Starting phenix.real_space_refine
on Wed Mar  4 02:49:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y90_10731/03_2026/6y90_10731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y90_10731/03_2026/6y90_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_10731/03_2026/6y90_10731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y90_10731/03_2026/6y90_10731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y90_10731/03_2026/6y90_10731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y90_10731/03_2026/6y90_10731.cif"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.83, per 1000 atoms: 0.29
  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=12, 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
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 148 " - pdb=" SG  CYS H 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 224 " - pdb=" SG  CYS L 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 133 " - pdb=" SG  CYS L 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: 0.91
  Conformation dependent library (CDL) restraints added in 484.8 milliseconds
  

  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: 0.34
  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: 1.51

  Time building geometry restraints manager: 1.19 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: 5891
       20.87 -    41.75: 441
       41.75 -    62.62: 74
       62.62 -    83.49: 16
       83.49 -   104.36: 6
  Dihedral angle restraints: 6428
    sinusoidal: 2906
      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 6425 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:
        2.27 -     2.79: 2180
        2.79 -     3.32: 8677
        3.32 -     3.85: 15209
        3.85 -     4.37: 16780
        4.37 -     4.90: 29883
  Nonbonded interactions: 72729
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 163 "
            pdb=" OH  TYR B 182 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OD1 ASP C  90 "
            pdb=" OH  TYR C  94 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD1 ASP H  90 "
            pdb=" OH  TYR H  94 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD1 ASN L 136 "
            pdb=" OG  SER L 173 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OD1 ASN D 136 "
            pdb=" OG  SER D 173 "
     model   vdw
     2.287 3.040
  ... (remaining 72724 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 45 through 303 or resid 306 through 309))
  selection = (chain 'B' and (resid 45 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 CAK or name CAL or name CAM \ 
 or name CAN or name CAO or name CAP or name CAQ or name 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 CBF or name CBG or name CBH \ 
 or name CBI or name OAF or name OAG or name OAH or name OAW)) or resid 306 thro \ 
ugh 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.940
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.270
-------------------------------------------------------------------------------
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  10032  Z= 0.333
  Angle     :  0.902  14.163  13614  Z= 0.356
  Chirality :  0.068   0.480   1524
  Planarity :  0.003   0.032   1642
  Dihedral  : 14.795 104.364   4140
  Min Nonbonded Distance : 2.268

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG B 156 
 TYR   0.024   0.001   TYR A  94 
 PHE   0.018   0.001   PHE A  62 
 TRP   0.009   0.001   TRP B  89 
 HIS   0.002   0.000   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 (10018)
  covalent geometry    : angle       0.90266 (13590)
  SS BOND              : bond        0.00553 (   12)
  SS BOND              : angle       0.50249 (   24)
  hydrogen bonds       : bond        0.23071 (  385)
  hydrogen bonds       : angle       8.17755 ( 1077)
  Misc. bond           : bond        0.00363 (    2)

*********************** 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  : 0.301 
Fit side-chains
REVERT: B  106 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7931 (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: 0.8115 (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: 0.0922
  time to fit residues: 25.3042
Evaluate side-chains
  154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:   40.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 HIS
B 166 ASN
B 181 GLN
B 214 ASN
C 207 ASN
** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 ASN
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 = 0.4430 r_free = 0.4430 target = 0.191015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.144433 restraints weight = 16809.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.146335 restraints weight = 9950.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.147878 restraints weight = 5889.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.148746 restraints weight = 4937.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.148797 restraints weight = 4398.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10032  Z= 0.182
  Angle     :  0.665   9.082  13614  Z= 0.317
  Chirality :  0.044   0.226   1524
  Planarity :  0.004   0.034   1642
  Dihedral  : 11.124  72.435   2056
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.83 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.25), residues: 1206
  helix:  1.54 (0.33), residues: 254
  sheet:  0.34 (0.28), residues: 372
  loop : -0.93 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L 107 
 TYR   0.019   0.002   TYR A  94 
 PHE   0.017   0.002   PHE B 146 
 TRP   0.012   0.002   TRP H 106 
 HIS   0.005   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (10018)
  covalent geometry    : angle       0.66467 (13590)
  SS BOND              : bond        0.00364 (   12)
  SS BOND              : angle       1.03248 (   24)
  hydrogen bonds       : bond        0.04293 (  385)
  hydrogen bonds       : angle       5.80950 ( 1077)
  Misc. bond           : bond        0.00258 (    2)

*********************** 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
  180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 168
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   46 MET cc_start: 0.5876 (pmm) cc_final: 0.5631 (ptp)
REVERT: A   50 LYS cc_start: 0.8019 (ttmt) cc_final: 0.6878 (pttp)
REVERT: B   50 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7818 (ttmm)
REVERT: B  106 LYS cc_start: 0.8517 (mmmt) cc_final: 0.7903 (pttp)
REVERT: C   48 ILE cc_start: 0.8637 (tp) cc_final: 0.8358 (tp)
REVERT: D   21 MET cc_start: 0.7963 (ptp) cc_final: 0.7745 (ptp)
REVERT: D  168 LYS cc_start: 0.7809 (tttm) cc_final: 0.7167 (tppt)
REVERT: H   48 ILE cc_start: 0.8695 (tp) cc_final: 0.8424 (tp)
REVERT: H   62 GLN cc_start: 0.8019 (mt0) cc_final: 0.7782 (mt0)
REVERT: L   89 GLN cc_start: 0.8448 (pp30) cc_final: 0.8223 (pp30)
  outliers start: 12
  outliers final: 7
  residues processed: 173
  average time/residue: 0.0850
  time to fit residues: 21.4956
Evaluate side-chains
  160 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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   19 VAL
Chi-restraints excluded: chain D residue   37 GLN
Chi-restraints excluded: chain L residue   19 VAL
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 32 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 94 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 119 optimal weight:    1.9990
   chunk 110 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
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  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 166 ASN
B 181 GLN
** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.192957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.153394 restraints weight = 16715.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.152615 restraints weight = 10022.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.153486 restraints weight = 9351.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.153833 restraints weight = 5640.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.154604 restraints weight = 5016.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10032  Z= 0.115
  Angle     :  0.573   7.936  13614  Z= 0.271
  Chirality :  0.043   0.241   1524
  Planarity :  0.004   0.040   1642
  Dihedral  : 10.074  59.719   2050
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.97 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.25), residues: 1206
  helix:  1.50 (0.34), residues: 250
  sheet:  0.31 (0.27), residues: 370
  loop : -0.81 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  60 
 TYR   0.016   0.001   TYR A  94 
 PHE   0.015   0.001   PHE B 146 
 TRP   0.012   0.001   TRP B  89 
 HIS   0.002   0.001   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10018)
  covalent geometry    : angle       0.57259 (13590)
  SS BOND              : bond        0.00361 (   12)
  SS BOND              : angle       0.89764 (   24)
  hydrogen bonds       : bond        0.03576 (  385)
  hydrogen bonds       : angle       5.25087 ( 1077)
  Misc. bond           : bond        0.00240 (    2)

*********************** 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
  182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8245 (ttmt) cc_final: 0.6815 (pttp)
REVERT: B  106 LYS cc_start: 0.8495 (mmmt) cc_final: 0.7833 (pttm)
REVERT: C   48 ILE cc_start: 0.8550 (tp) cc_final: 0.8338 (tp)
REVERT: C   64 PHE cc_start: 0.6390 (m-10) cc_final: 0.5880 (m-10)
REVERT: D   89 GLN cc_start: 0.8348 (pp30) cc_final: 0.8125 (pp30)
REVERT: H   48 ILE cc_start: 0.8647 (tp) cc_final: 0.8362 (tp)
REVERT: H   62 GLN cc_start: 0.7994 (mt0) cc_final: 0.7792 (mt0)
REVERT: H   64 PHE cc_start: 0.6464 (m-10) cc_final: 0.5986 (m-10)
REVERT: L   89 GLN cc_start: 0.8371 (pp30) cc_final: 0.8125 (pp30)
  outliers start: 19
  outliers final: 12
  residues processed: 175
  average time/residue: 0.0793
  time to fit residues: 20.5839
Evaluate side-chains
  165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  177 SER
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   88 SER
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 26 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 111 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0970
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 166 ASN
B 181 GLN
C 208 HIS
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.190078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.144335 restraints weight = 17001.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.146131 restraints weight = 8948.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.146533 restraints weight = 6209.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.147083 restraints weight = 5033.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.147300 restraints weight = 4416.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10032  Z= 0.126
  Angle     :  0.563  13.902  13614  Z= 0.268
  Chirality :  0.043   0.219   1524
  Planarity :  0.003   0.037   1642
  Dihedral  :  9.621  59.667   2050
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.57 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.25), residues: 1206
  helix:  1.55 (0.33), residues: 248
  sheet:  0.33 (0.26), residues: 412
  loop : -0.70 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  60 
 TYR   0.015   0.001   TYR L  31 
 PHE   0.011   0.001   PHE B 203 
 TRP   0.011   0.001   TRP B  89 
 HIS   0.002   0.001   HIS H 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10018)
  covalent geometry    : angle       0.56223 (13590)
  SS BOND              : bond        0.00302 (   12)
  SS BOND              : angle       0.80634 (   24)
  hydrogen bonds       : bond        0.03317 (  385)
  hydrogen bonds       : angle       4.93440 ( 1077)
  Misc. bond           : bond        0.00288 (    2)

*********************** 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
  177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8269 (ttmt) cc_final: 0.6781 (pttp)
REVERT: A   59 ASN cc_start: 0.8788 (m-40) cc_final: 0.8495 (m-40)
REVERT: B  106 LYS cc_start: 0.8526 (mmmt) cc_final: 0.7781 (pttm)
REVERT: C   64 PHE cc_start: 0.6553 (m-80) cc_final: 0.6226 (m-10)
REVERT: H   62 GLN cc_start: 0.8086 (mt0) cc_final: 0.7879 (mt0)
REVERT: H   64 PHE cc_start: 0.6686 (m-80) cc_final: 0.6314 (m-10)
  outliers start: 19
  outliers final: 11
  residues processed: 169
  average time/residue: 0.0799
  time to fit residues: 20.0425
Evaluate side-chains
  156 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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 A residue  189 LEU
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 L residue   19 VAL
Chi-restraints excluded: chain L residue   21 MET
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 70 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 117 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 112 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 101 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 166 ASN
C  33 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 = 0.4337 r_free = 0.4337 target = 0.183425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.137343 restraints weight = 16878.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.138038 restraints weight = 9286.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.138866 restraints weight = 6529.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.139078 restraints weight = 5615.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139547 restraints weight = 4869.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10032  Z= 0.218
  Angle     :  0.667  12.992  13614  Z= 0.323
  Chirality :  0.046   0.240   1524
  Planarity :  0.004   0.044   1642
  Dihedral  :  9.959  59.609   2050
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.11 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.25), residues: 1206
  helix:  1.17 (0.32), residues: 254
  sheet:  0.29 (0.26), residues: 422
  loop : -0.90 (0.29), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  60 
 TYR   0.021   0.002   TYR C 107 
 PHE   0.014   0.001   PHE B  45 
 TRP   0.014   0.002   TRP B  89 
 HIS   0.004   0.001   HIS H 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (10018)
  covalent geometry    : angle       0.66600 (13590)
  SS BOND              : bond        0.00376 (   12)
  SS BOND              : angle       1.04869 (   24)
  hydrogen bonds       : bond        0.03678 (  385)
  hydrogen bonds       : angle       5.04229 ( 1077)
  Misc. bond           : bond        0.00275 (    2)

*********************** 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
  183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8334 (ttmt) cc_final: 0.6861 (pttp)
REVERT: B  106 LYS cc_start: 0.8597 (mmmt) cc_final: 0.7743 (pttm)
REVERT: C   64 PHE cc_start: 0.6882 (m-80) cc_final: 0.6670 (m-80)
  outliers start: 26
  outliers final: 14
  residues processed: 176
  average time/residue: 0.0917
  time to fit residues: 23.5010
Evaluate side-chains
  161 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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 A residue  189 LEU
Chi-restraints excluded: chain B residue  141 ILE
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   37 GLN
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain L residue   19 VAL
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 71 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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**
B 166 ASN
D  37 GLN
L  37 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.180075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.135911 restraints weight = 16797.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.135038 restraints weight = 10121.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.136012 restraints weight = 7253.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.136462 restraints weight = 5490.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.136748 restraints weight = 4704.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  10032  Z= 0.271
  Angle     :  0.724  11.704  13614  Z= 0.351
  Chirality :  0.048   0.231   1524
  Planarity :  0.004   0.035   1642
  Dihedral  : 10.385  59.922   2050
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.85 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.25), residues: 1206
  helix:  0.88 (0.32), residues: 254
  sheet:  0.21 (0.26), residues: 422
  loop : -1.06 (0.29), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  60 
 TYR   0.023   0.002   TYR C 107 
 PHE   0.018   0.002   PHE B  45 
 TRP   0.017   0.002   TRP B  89 
 HIS   0.005   0.001   HIS H 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 (10018)
  covalent geometry    : angle       0.72345 (13590)
  SS BOND              : bond        0.00382 (   12)
  SS BOND              : angle       1.16635 (   24)
  hydrogen bonds       : bond        0.03988 (  385)
  hydrogen bonds       : angle       5.24408 ( 1077)
  Misc. bond           : bond        0.00319 (    2)

*********************** 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
  191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8308 (ttmt) cc_final: 0.6898 (pttp)
REVERT: D   32 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8147 (tp)
REVERT: L   80 GLU cc_start: 0.8170 (tt0) cc_final: 0.7599 (mp0)
  outliers start: 36
  outliers final: 26
  residues processed: 182
  average time/residue: 0.0887
  time to fit residues: 23.8838
Evaluate side-chains
  168 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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 A residue  186 ILE
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   51 ILE
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   32 ILE
Chi-restraints excluded: chain D residue   37 GLN
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   51 ILE
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   86 LEU
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:   20.0000
   chunk 46 optimal weight:    7.9990
   chunk 18 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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  56 GLN
** 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 = 0.4348 r_free = 0.4348 target = 0.184372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.138294 restraints weight = 16671.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.139610 restraints weight = 9137.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.140139 restraints weight = 6206.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.140406 restraints weight = 5142.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.140753 restraints weight = 4488.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10032  Z= 0.132
  Angle     :  0.638  11.469  13614  Z= 0.303
  Chirality :  0.044   0.208   1524
  Planarity :  0.003   0.030   1642
  Dihedral  :  9.916  59.143   2050
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.25), residues: 1206
  helix:  0.97 (0.32), residues: 248
  sheet:  0.26 (0.26), residues: 418
  loop : -0.95 (0.29), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  60 
 TYR   0.023   0.001   TYR A  94 
 PHE   0.014   0.001   PHE B 146 
 TRP   0.015   0.001   TRP B  89 
 HIS   0.001   0.001   HIS H 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10018)
  covalent geometry    : angle       0.63704 (13590)
  SS BOND              : bond        0.00372 (   12)
  SS BOND              : angle       0.89057 (   24)
  hydrogen bonds       : bond        0.03458 (  385)
  hydrogen bonds       : angle       4.99843 ( 1077)
  Misc. bond           : bond        0.00264 (    2)

*********************** 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
  184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8274 (ttmt) cc_final: 0.6814 (pttp)
REVERT: B  105 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6685 (mt-10)
REVERT: B  106 LYS cc_start: 0.8443 (mmmt) cc_final: 0.6989 (pptt)
REVERT: D   32 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.8011 (tp)
  outliers start: 29
  outliers final: 21
  residues processed: 176
  average time/residue: 0.0853
  time to fit residues: 21.9028
Evaluate side-chains
  170 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
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 A residue  189 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 B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   32 ILE
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 L residue   10 ILE
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   41 SER
Chi-restraints excluded: chain L residue   62 SER
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 19 optimal weight:    0.3980
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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**
** B 204 GLN ** 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 = 0.4349 r_free = 0.4349 target = 0.184521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.138913 restraints weight = 16773.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.140139 restraints weight = 8987.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.140583 restraints weight = 6389.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.141482 restraints weight = 4995.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.141289 restraints weight = 4588.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10032  Z= 0.137
  Angle     :  0.633  10.607  13614  Z= 0.303
  Chirality :  0.044   0.201   1524
  Planarity :  0.003   0.029   1642
  Dihedral  :  9.671  57.282   2050
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.06 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.25), residues: 1206
  helix:  0.96 (0.32), residues: 248
  sheet:  0.30 (0.26), residues: 404
  loop : -0.97 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  60 
 TYR   0.021   0.001   TYR B  94 
 PHE   0.015   0.001   PHE B 146 
 TRP   0.014   0.001   TRP B  89 
 HIS   0.002   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10018)
  covalent geometry    : angle       0.63277 (13590)
  SS BOND              : bond        0.00323 (   12)
  SS BOND              : angle       0.87593 (   24)
  hydrogen bonds       : bond        0.03378 (  385)
  hydrogen bonds       : angle       4.94175 ( 1077)
  Misc. bond           : bond        0.00251 (    2)

*********************** 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: 29
    poor density    : 153
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8271 (ttmt) cc_final: 0.6825 (pttp)
REVERT: B  106 LYS cc_start: 0.8501 (mmmt) cc_final: 0.7041 (pptt)
  outliers start: 29
  outliers final: 24
  residues processed: 173
  average time/residue: 0.0864
  time to fit residues: 21.8931
Evaluate side-chains
  173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  189 LEU
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 B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain D residue   10 ILE
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   37 GLN
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   88 SER
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 116 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   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**
** B 204 GLN ** 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 = 0.4333 r_free = 0.4333 target = 0.183139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.137098 restraints weight = 16763.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.138274 restraints weight = 9360.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.139013 restraints weight = 6088.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.139546 restraints weight = 5074.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139776 restraints weight = 4612.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10032  Z= 0.174
  Angle     :  0.654  10.810  13614  Z= 0.315
  Chirality :  0.045   0.207   1524
  Planarity :  0.004   0.031   1642
  Dihedral  :  9.649  59.116   2050
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.25 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.25), residues: 1206
  helix:  0.89 (0.32), residues: 248
  sheet:  0.30 (0.26), residues: 410
  loop : -0.97 (0.29), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  60 
 TYR   0.028   0.002   TYR A  94 
 PHE   0.014   0.001   PHE B 146 
 TRP   0.015   0.001   TRP B  89 
 HIS   0.003   0.001   HIS H 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10018)
  covalent geometry    : angle       0.65323 (13590)
  SS BOND              : bond        0.00302 (   12)
  SS BOND              : angle       0.94559 (   24)
  hydrogen bonds       : bond        0.03472 (  385)
  hydrogen bonds       : angle       4.96800 ( 1077)
  Misc. bond           : bond        0.00256 (    2)

*********************** 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
  181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8303 (ttmt) cc_final: 0.6824 (pttp)
REVERT: A   72 ILE cc_start: 0.9333 (mm) cc_final: 0.9084 (mm)
REVERT: B  106 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7157 (pptt)
REVERT: C   10 GLU cc_start: 0.8342 (pm20) cc_final: 0.7856 (pm20)
REVERT: L   80 GLU cc_start: 0.8130 (tt0) cc_final: 0.7573 (mp0)
  outliers start: 30
  outliers final: 26
  residues processed: 172
  average time/residue: 0.0845
  time to fit residues: 21.1436
Evaluate side-chains
  173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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 A residue  186 ILE
Chi-restraints excluded: chain A residue  189 LEU
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 B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   48 ILE
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   41 SER
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   51 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 105 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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  56 GLN
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
L  37 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.185491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.145742 restraints weight = 16824.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.145380 restraints weight = 12352.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.145855 restraints weight = 11346.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.147183 restraints weight = 6750.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.147466 restraints weight = 5646.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10032  Z= 0.123
  Angle     :  0.635  12.542  13614  Z= 0.305
  Chirality :  0.045   0.220   1524
  Planarity :  0.003   0.029   1642
  Dihedral  :  9.380  59.480   2050
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.25), residues: 1206
  helix:  0.89 (0.32), residues: 248
  sheet:  0.34 (0.27), residues: 404
  loop : -0.99 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  60 
 TYR   0.031   0.001   TYR A  94 
 PHE   0.015   0.001   PHE B 203 
 TRP   0.017   0.001   TRP A  85 
 HIS   0.002   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10018)
  covalent geometry    : angle       0.63518 (13590)
  SS BOND              : bond        0.00283 (   12)
  SS BOND              : angle       0.79279 (   24)
  hydrogen bonds       : bond        0.03337 (  385)
  hydrogen bonds       : angle       4.96450 ( 1077)
  Misc. bond           : bond        0.00228 (    2)

********************** 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
  179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8286 (ttmt) cc_final: 0.6844 (pttp)
REVERT: A   72 ILE cc_start: 0.9298 (mm) cc_final: 0.9051 (mm)
REVERT: A  145 HIS cc_start: 0.5783 (p90) cc_final: 0.5559 (p-80)
REVERT: B  105 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6508 (mt-10)
REVERT: B  106 LYS cc_start: 0.8511 (mmmt) cc_final: 0.7154 (pptt)
REVERT: L   80 GLU cc_start: 0.8125 (tt0) cc_final: 0.7506 (mp0)
  outliers start: 27
  outliers final: 24
  residues processed: 168
  average time/residue: 0.0817
  time to fit residues: 20.0415
Evaluate side-chains
  173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  137 ASP
Chi-restraints excluded: chain A residue  166 ASN
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  189 LEU
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 B residue  177 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain D residue   10 ILE
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   51 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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**
** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.184628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.144434 restraints weight = 16695.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.144145 restraints weight = 12379.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.144639 restraints weight = 11482.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.145970 restraints weight = 6838.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.146250 restraints weight = 5681.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10032  Z= 0.145
  Angle     :  0.634  10.911  13614  Z= 0.306
  Chirality :  0.045   0.209   1524
  Planarity :  0.004   0.029   1642
  Dihedral  :  9.295  59.977   2050
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.25), residues: 1206
  helix:  0.90 (0.32), residues: 248
  sheet:  0.34 (0.26), residues: 404
  loop : -0.97 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  60 
 TYR   0.027   0.001   TYR A  94 
 PHE   0.014   0.001   PHE B 203 
 TRP   0.014   0.001   TRP A  85 
 HIS   0.002   0.001   HIS H 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10018)
  covalent geometry    : angle       0.63334 (13590)
  SS BOND              : bond        0.00258 (   12)
  SS BOND              : angle       0.84815 (   24)
  hydrogen bonds       : bond        0.03341 (  385)
  hydrogen bonds       : angle       4.95362 ( 1077)
  Misc. bond           : bond        0.00234 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1704.85 seconds
wall clock time: 30 minutes 15.48 seconds (1815.48 seconds total)