Starting phenix.real_space_refine
on Fri Feb 14 14:13:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y90_10731/02_2025/6y90_10731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y90_10731/02_2025/6y90_10731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y90_10731/02_2025/6y90_10731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y90_10731/02_2025/6y90_10731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y90_10731/02_2025/6y90_10731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y90_10731/02_2025/6y90_10731.cif"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.057
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      56      5.16       5
     C    6368      2.51       5
     N    1520      2.21       5
     O    1832      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9778
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1341
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 7, 'TRANS': 164}
    Chain: "B"
      Number of atoms: 1341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1341
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 7, 'TRANS': 164}
    Chain: "C"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1669
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 210}
    Chain: "D"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1623
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199}
    Chain: "A"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 256
          Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 256
          Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    H, L
  Time building chain proxies: 7.42, per 1000 atoms: 0.76
  Number of scatterers: 9778
  At special positions: 0
  Unit cell: (103.378, 142.45, 134.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     P       2     15.00
     O    1832      8.00
     N    1520      7.00
     C    6368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 167 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 167 " - pdb=" SG  CYS B 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 148 " - pdb=" SG  CYS C 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 224 " - pdb=" SG  CYS D 213 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 193 " 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2252

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 20 sheets defined
      24.7% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 4.004A  pdb=" N   VAL A  84 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 102
      removed outlier: 3.805A  pdb=" N   TRP A  89 " --> pdb=" O   TRP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 143
      removed outlier: 4.010A  pdb=" N   MET A 117 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ILE A 118 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 177 through 215
      removed outlier: 3.859A  pdb=" N   CYS A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 71
      removed outlier: 3.567A  pdb=" N   LEU B  52 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   MET B  71 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.707A  pdb=" N   VAL B  84 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 102
      removed outlier: 3.889A  pdb=" N   TRP B  89 " --> pdb=" O   TRP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 143
      removed outlier: 4.054A  pdb=" N   MET B 117 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ILE B 118 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 157
    Processing helix  chain 'B' and resid 171 through 175
    Processing helix  chain 'B' and resid 177 through 215
      removed outlier: 3.729A  pdb=" N   CYS B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 82
    Processing helix  chain 'D' and resid 120 through 127
      removed outlier: 3.540A  pdb=" N   LEU D 124 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY D 127 " --> pdb=" O   GLN D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 188
    Processing helix  chain 'L' and resid 78 through 82
    Processing helix  chain 'L' and resid 120 through 127
      removed outlier: 3.539A  pdb=" N   LEU L 124 " --> pdb=" O   SER L 120 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY L 127 " --> pdb=" O   GLN L 123 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 181 through 188
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5
      removed outlier: 3.752A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 59
      removed outlier: 3.620A  pdb=" N   ILE C  48 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102
      removed outlier: 3.817A  pdb=" N   ASP C 105 " --> pdb=" O   TYR C 102 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 128 through 132
      removed outlier: 3.881A  pdb=" N   SER C 128 " --> pdb=" O   LYS C 151 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY C 147 " --> pdb=" O   LEU C 132 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER C 188 " --> pdb=" O   CYS C 148 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   TYR C 184 " --> pdb=" O   ASP C 152 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   SER C 185 " --> pdb=" O   ALA C 176 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ALA C 176 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER C 187 " --> pdb=" O   PHE C 174 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 159 through 160
      removed outlier: 3.537A  pdb=" N   THR C 159 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.668A  pdb=" N   THR D  22 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.558A  pdb=" N   LEU D  11 " --> pdb=" O   LYS D 102 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR D  84 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   GLN D  36 " --> pdb=" O   PRO D  45 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TYR D  48 " --> pdb=" O   ASN D  52 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 113 through 117
      removed outlier: 3.516A  pdb=" N   SER D 113 " --> pdb=" O   ASN D 136 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASN D 136 " --> pdb=" O   SER D 113 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL D 132 " --> pdb=" O   PHE D 117 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA D 129 " --> pdb=" O   LEU D 180 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU D 180 " --> pdb=" O   ALA D 129 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER D 176 " --> pdb=" O   CYS D 133 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU D 135 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU D 174 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER D 161 " --> pdb=" O   SER D 175 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR D 177 " --> pdb=" O   GLN D 159 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLN D 159 " --> pdb=" O   THR D 177 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154
      removed outlier: 3.953A  pdb=" N   TRP D 147 " --> pdb=" O   GLN D 154 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS D 144 " --> pdb=" O   THR D 196 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLU D 194 " --> pdb=" O   GLN D 146 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR D 191 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE D 208 " --> pdb=" O   TYR D 191 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   CYS D 193 " --> pdb=" O   LYS D 206 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LYS D 206 " --> pdb=" O   CYS D 193 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.753A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59
      removed outlier: 3.620A  pdb=" N   ILE H  48 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 100 through 102
      removed outlier: 3.819A  pdb=" N   ASP H 105 " --> pdb=" O   TYR H 102 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 128 through 132
      removed outlier: 3.881A  pdb=" N   SER H 128 " --> pdb=" O   LYS H 151 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   SER H 188 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TYR H 184 " --> pdb=" O   ASP H 152 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   SER H 185 " --> pdb=" O   ALA H 176 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   ALA H 176 " --> pdb=" O   SER H 185 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER H 187 " --> pdb=" O   PHE H 174 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 159 through 160
      removed outlier: 3.537A  pdb=" N   THR H 159 " --> pdb=" O   ASN H 207 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.668A  pdb=" N   THR L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  74 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.558A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 102 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR L  84 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   GLN L  36 " --> pdb=" O   PRO L  45 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   TYR L  48 " --> pdb=" O   ASN L  52 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 113 through 117
      removed outlier: 3.516A  pdb=" N   SER L 113 " --> pdb=" O   ASN L 136 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASN L 136 " --> pdb=" O   SER L 113 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL L 132 " --> pdb=" O   PHE L 117 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA L 129 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU L 180 " --> pdb=" O   ALA L 129 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER L 176 " --> pdb=" O   CYS L 133 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU L 135 " --> pdb=" O   LEU L 174 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU L 174 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER L 161 " --> pdb=" O   SER L 175 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   THR L 177 " --> pdb=" O   GLN L 159 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLN L 159 " --> pdb=" O   THR L 177 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 152 through 154
      removed outlier: 3.954A  pdb=" N   TRP L 147 " --> pdb=" O   GLN L 154 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS L 144 " --> pdb=" O   THR L 196 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLU L 194 " --> pdb=" O   GLN L 146 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR L 191 " --> pdb=" O   PHE L 208 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE L 208 " --> pdb=" O   TYR L 191 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   CYS L 193 " --> pdb=" O   LYS L 206 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LYS L 206 " --> pdb=" O   CYS L 193 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1077 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: 2.73

  Time building geometry restraints manager: 2.71 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1498
        1.31 -     1.44: 2686
        1.44 -     1.56: 5745
        1.56 -     1.69: 5
        1.69 -     1.81: 84
  Bond restraints: 10018
  Sorted by residual:
  bond pdb=" CAZ Y01 A 303 "
       pdb=" CBH Y01 A 303 "
    ideal  model  delta    sigma   weight residual
    1.519  1.405  0.114 2.00e-02 2.50e+03 3.26e+01
  bond pdb=" CAZ Y01 B 304 "
       pdb=" CBH Y01 B 304 "
    ideal  model  delta    sigma   weight residual
    1.519  1.405  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" CAZ Y01 A 302 "
       pdb=" CBH Y01 A 302 "
    ideal  model  delta    sigma   weight residual
    1.519  1.406  0.113 2.00e-02 2.50e+03 3.18e+01
  bond pdb=" CAZ Y01 B 301 "
       pdb=" CBH Y01 B 301 "
    ideal  model  delta    sigma   weight residual
    1.519  1.406  0.113 2.00e-02 2.50e+03 3.17e+01
  bond pdb=" CAZ Y01 B 302 "
       pdb=" CBH Y01 B 302 "
    ideal  model  delta    sigma   weight residual
    1.519  1.406  0.113 2.00e-02 2.50e+03 3.17e+01
  ... (remaining 10013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 13126
        2.83 -     5.67: 438
        5.67 -     8.50: 18
        8.50 -    11.33: 6
       11.33 -    14.16: 2
  Bond angle restraints: 13590
  Sorted by residual:
  angle pdb=" O12 PC1 A 304 "
        pdb=" P   PC1 A 304 "
        pdb=" O14 PC1 A 304 "
      ideal   model   delta    sigma   weight residual
     123.67  109.51   14.16 3.00e+00 1.11e-01 2.23e+01
  angle pdb=" O12 PC1 B 305 "
        pdb=" P   PC1 B 305 "
        pdb=" O14 PC1 B 305 "
      ideal   model   delta    sigma   weight residual
     123.67  109.53   14.14 3.00e+00 1.11e-01 2.22e+01
  angle pdb=" CAY Y01 A 303 "
        pdb=" OAW Y01 A 303 "
        pdb=" CBC Y01 A 303 "
      ideal   model   delta    sigma   weight residual
     119.39  109.59    9.80 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" CAY Y01 B 304 "
        pdb=" OAW Y01 B 304 "
        pdb=" CBC Y01 B 304 "
      ideal   model   delta    sigma   weight residual
     119.39  109.65    9.74 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" C22 PC1 B 305 "
        pdb=" C21 PC1 B 305 "
        pdb=" O21 PC1 B 305 "
      ideal   model   delta    sigma   weight residual
     111.12  119.88   -8.76 3.00e+00 1.11e-01 8.52e+00
  ... (remaining 13585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.87: 5881
       20.87 -    41.75: 436
       41.75 -    62.62: 74
       62.62 -    83.49: 16
       83.49 -   104.36: 6
  Dihedral angle restraints: 6413
    sinusoidal: 2891
      harmonic: 3522
  Sorted by residual:
  dihedral pdb=" CA  PHE B 146 "
           pdb=" C   PHE B 146 "
           pdb=" N   LEU B 147 "
           pdb=" CA  LEU B 147 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CAR Y01 A 303 "
           pdb=" CAV Y01 A 303 "
           pdb=" CBC Y01 A 303 "
           pdb=" CAZ Y01 A 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.40  -48.96  104.36     1      3.00e+01 1.11e-03 1.33e+01
  dihedral pdb=" CAR Y01 B 304 "
           pdb=" CAV Y01 B 304 "
           pdb=" CBC Y01 B 304 "
           pdb=" CAZ Y01 B 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.40  -48.94  104.34     1      3.00e+01 1.11e-03 1.33e+01
  ... (remaining 6410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1428
       0.096 -    0.192: 62
       0.192 -    0.288: 5
       0.288 -    0.384: 15
       0.384 -    0.480: 14
  Chirality restraints: 1524
  Sorted by residual:
  chirality pdb=" CBH Y01 B 301 "
            pdb=" CAT Y01 B 301 "
            pdb=" CAZ Y01 B 301 "
            pdb=" CBF Y01 B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.37   -0.48 2.00e-01 2.50e+01 5.76e+00
  chirality pdb=" CBH Y01 A 310 "
            pdb=" CAT Y01 A 310 "
            pdb=" CAZ Y01 A 310 "
            pdb=" CBF Y01 A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.38   -0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CBG Y01 B 301 "
            pdb=" CAQ Y01 B 301 "
            pdb=" CBD Y01 B 301 "
            pdb=" CBI Y01 B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.81    0.47 2.00e-01 2.50e+01 5.62e+00
  ... (remaining 1521 not shown)

  Planarity restraints: 1642
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  94 "   -0.007 2.00e-02 2.50e+03   1.03e-02 2.11e+00
        pdb=" CG  TYR A  94 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  94 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  94 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  94 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  57 "    0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO L  58 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO L  58 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO L  58 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  57 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO D  58 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO D  58 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D  58 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1639 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 63
        2.61 -     3.18: 7852
        3.18 -     3.75: 14206
        3.75 -     4.33: 18745
        4.33 -     4.90: 31878
  Nonbonded interactions: 72744
  Sorted by model distance:
  nonbonded pdb=" SG  CYS H 148 "
            pdb=" SG  CYS H 204 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS L 133 "
            pdb=" SG  CYS L 193 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS L  23 "
            pdb=" SG  CYS L  87 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS H  22 "
            pdb=" SG  CYS H  96 "
     model   vdw
     2.033 3.760
  nonbonded pdb=" SG  CYS H 224 "
            pdb=" SG  CYS L 213 "
     model   vdw
     2.043 3.760
  ... (remaining 72739 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: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 45 through 216 or resid 301 through 303 or resid 306 throu \ 
gh 309))
  selection = (chain 'B' and (resid 45 through 216 or resid 301 through 302 or (resid 303 and  \ 
(name CAA or name CAB or name CAD or name CAE or name CAI or name CAJ or name CA \ 
K or name CAL or name CAM or name CAN or name CAO or name CAP or name CAQ or nam \ 
e CAR or name CAS or name CAT or name CAU or name CAV or name CAX or name CAY or \ 
 name CAZ or name CBA or name CBB or name CBC or name CBD or name CBE or name CB \ 
F or name CBG or name CBH or name CBI or name OAF or name OAG or name OAH or nam \ 
e OAW)) or resid 306 through 309))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.530
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.480
  Find NCS groups from input model:        0.410
  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:   31.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
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      :  0.007   0.114  10018  Z= 0.430
  Angle     :  0.903  14.163  13590  Z= 0.356
  Chirality :  0.068   0.480   1524
  Planarity :  0.003   0.032   1642
  Dihedral  : 14.795 104.364   4140
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.00 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.25), residues: 1206
  helix:  2.02 (0.35), residues: 234
  sheet:  0.31 (0.28), residues: 352
  loop : -0.72 (0.26), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  89 
 HIS   0.002   0.000   HIS B 145 
 PHE   0.018   0.001   PHE A  62 
 TYR   0.024   0.001   TYR A  94 
 ARG   0.001   0.000   ARG B 156 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 191
  time to evaluate  : 1.060 
Fit side-chains
REVERT: B  106 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7933 (pttm)
REVERT: B  142 LYS cc_start: 0.8655 (tppt) cc_final: 0.8315 (tptt)
REVERT: D   89 GLN cc_start: 0.8320 (pp30) cc_final: 0.8114 (pp30)
REVERT: H   62 GLN cc_start: 0.7764 (mt0) cc_final: 0.7519 (mt0)
REVERT: L   89 GLN cc_start: 0.8291 (pp30) cc_final: 0.8079 (pp30)
  outliers start: 2
  outliers final: 2
  residues processed: 191
  average time/residue: 0.2083
  time to fit residues: 56.6919
Evaluate side-chains
  153 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain H residue   34 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 90 optimal weight:   40.0000
   chunk 50 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:   40.0000
   chunk 94 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 181 GLN
A 214 ASN
B  59 ASN
B 158 HIS
B 181 GLN
B 214 ASN
C 207 ASN
C 208 HIS
H  33 ASN
H 207 ASN
H 208 HIS
L   1 GLN
L 137 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.196854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.157240 restraints weight = 17129.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.156463 restraints weight = 11008.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.157454 restraints weight = 9908.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10018  Z= 0.200
  Angle     :  0.613   8.738  13590  Z= 0.290
  Chirality :  0.043   0.262   1524
  Planarity :  0.003   0.035   1642
  Dihedral  : 11.103  76.591   2056
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.63 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1206
  helix:  1.67 (0.34), residues: 248
  sheet:  0.42 (0.28), residues: 370
  loop : -0.83 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  89 
 HIS   0.003   0.001   HIS C 172 
 PHE   0.016   0.001   PHE B 146 
 TYR   0.021   0.001   TYR A  94 
 ARG   0.005   0.001   ARG L  76 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A   46 MET cc_start: 0.5940 (pmm) cc_final: 0.5481 (ptp)
REVERT: A   50 LYS cc_start: 0.7992 (ttmt) cc_final: 0.6953 (pttm)
REVERT: A  119 MET cc_start: 0.6673 (mmt) cc_final: 0.6332 (mmt)
REVERT: B   50 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7355 (ttmm)
REVERT: B   57 ILE cc_start: 0.9084 (mm) cc_final: 0.8882 (mm)
REVERT: B  106 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7996 (pttp)
REVERT: C   48 ILE cc_start: 0.8570 (tp) cc_final: 0.8306 (tp)
REVERT: D   89 GLN cc_start: 0.8414 (pp30) cc_final: 0.8113 (pp30)
REVERT: D  168 LYS cc_start: 0.7770 (tttm) cc_final: 0.7139 (tppt)
REVERT: H   48 ILE cc_start: 0.8633 (tp) cc_final: 0.8310 (tp)
REVERT: H   62 GLN cc_start: 0.7993 (mt0) cc_final: 0.7764 (mt0)
REVERT: L   89 GLN cc_start: 0.8395 (pp30) cc_final: 0.8097 (pp30)
  outliers start: 10
  outliers final: 5
  residues processed: 179
  average time/residue: 0.2073
  time to fit residues: 53.9779
Evaluate side-chains
  157 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 48 optimal weight:    8.9990
   chunk 55 optimal weight:   20.0000
   chunk 81 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 140 ASN
A 181 GLN
A 214 ASN
B 166 ASN
B 181 GLN
C  33 ASN
L  37 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.183559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133657 restraints weight = 16782.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136885 restraints weight = 8300.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.139022 restraints weight = 5558.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10018  Z= 0.357
  Angle     :  0.686  11.280  13590  Z= 0.332
  Chirality :  0.046   0.235   1524
  Planarity :  0.004   0.040   1642
  Dihedral  : 10.486  58.744   2050
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.03 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.25), residues: 1206
  helix:  1.38 (0.33), residues: 254
  sheet:  0.32 (0.26), residues: 414
  loop : -0.86 (0.28), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  89 
 HIS   0.005   0.001   HIS H 172 
 PHE   0.016   0.002   PHE B  45 
 TYR   0.022   0.002   TYR C 107 
 ARG   0.007   0.001   ARG D  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 1.050 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8366 (ttmt) cc_final: 0.6890 (pttp)
REVERT: B  106 LYS cc_start: 0.8494 (mmmt) cc_final: 0.7848 (pptt)
REVERT: H   64 PHE cc_start: 0.6938 (m-10) cc_final: 0.6550 (m-10)
REVERT: L   89 GLN cc_start: 0.8534 (pp30) cc_final: 0.8247 (pp30)
  outliers start: 22
  outliers final: 13
  residues processed: 176
  average time/residue: 0.1942
  time to fit residues: 50.0121
Evaluate side-chains
  156 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0170
   chunk 70 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 118 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   overall best weight:    1.6026

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 ASN
A 181 GLN
A 214 ASN
B 166 ASN
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.185040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.135218 restraints weight = 16653.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.138707 restraints weight = 8076.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.140776 restraints weight = 5340.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10018  Z= 0.238
  Angle     :  0.614  13.267  13590  Z= 0.293
  Chirality :  0.044   0.264   1524
  Planarity :  0.004   0.037   1642
  Dihedral  : 10.156  58.994   2050
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.30 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.25), residues: 1206
  helix:  1.28 (0.32), residues: 254
  sheet:  0.28 (0.26), residues: 418
  loop : -0.93 (0.29), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  89 
 HIS   0.002   0.001   HIS C  35 
 PHE   0.016   0.001   PHE B 146 
 TYR   0.018   0.001   TYR A  94 
 ARG   0.004   0.000   ARG D  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8304 (ttmt) cc_final: 0.6833 (pttp)
REVERT: B  106 LYS cc_start: 0.8525 (mmmt) cc_final: 0.7823 (pptt)
REVERT: B  109 ARG cc_start: 0.6642 (tmt-80) cc_final: 0.6225 (tpm170)
  outliers start: 30
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1970
  time to fit residues: 50.9525
Evaluate side-chains
  163 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 98 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 86 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 77 optimal weight:    0.2980
   chunk 119 optimal weight:    4.9990
   chunk 100 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 48 optimal weight:    0.2980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 ASN
A 214 ASN
B 166 ASN
L  37 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.185468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.135471 restraints weight = 16610.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.138938 restraints weight = 8063.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.140882 restraints weight = 5327.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10018  Z= 0.217
  Angle     :  0.619  10.919  13590  Z= 0.292
  Chirality :  0.044   0.237   1524
  Planarity :  0.003   0.031   1642
  Dihedral  :  9.898  59.862   2050
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.42 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.25), residues: 1206
  helix:  1.26 (0.33), residues: 248
  sheet:  0.34 (0.26), residues: 414
  loop : -0.88 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  89 
 HIS   0.002   0.001   HIS H 172 
 PHE   0.015   0.001   PHE H  64 
 TYR   0.016   0.001   TYR B  94 
 ARG   0.004   0.000   ARG D  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8288 (ttmt) cc_final: 0.6807 (pttp)
REVERT: B  106 LYS cc_start: 0.8517 (mmmt) cc_final: 0.7857 (pttp)
REVERT: B  109 ARG cc_start: 0.6668 (tmt-80) cc_final: 0.6214 (tpm170)
REVERT: C   64 PHE cc_start: 0.7290 (m-10) cc_final: 0.7029 (m-10)
  outliers start: 27
  outliers final: 22
  residues processed: 177
  average time/residue: 0.2036
  time to fit residues: 51.5872
Evaluate side-chains
  171 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0670
   chunk 63 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 120 ASN
A 181 GLN
A 214 ASN
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  52 ASN
L  37 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.188342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.138979 restraints weight = 16722.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.142473 restraints weight = 7938.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.144594 restraints weight = 5224.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10018  Z= 0.165
  Angle     :  0.577  10.016  13590  Z= 0.277
  Chirality :  0.043   0.202   1524
  Planarity :  0.003   0.029   1642
  Dihedral  :  9.500  59.717   2050
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.39 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.25), residues: 1206
  helix:  1.29 (0.33), residues: 248
  sheet:  0.50 (0.26), residues: 402
  loop : -0.87 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  89 
 HIS   0.002   0.001   HIS C  35 
 PHE   0.013   0.001   PHE H  64 
 TYR   0.010   0.001   TYR H 107 
 ARG   0.003   0.000   ARG D  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8263 (ttmt) cc_final: 0.6809 (pttp)
REVERT: A  181 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8265 (mm-40)
REVERT: B  106 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7839 (pttp)
REVERT: B  109 ARG cc_start: 0.6559 (tmt-80) cc_final: 0.6197 (tpm170)
  outliers start: 23
  outliers final: 15
  residues processed: 171
  average time/residue: 0.2058
  time to fit residues: 50.9453
Evaluate side-chains
  161 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain L residue   62 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 69 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 105 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 103 optimal weight:    0.6980
   chunk 116 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0170
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.189603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.142528 restraints weight = 17093.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.144024 restraints weight = 9798.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.145530 restraints weight = 5885.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10018  Z= 0.159
  Angle     :  0.565   9.228  13590  Z= 0.274
  Chirality :  0.043   0.192   1524
  Planarity :  0.003   0.048   1642
  Dihedral  :  9.156  58.644   2050
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.25 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.25), residues: 1206
  helix:  1.09 (0.32), residues: 260
  sheet:  0.57 (0.26), residues: 402
  loop : -0.89 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  89 
 HIS   0.002   0.000   HIS B 145 
 PHE   0.012   0.001   PHE H  64 
 TYR   0.011   0.001   TYR A  94 
 ARG   0.007   0.000   ARG L  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8277 (ttmt) cc_final: 0.6792 (pttp)
REVERT: A   59 ASN cc_start: 0.8822 (m-40) cc_final: 0.8576 (m-40)
REVERT: B  106 LYS cc_start: 0.8589 (mmmt) cc_final: 0.7769 (pttm)
REVERT: B  109 ARG cc_start: 0.6843 (tmt-80) cc_final: 0.6060 (tpm170)
REVERT: L   80 GLU cc_start: 0.7960 (tt0) cc_final: 0.7434 (mp0)
  outliers start: 23
  outliers final: 19
  residues processed: 173
  average time/residue: 0.1914
  time to fit residues: 48.4623
Evaluate side-chains
  170 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   36 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   87 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0870
   chunk 103 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 181 GLN
A 214 ASN
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.184390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136721 restraints weight = 16978.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.138981 restraints weight = 9027.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.140098 restraints weight = 5538.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10018  Z= 0.273
  Angle     :  0.615   8.510  13590  Z= 0.301
  Chirality :  0.045   0.206   1524
  Planarity :  0.004   0.042   1642
  Dihedral  :  9.277  59.452   2050
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.06 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.25), residues: 1206
  helix:  0.95 (0.32), residues: 260
  sheet:  0.28 (0.26), residues: 426
  loop : -0.78 (0.29), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  89 
 HIS   0.003   0.001   HIS H 208 
 PHE   0.012   0.001   PHE B  45 
 TYR   0.019   0.001   TYR H 107 
 ARG   0.005   0.000   ARG L  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8340 (ttmt) cc_final: 0.6851 (pttp)
REVERT: B  106 LYS cc_start: 0.8657 (mmmt) cc_final: 0.7784 (pttm)
REVERT: B  109 ARG cc_start: 0.6767 (tmt-80) cc_final: 0.6290 (tpm170)
REVERT: L   80 GLU cc_start: 0.8046 (tt0) cc_final: 0.7493 (mp0)
  outliers start: 30
  outliers final: 24
  residues processed: 174
  average time/residue: 0.1961
  time to fit residues: 49.7083
Evaluate side-chains
  175 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   36 GLN
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   87 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 56 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 48 optimal weight:   30.0000
   chunk 59 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.186736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.137479 restraints weight = 16998.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.141065 restraints weight = 8042.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.143257 restraints weight = 5256.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10018  Z= 0.188
  Angle     :  0.599  10.375  13590  Z= 0.289
  Chirality :  0.043   0.202   1524
  Planarity :  0.003   0.033   1642
  Dihedral  :  9.007  57.985   2050
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.74 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1206
  helix:  1.01 (0.32), residues: 260
  sheet:  0.50 (0.26), residues: 402
  loop : -0.94 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  89 
 HIS   0.002   0.001   HIS B 145 
 PHE   0.020   0.001   PHE H  64 
 TYR   0.031   0.001   TYR A  94 
 ARG   0.006   0.000   ARG L  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 1.142 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8313 (ttmt) cc_final: 0.6832 (pttp)
REVERT: B  106 LYS cc_start: 0.8506 (mmmt) cc_final: 0.7783 (pttm)
REVERT: L   80 GLU cc_start: 0.7906 (tt0) cc_final: 0.7453 (mp0)
REVERT: L  164 GLU cc_start: 0.7978 (tp30) cc_final: 0.7729 (tp30)
  outliers start: 27
  outliers final: 26
  residues processed: 177
  average time/residue: 0.1951
  time to fit residues: 50.2137
Evaluate side-chains
  181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   36 GLN
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   87 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 117 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.184277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.134739 restraints weight = 16950.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.138218 restraints weight = 8121.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.140326 restraints weight = 5350.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.3609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10018  Z= 0.271
  Angle     :  0.636  10.285  13590  Z= 0.309
  Chirality :  0.045   0.208   1524
  Planarity :  0.004   0.035   1642
  Dihedral  :  9.039  58.472   2050
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.22 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.25), residues: 1206
  helix:  0.94 (0.32), residues: 260
  sheet:  0.31 (0.26), residues: 422
  loop : -0.86 (0.29), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  89 
 HIS   0.003   0.001   HIS H 208 
 PHE   0.015   0.001   PHE H  64 
 TYR   0.026   0.001   TYR A  94 
 ARG   0.005   0.000   ARG L  60 

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 1.058 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8362 (ttmt) cc_final: 0.6854 (pttp)
REVERT: B  106 LYS cc_start: 0.8552 (mmmt) cc_final: 0.7744 (pttm)
REVERT: L   80 GLU cc_start: 0.8019 (tt0) cc_final: 0.7454 (mp0)
REVERT: L  164 GLU cc_start: 0.8034 (tp30) cc_final: 0.7786 (tp30)
  outliers start: 29
  outliers final: 25
  residues processed: 178
  average time/residue: 0.1925
  time to fit residues: 49.9281
Evaluate side-chains
  180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain B residue   45 PHE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  119 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   36 GLN
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   87 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 31 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 119 optimal weight:    8.9990
   chunk 89 optimal weight:    0.5980
   chunk 115 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 166 ASN
A 214 ASN
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.186740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.142642 restraints weight = 16809.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.141368 restraints weight = 9373.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.142609 restraints weight = 7293.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10018  Z= 0.190
  Angle     :  0.615  10.870  13590  Z= 0.296
  Chirality :  0.044   0.208   1524
  Planarity :  0.003   0.029   1642
  Dihedral  :  8.817  59.018   2050
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.83 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.25), residues: 1206
  helix:  0.97 (0.32), residues: 260
  sheet:  0.45 (0.26), residues: 402
  loop : -0.93 (0.29), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  89 
 HIS   0.002   0.001   HIS C  35 
 PHE   0.018   0.001   PHE H  64 
 TYR   0.034   0.001   TYR B  94 
 ARG   0.005   0.000   ARG L  60 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3357.90 seconds
wall clock time: 61 minutes 5.23 seconds (3665.23 seconds total)