7289  Z= 0.248
  Angle     :  0.710   9.520   9941  Z= 0.341
  Chirality :  0.047   0.395   1128
  Planarity :  0.006   0.098   1256
  Dihedral  :  7.458  57.981   1167
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.43 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.83 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.28), residues: 855
  helix:  2.67 (0.42), residues: 142
  sheet: -0.63 (0.32), residues: 235
  loop : -1.71 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.002   TRP B 310 
 HIS   0.003   0.001   HIS D 117 
 PHE   0.021   0.002   PHE B  72 
 TYR   0.030   0.002   TYR B 295 
 ARG   0.007   0.001   ARG B 300 

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7199 (mm)
REVERT: D  132 MET cc_start: 0.7729 (ppp) cc_final: 0.7295 (ppp)
REVERT: D  140 MET cc_start: 0.8459 (tmm) cc_final: 0.8152 (tmm)
REVERT: A  194 GLN cc_start: 0.7673 (mp10) cc_final: 0.6867 (mt0)
REVERT: A  210 MET cc_start: 0.6397 (mmp) cc_final: 0.6147 (mmm)
REVERT: A  217 TRP cc_start: 0.8080 (m100) cc_final: 0.6621 (m100)
REVERT: B   76 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7208 (tttp)
REVERT: B  146 TRP cc_start: 0.8784 (p90) cc_final: 0.8360 (p90)
REVERT: B  244 TRP cc_start: 0.7265 (p90) cc_final: 0.7012 (p90)
  outliers start: 29
  outliers final: 24
  residues processed: 111
  average time/residue: 0.1902
  time to fit residues: 29.4675
Evaluate side-chains
  112 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  189 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain C residue  211 TYR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  164 TRP
Chi-restraints excluded: chain B residue  182 CYS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  265 ASP
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  296 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 51 optimal weight:    0.4980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 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 = 0.4316 r_free = 0.4316 target = 0.170549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.149466 restraints weight = 15316.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.152482 restraints weight = 9535.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.154579 restraints weight = 6777.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.6099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7289  Z= 0.205
  Angle     :  0.679   9.555   9941  Z= 0.325
  Chirality :  0.046   0.384   1128
  Planarity :  0.006   0.098   1256
  Dihedral  :  7.237  57.518   1167
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.08 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.31 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.29), residues: 855
  helix:  2.69 (0.42), residues: 142
  sheet: -0.63 (0.32), residues: 243
  loop : -1.67 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP B 310 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.021   0.001   PHE B  72 
 TYR   0.025   0.001   TYR B 295 
 ARG   0.004   0.000   ARG C 171 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2498.73 seconds
wall clock time: 44 minutes 2.33 seconds (2642.33 seconds total)