Starting phenix.real_space_refine
on Tue Sep 24 11:16:29 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/09_2024/6tau_10428.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/09_2024/6tau_10428.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/09_2024/6tau_10428.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/09_2024/6tau_10428.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/09_2024/6tau_10428.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tau_10428/09_2024/6tau_10428.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    5172      2.51       5
     N    1428      2.21       5
     O    1524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 91 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8148
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1358
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
    Chain: "B"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1358
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
    Chain: "C"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1358
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
    Chain: "D"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1358
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
    Chain: "E"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1358
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
    Chain: "F"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1358
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
  Time building chain proxies: 5.19, per 1000 atoms: 0.64
  Number of scatterers: 8148
  At special positions: 0
  Unit cell: (131.86, 63.848, 129.084, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1524      8.00
     N    1428      7.00
     C    5172      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      67.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 63
      removed outlier: 3.700A  pdb=" N   VAL A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 72
      removed outlier: 3.718A  pdb=" N   LEU A  70 " --> pdb=" O   ASP A  66 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LYS A  71 " --> pdb=" O   LYS A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 76
    Processing helix  chain 'A' and resid 80 through 86
    Processing helix  chain 'A' and resid 88 through 92
      removed outlier: 3.611A  pdb=" N   ALA A  92 " --> pdb=" O   ARG A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 107
      removed outlier: 3.785A  pdb=" N   LEU A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 120
      removed outlier: 3.844A  pdb=" N   ILE A 115 " --> pdb=" O   PRO A 111 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE A 120 " --> pdb=" O   TYR A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 142
      removed outlier: 3.518A  pdb=" N   PHE A 133 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 161
      removed outlier: 3.839A  pdb=" N   GLU A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASP A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 168
      removed outlier: 3.615A  pdb=" N   GLU A 168 " --> pdb=" O   PRO A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 192
      removed outlier: 4.163A  pdb=" N   LEU A 182 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR A 187 " --> pdb=" O   ASP A 183 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL A 188 " --> pdb=" O   ARG A 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 63
      removed outlier: 3.570A  pdb=" N   VAL B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLU B  60 " --> pdb=" O   GLU B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 76
      removed outlier: 3.875A  pdb=" N   LEU B  75 " --> pdb=" O   GLY B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 88
      removed outlier: 3.515A  pdb=" N   TRP B  84 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LYS B  86 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY B  87 " --> pdb=" O   VAL B  83 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL B  88 " --> pdb=" O   TRP B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 92
    Processing helix  chain 'B' and resid 94 through 107
      removed outlier: 3.965A  pdb=" N   PHE B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 120
      removed outlier: 3.641A  pdb=" N   ILE B 115 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   PHE B 120 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 142
      removed outlier: 3.592A  pdb=" N   PHE B 133 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 162
      removed outlier: 3.808A  pdb=" N   GLU B 154 " --> pdb=" O   ASP B 150 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU B 155 " --> pdb=" O   GLU B 151 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ASP B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   PHE B 157 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 192
      removed outlier: 4.223A  pdb=" N   LEU B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   THR B 187 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL B 188 " --> pdb=" O   ARG B 184 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG B 192 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 63
      removed outlier: 3.783A  pdb=" N   VAL C  48 " --> pdb=" O   ASP C  44 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU C  60 " --> pdb=" O   GLU C  56 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY C  63 " --> pdb=" O   LYS C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 72
      removed outlier: 4.195A  pdb=" N   LYS C  71 " --> pdb=" O   LYS C  67 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLY C  72 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 67 through 72'
    Processing helix  chain 'C' and resid 73 through 76
    Processing helix  chain 'C' and resid 79 through 88
      removed outlier: 3.988A  pdb=" N   VAL C  83 " --> pdb=" O   SER C  79 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY C  87 " --> pdb=" O   VAL C  83 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL C  88 " --> pdb=" O   TRP C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 107
      removed outlier: 3.888A  pdb=" N   HIS C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE C 106 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 119
      removed outlier: 3.782A  pdb=" N   ILE C 115 " --> pdb=" O   PRO C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 142
      removed outlier: 3.790A  pdb=" N   PHE C 133 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 162
      removed outlier: 4.078A  pdb=" N   GLU C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU C 155 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ASP C 156 " --> pdb=" O   GLU C 152 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE C 157 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 168
      removed outlier: 3.696A  pdb=" N   ARG C 167 " --> pdb=" O   GLN C 163 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLU C 168 " --> pdb=" O   PRO C 164 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 163 through 168'
    Processing helix  chain 'C' and resid 177 through 192
      removed outlier: 4.003A  pdb=" N   LEU C 181 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LEU C 182 " --> pdb=" O   PHE C 178 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR C 187 " --> pdb=" O   ASP C 183 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   VAL C 188 " --> pdb=" O   ARG C 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 63
      removed outlier: 3.700A  pdb=" N   VAL D  48 " --> pdb=" O   ASP D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 72
      removed outlier: 3.718A  pdb=" N   LEU D  70 " --> pdb=" O   ASP D  66 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LYS D  71 " --> pdb=" O   LYS D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 76
    Processing helix  chain 'D' and resid 80 through 86
    Processing helix  chain 'D' and resid 88 through 92
      removed outlier: 3.611A  pdb=" N   ALA D  92 " --> pdb=" O   ARG D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 107
      removed outlier: 3.785A  pdb=" N   LEU D 102 " --> pdb=" O   ALA D  98 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG D 103 " --> pdb=" O   LEU D  99 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE D 106 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 120
      removed outlier: 3.845A  pdb=" N   ILE D 115 " --> pdb=" O   PRO D 111 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   PHE D 120 " --> pdb=" O   TYR D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 142
      removed outlier: 3.518A  pdb=" N   PHE D 133 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 162
      removed outlier: 3.777A  pdb=" N   PHE D 157 " --> pdb=" O   THR D 153 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE D 158 " --> pdb=" O   GLU D 154 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TYR D 159 " --> pdb=" O   LEU D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 163 through 168
      removed outlier: 3.614A  pdb=" N   GLU D 168 " --> pdb=" O   PRO D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 192
      removed outlier: 4.162A  pdb=" N   LEU D 182 " --> pdb=" O   PHE D 178 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR D 187 " --> pdb=" O   ASP D 183 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL D 188 " --> pdb=" O   ARG D 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 63
      removed outlier: 3.570A  pdb=" N   VAL E  48 " --> pdb=" O   ASP E  44 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLU E  60 " --> pdb=" O   GLU E  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 72 through 76
      removed outlier: 3.876A  pdb=" N   LEU E  75 " --> pdb=" O   GLY E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 80 through 88
      removed outlier: 3.515A  pdb=" N   TRP E  84 " --> pdb=" O   ILE E  80 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LYS E  86 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY E  87 " --> pdb=" O   VAL E  83 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL E  88 " --> pdb=" O   TRP E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 92
    Processing helix  chain 'E' and resid 94 through 107
      removed outlier: 3.965A  pdb=" N   PHE E 106 " --> pdb=" O   LEU E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 120
      removed outlier: 3.641A  pdb=" N   ILE E 115 " --> pdb=" O   PRO E 111 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   PHE E 120 " --> pdb=" O   TYR E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 142
      removed outlier: 3.592A  pdb=" N   PHE E 133 " --> pdb=" O   VAL E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 150 through 162
      removed outlier: 3.625A  pdb=" N   GLU E 154 " --> pdb=" O   ASP E 150 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU E 155 " --> pdb=" O   GLU E 151 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ASP E 156 " --> pdb=" O   GLU E 152 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   PHE E 157 " --> pdb=" O   THR E 153 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE E 158 " --> pdb=" O   GLU E 154 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 192
      removed outlier: 4.222A  pdb=" N   LEU E 182 " --> pdb=" O   PHE E 178 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   THR E 187 " --> pdb=" O   ASP E 183 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL E 188 " --> pdb=" O   ARG E 184 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG E 192 " --> pdb=" O   VAL E 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 44 through 63
      removed outlier: 3.783A  pdb=" N   VAL F  48 " --> pdb=" O   ASP F  44 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU F  60 " --> pdb=" O   GLU F  56 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY F  63 " --> pdb=" O   LYS F  59 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 72
      removed outlier: 4.195A  pdb=" N   LYS F  71 " --> pdb=" O   LYS F  67 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLY F  72 " --> pdb=" O   ASP F  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 67 through 72'
    Processing helix  chain 'F' and resid 73 through 76
    Processing helix  chain 'F' and resid 79 through 88
      removed outlier: 3.988A  pdb=" N   VAL F  83 " --> pdb=" O   SER F  79 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY F  87 " --> pdb=" O   VAL F  83 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL F  88 " --> pdb=" O   TRP F  84 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 94 through 107
      removed outlier: 3.889A  pdb=" N   HIS F 105 " --> pdb=" O   LEU F 101 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE F 106 " --> pdb=" O   LEU F 102 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 119
      removed outlier: 3.783A  pdb=" N   ILE F 115 " --> pdb=" O   PRO F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 142
      removed outlier: 3.791A  pdb=" N   PHE F 133 " --> pdb=" O   VAL F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 150 through 162
      removed outlier: 3.941A  pdb=" N   GLU F 154 " --> pdb=" O   ASP F 150 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   MET F 162 " --> pdb=" O   ILE F 158 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 163 through 168
      removed outlier: 3.696A  pdb=" N   ARG F 167 " --> pdb=" O   GLN F 163 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   GLU F 168 " --> pdb=" O   PRO F 164 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 163 through 168'
    Processing helix  chain 'F' and resid 177 through 192
      removed outlier: 4.004A  pdb=" N   LEU F 181 " --> pdb=" O   THR F 177 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LEU F 182 " --> pdb=" O   PHE F 178 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR F 187 " --> pdb=" O   ASP F 183 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   VAL F 188 " --> pdb=" O   ARG F 184 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    924 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: 1.82

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2673
        1.34 -     1.46: 1681
        1.46 -     1.58: 3938
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 8328
  Sorted by residual:
  bond pdb=" N   MET A 162 "
       pdb=" CA  MET A 162 "
    ideal  model  delta    sigma   weight residual
    1.454  1.514 -0.059 1.15e-02 7.56e+03 2.66e+01
  bond pdb=" C   GLU C 154 "
       pdb=" O   GLU C 154 "
    ideal  model  delta    sigma   weight residual
    1.237  1.295 -0.058 1.17e-02 7.31e+03 2.48e+01
  bond pdb=" C   ILE C 158 "
       pdb=" O   ILE C 158 "
    ideal  model  delta    sigma   weight residual
    1.237  1.290 -0.053 1.17e-02 7.31e+03 2.03e+01
  bond pdb=" N   MET F 162 "
       pdb=" CA  MET F 162 "
    ideal  model  delta    sigma   weight residual
    1.453  1.511 -0.058 1.31e-02 5.83e+03 1.94e+01
  bond pdb=" N   MET C 162 "
       pdb=" CA  MET C 162 "
    ideal  model  delta    sigma   weight residual
    1.456  1.506 -0.050 1.25e-02 6.40e+03 1.61e+01
  ... (remaining 8323 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 10812
        2.40 -     4.80: 341
        4.80 -     7.20: 52
        7.20 -     9.59: 7
        9.59 -    11.99: 2
  Bond angle restraints: 11214
  Sorted by residual:
  angle pdb=" C   MET C 162 "
        pdb=" N   GLN C 163 "
        pdb=" CA  GLN C 163 "
      ideal   model   delta    sigma   weight residual
     120.60  132.59  -11.99 1.53e+00 4.27e-01 6.14e+01
  angle pdb=" C   MET E 162 "
        pdb=" N   GLN E 163 "
        pdb=" CA  GLN E 163 "
      ideal   model   delta    sigma   weight residual
     120.39  130.35   -9.96 1.39e+00 5.18e-01 5.14e+01
  angle pdb=" N   PHE D 157 "
        pdb=" CA  PHE D 157 "
        pdb=" C   PHE D 157 "
      ideal   model   delta    sigma   weight residual
     111.07  117.01   -5.94 1.07e+00 8.73e-01 3.08e+01
  angle pdb=" N   MET C 162 "
        pdb=" CA  MET C 162 "
        pdb=" C   MET C 162 "
      ideal   model   delta    sigma   weight residual
     110.35  117.56   -7.21 1.36e+00 5.41e-01 2.81e+01
  angle pdb=" C   MET A 162 "
        pdb=" N   GLN A 163 "
        pdb=" CA  GLN A 163 "
      ideal   model   delta    sigma   weight residual
     120.86  128.51   -7.65 1.60e+00 3.91e-01 2.28e+01
  ... (remaining 11209 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 4491
       17.72 -    35.44: 449
       35.44 -    53.16: 70
       53.16 -    70.88: 26
       70.88 -    88.60: 16
  Dihedral angle restraints: 5052
    sinusoidal: 2166
      harmonic: 2886
  Sorted by residual:
  dihedral pdb=" CA  LYS F  78 "
           pdb=" C   LYS F  78 "
           pdb=" N   SER F  79 "
           pdb=" CA  SER F  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.52  -22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  LYS C  78 "
           pdb=" C   LYS C  78 "
           pdb=" N   SER C  79 "
           pdb=" CA  SER C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.53  -22.47     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  SER C 107 "
           pdb=" C   SER C 107 "
           pdb=" N   PRO C 108 "
           pdb=" CA  PRO C 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.70  -19.30     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 5049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 937
       0.055 -    0.110: 159
       0.110 -    0.164: 68
       0.164 -    0.219: 17
       0.219 -    0.274: 7
  Chirality restraints: 1188
  Sorted by residual:
  chirality pdb=" CB  THR D 109 "
            pdb=" CA  THR D 109 "
            pdb=" OG1 THR D 109 "
            pdb=" CG2 THR D 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CB  THR A 109 "
            pdb=" CA  THR A 109 "
            pdb=" OG1 THR A 109 "
            pdb=" CG2 THR A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  THR A 109 "
            pdb=" N   THR A 109 "
            pdb=" C   THR A 109 "
            pdb=" CB  THR A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1185 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F 155 "    0.019 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   LEU F 155 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   LEU F 155 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASP F 156 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 155 "   -0.018 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   LEU D 155 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LEU D 155 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP D 156 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E 163 "    0.054 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO E 164 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO E 164 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO E 164 "    0.045 5.00e-02 4.00e+02
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        1.28 -     2.01: 4
        2.01 -     2.73: 528
        2.73 -     3.45: 10972
        3.45 -     4.18: 15381
        4.18 -     4.90: 27118
  Nonbonded interactions: 54003
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 156 "
            pdb=" NH2 ARG A 172 "
     model   vdw
     1.283 3.120
  nonbonded pdb=" O   ASP A 150 "
            pdb=" OE2 GLU A 154 "
     model   vdw
     1.337 3.040
  nonbonded pdb=" O   ASP A 150 "
            pdb=" CD  GLU A 154 "
     model   vdw
     1.634 3.270
  nonbonded pdb=" O   ASP A 150 "
            pdb=" OE1 GLU A 154 "
     model   vdw
     1.719 3.040
  nonbonded pdb=" O   PHE B 157 "
            pdb=" CD2 LEU B 161 "
     model   vdw
     2.090 3.460
  ... (remaining 53998 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.150
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.700
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
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      :  0.006   0.059   8328  Z= 0.379
  Angle     :  0.992  11.992  11214  Z= 0.647
  Chirality :  0.056   0.274   1188
  Planarity :  0.009   0.082   1446
  Dihedral  : 15.437  88.596   3180
  Min Nonbonded Distance : 1.283

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  5.74 %
    Favored  : 94.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.23 (0.19), residues: 972
  helix: -2.49 (0.17), residues: 512
  sheet:  None (None), residues: 0
  loop : -3.19 (0.20), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  95 
 HIS   0.005   0.001   HIS E 173 
 PHE   0.016   0.002   PHE E  77 
 TYR   0.018   0.002   TYR F 126 
 ARG   0.002   0.000   ARG E 148 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 204
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 GLU cc_start: 0.7822 (tp30) cc_final: 0.7499 (tp30)
REVERT: B   50 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6793 (tm-30)
REVERT: B  117 MET cc_start: 0.7398 (tpt) cc_final: 0.6139 (mtt)
REVERT: B  123 LYS cc_start: 0.8106 (mttt) cc_final: 0.7882 (mtpp)
REVERT: C   43 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7970 (mtp85)
REVERT: C   90 ARG cc_start: 0.8341 (ptt90) cc_final: 0.8107 (ptt-90)
REVERT: E   50 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7231 (tp30)
REVERT: E  117 MET cc_start: 0.7716 (tpt) cc_final: 0.6373 (mtt)
REVERT: F  168 GLU cc_start: 0.7779 (pp20) cc_final: 0.7480 (pp20)
  outliers start: 2
  outliers final: 1
  residues processed: 206
  average time/residue: 0.3006
  time to fit residues: 75.7909
Evaluate side-chains
  158 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  155 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 105 HIS
A 124 GLN
B 114 GLN
** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 GLN
E 114 GLN
E 163 GLN
** F  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8328  Z= 0.320
  Angle     :  0.647   9.486  11214  Z= 0.350
  Chirality :  0.045   0.187   1188
  Planarity :  0.006   0.064   1446
  Dihedral  :  4.975  23.671   1100
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.61 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.23), residues: 972
  helix: -0.76 (0.20), residues: 532
  sheet:  None (None), residues: 0
  loop : -2.62 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  95 
 HIS   0.005   0.001   HIS B 173 
 PHE   0.025   0.002   PHE B 120 
 TYR   0.022   0.002   TYR B 166 
 ARG   0.006   0.001   ARG D 184 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A  128 GLU cc_start: 0.7540 (tp30) cc_final: 0.7283 (tp30)
REVERT: C   90 ARG cc_start: 0.8400 (ptt90) cc_final: 0.8140 (ptt-90)
REVERT: C  118 GLU cc_start: 0.8495 (tp30) cc_final: 0.7935 (tp30)
REVERT: D  162 MET cc_start: 0.6776 (mpp) cc_final: 0.6304 (mmm)
REVERT: F   50 GLU cc_start: 0.7839 (tt0) cc_final: 0.7636 (tt0)
  outliers start: 17
  outliers final: 10
  residues processed: 190
  average time/residue: 0.2647
  time to fit residues: 63.4340
Evaluate side-chains
  171 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 27 optimal weight:    0.2980
   chunk 72 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 GLN
C  45 HIS
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  45 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8328  Z= 0.157
  Angle     :  0.528   7.612  11214  Z= 0.282
  Chirality :  0.040   0.181   1188
  Planarity :  0.005   0.056   1446
  Dihedral  :  4.203  23.997   1098
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.75 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.25), residues: 972
  helix:  0.25 (0.21), residues: 520
  sheet:  None (None), residues: 0
  loop : -2.03 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  95 
 HIS   0.008   0.001   HIS B 173 
 PHE   0.021   0.001   PHE A 133 
 TYR   0.011   0.001   TYR E 159 
 ARG   0.005   0.000   ARG C  43 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A  117 MET cc_start: 0.7906 (tpp) cc_final: 0.7104 (ttp)
REVERT: B  117 MET cc_start: 0.7528 (tpp) cc_final: 0.7262 (tpp)
REVERT: B  123 LYS cc_start: 0.7925 (mttt) cc_final: 0.7661 (mtpp)
REVERT: B  162 MET cc_start: 0.7749 (mmm) cc_final: 0.7255 (mmm)
REVERT: C   67 LYS cc_start: 0.8376 (tptt) cc_final: 0.8173 (tptt)
REVERT: C   90 ARG cc_start: 0.8336 (ptt90) cc_final: 0.8134 (ptt-90)
REVERT: D  117 MET cc_start: 0.7910 (tpp) cc_final: 0.6867 (ttp)
REVERT: D  162 MET cc_start: 0.6352 (mpp) cc_final: 0.6058 (mmm)
REVERT: E  117 MET cc_start: 0.7440 (tpp) cc_final: 0.7198 (tpp)
REVERT: E  174 GLU cc_start: 0.7958 (mp0) cc_final: 0.7316 (pm20)
REVERT: F   67 LYS cc_start: 0.8500 (tptt) cc_final: 0.8179 (tptt)
  outliers start: 19
  outliers final: 14
  residues processed: 175
  average time/residue: 0.2745
  time to fit residues: 60.0846
Evaluate side-chains
  164 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain B residue   71 LYS
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0170
   chunk 58 optimal weight:    0.0010
   chunk 87 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    1.3628

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8328  Z= 0.195
  Angle     :  0.521   6.754  11214  Z= 0.280
  Chirality :  0.040   0.183   1188
  Planarity :  0.004   0.052   1446
  Dihedral  :  4.090  22.874   1098
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.55 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.25), residues: 972
  helix:  0.63 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.09 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  95 
 HIS   0.008   0.001   HIS B 173 
 PHE   0.015   0.001   PHE A 133 
 TYR   0.011   0.001   TYR C 113 
 ARG   0.005   0.000   ARG C  43 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  117 MET cc_start: 0.8007 (tpp) cc_final: 0.7107 (ttp)
REVERT: B  117 MET cc_start: 0.7585 (tpp) cc_final: 0.7221 (tpp)
REVERT: C   90 ARG cc_start: 0.8312 (ptt90) cc_final: 0.8089 (ptt-90)
REVERT: D   52 ILE cc_start: 0.7882 (tt) cc_final: 0.7610 (tt)
REVERT: D   91 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6889 (t70)
REVERT: D  117 MET cc_start: 0.8022 (tpp) cc_final: 0.6921 (ttp)
REVERT: D  162 MET cc_start: 0.6655 (tpp) cc_final: 0.6433 (mmm)
REVERT: E  117 MET cc_start: 0.7480 (tpp) cc_final: 0.7095 (tpp)
  outliers start: 19
  outliers final: 11
  residues processed: 168
  average time/residue: 0.2651
  time to fit residues: 56.9095
Evaluate side-chains
  160 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain D residue   91 ASP
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 47 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 105 HIS
D 105 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   8328  Z= 0.402
  Angle     :  0.670  10.112  11214  Z= 0.355
  Chirality :  0.046   0.191   1188
  Planarity :  0.005   0.053   1446
  Dihedral  :  4.711  26.323   1098
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.23 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.26), residues: 972
  helix:  0.63 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.94 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E  95 
 HIS   0.009   0.002   HIS A 173 
 PHE   0.025   0.003   PHE B 120 
 TYR   0.022   0.002   TYR F 166 
 ARG   0.006   0.001   ARG D 184 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 0.980 
Fit side-chains
REVERT: A  117 MET cc_start: 0.8116 (tpp) cc_final: 0.7326 (ttp)
REVERT: B   50 GLU cc_start: 0.7547 (tp30) cc_final: 0.7155 (tm-30)
REVERT: B  117 MET cc_start: 0.7721 (tpp) cc_final: 0.7274 (tpp)
REVERT: B  162 MET cc_start: 0.7812 (mmm) cc_final: 0.7286 (mmm)
REVERT: C   90 ARG cc_start: 0.8370 (ptt90) cc_final: 0.8152 (ptt-90)
REVERT: C  118 GLU cc_start: 0.8463 (tp30) cc_final: 0.7897 (tp30)
REVERT: C  180 GLU cc_start: 0.7268 (mp0) cc_final: 0.7034 (mm-30)
REVERT: D   52 ILE cc_start: 0.8088 (tt) cc_final: 0.7827 (tt)
REVERT: D   91 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6952 (t70)
REVERT: D  117 MET cc_start: 0.8201 (tpp) cc_final: 0.6995 (ttp)
REVERT: E  117 MET cc_start: 0.7699 (tpp) cc_final: 0.7267 (tpp)
REVERT: E  174 GLU cc_start: 0.8121 (mp0) cc_final: 0.7781 (mp0)
REVERT: F  128 GLU cc_start: 0.8052 (tp30) cc_final: 0.7844 (tp30)
  outliers start: 31
  outliers final: 18
  residues processed: 173
  average time/residue: 0.2497
  time to fit residues: 55.0275
Evaluate side-chains
  172 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain B residue   71 LYS
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   75 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain C residue  177 THR
Chi-restraints excluded: chain C residue  178 PHE
Chi-restraints excluded: chain D residue   91 ASP
Chi-restraints excluded: chain D residue  170 ILE
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 22 optimal weight:    8.9990
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0980
   chunk 43 optimal weight:    0.0670
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    8.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.5520

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8328  Z= 0.156
  Angle     :  0.541   8.209  11214  Z= 0.283
  Chirality :  0.040   0.181   1188
  Planarity :  0.004   0.052   1446
  Dihedral  :  4.071  25.096   1098
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.26 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.26), residues: 972
  helix:  1.08 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.64 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  95 
 HIS   0.009   0.001   HIS A 173 
 PHE   0.033   0.001   PHE A 133 
 TYR   0.008   0.001   TYR E 159 
 ARG   0.006   0.000   ARG F  90 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A  117 MET cc_start: 0.7795 (tpp) cc_final: 0.7059 (ttp)
REVERT: B  117 MET cc_start: 0.7563 (tpp) cc_final: 0.7112 (tpp)
REVERT: B  161 LEU cc_start: 0.8008 (mm) cc_final: 0.7801 (mm)
REVERT: B  162 MET cc_start: 0.7923 (mmm) cc_final: 0.7303 (mmm)
REVERT: C   67 LYS cc_start: 0.8490 (tptt) cc_final: 0.8226 (tptt)
REVERT: C  118 GLU cc_start: 0.8442 (tp30) cc_final: 0.7872 (tp30)
REVERT: D   91 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6876 (t70)
REVERT: D  117 MET cc_start: 0.7932 (tpp) cc_final: 0.6936 (ttp)
REVERT: E  117 MET cc_start: 0.7485 (tpp) cc_final: 0.7054 (tpp)
  outliers start: 21
  outliers final: 14
  residues processed: 168
  average time/residue: 0.2562
  time to fit residues: 54.7962
Evaluate side-chains
  165 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain C residue  178 PHE
Chi-restraints excluded: chain D residue   91 ASP
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 173 HIS
D 105 HIS
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8328  Z= 0.290
  Angle     :  0.608   9.479  11214  Z= 0.321
  Chirality :  0.044   0.236   1188
  Planarity :  0.004   0.053   1446
  Dihedral  :  4.377  27.042   1098
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 19.37 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.27), residues: 972
  helix:  1.11 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.63 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  95 
 HIS   0.010   0.001   HIS A 173 
 PHE   0.028   0.002   PHE A 133 
 TYR   0.016   0.002   TYR F 166 
 ARG   0.007   0.000   ARG D 184 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A  117 MET cc_start: 0.8024 (tpp) cc_final: 0.7279 (ttp)
REVERT: B   50 GLU cc_start: 0.7531 (tp30) cc_final: 0.7145 (tm-30)
REVERT: B  117 MET cc_start: 0.7682 (tpp) cc_final: 0.7224 (tpp)
REVERT: B  162 MET cc_start: 0.7814 (mmm) cc_final: 0.7608 (mmm)
REVERT: C   67 LYS cc_start: 0.8454 (tptt) cc_final: 0.8228 (tptt)
REVERT: C  118 GLU cc_start: 0.8504 (tp30) cc_final: 0.7895 (tp30)
REVERT: C  141 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7398 (tt)
REVERT: C  180 GLU cc_start: 0.7444 (mp0) cc_final: 0.7185 (mm-30)
REVERT: D   52 ILE cc_start: 0.8071 (tt) cc_final: 0.7844 (tt)
REVERT: D   91 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6908 (t70)
REVERT: D  117 MET cc_start: 0.8072 (tpp) cc_final: 0.6925 (ttp)
REVERT: E  117 MET cc_start: 0.7591 (tpp) cc_final: 0.7214 (tpp)
  outliers start: 26
  outliers final: 18
  residues processed: 167
  average time/residue: 0.2623
  time to fit residues: 55.7554
Evaluate side-chains
  173 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue   71 LYS
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain C residue  177 THR
Chi-restraints excluded: chain C residue  178 PHE
Chi-restraints excluded: chain D residue   91 ASP
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8328  Z= 0.181
  Angle     :  0.557   7.236  11214  Z= 0.292
  Chirality :  0.041   0.222   1188
  Planarity :  0.004   0.052   1446
  Dihedral  :  4.140  29.265   1098
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.95 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.27), residues: 972
  helix:  1.28 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.42 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  95 
 HIS   0.010   0.001   HIS A 173 
 PHE   0.024   0.001   PHE A 133 
 TYR   0.009   0.001   TYR C 166 
 ARG   0.012   0.000   ARG D 184 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  117 MET cc_start: 0.7856 (tpp) cc_final: 0.7100 (ttp)
REVERT: B   89 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7672 (ttm-80)
REVERT: B  117 MET cc_start: 0.7629 (tpp) cc_final: 0.7182 (tpp)
REVERT: C   67 LYS cc_start: 0.8475 (tptt) cc_final: 0.8234 (tptt)
REVERT: C  118 GLU cc_start: 0.8479 (tp30) cc_final: 0.7876 (tp30)
REVERT: D   91 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6924 (t70)
REVERT: D  117 MET cc_start: 0.7979 (tpp) cc_final: 0.6875 (ttp)
REVERT: E  117 MET cc_start: 0.7539 (tpp) cc_final: 0.7078 (tpp)
REVERT: E  174 GLU cc_start: 0.7738 (mp0) cc_final: 0.7415 (pm20)
REVERT: F  128 GLU cc_start: 0.8049 (tp30) cc_final: 0.7012 (tt0)
  outliers start: 20
  outliers final: 15
  residues processed: 160
  average time/residue: 0.2536
  time to fit residues: 51.5792
Evaluate side-chains
  163 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue   71 LYS
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain C residue  178 PHE
Chi-restraints excluded: chain D residue   91 ASP
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 67 optimal weight:    0.1980
   chunk 26 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0870
   chunk 85 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 91 optimal weight:    0.3980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8328  Z= 0.159
  Angle     :  0.545  10.175  11214  Z= 0.281
  Chirality :  0.040   0.210   1188
  Planarity :  0.004   0.054   1446
  Dihedral  :  3.812  27.286   1098
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.17 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.27), residues: 972
  helix:  1.52 (0.23), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.22 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  85 
 HIS   0.010   0.001   HIS A 173 
 PHE   0.023   0.001   PHE A 133 
 TYR   0.010   0.001   TYR D 113 
 ARG   0.013   0.000   ARG D 184 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  117 MET cc_start: 0.7761 (tpp) cc_final: 0.7100 (ttp)
REVERT: B   89 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7664 (ttm-80)
REVERT: B  117 MET cc_start: 0.7515 (tpp) cc_final: 0.7052 (tpp)
REVERT: C   67 LYS cc_start: 0.8575 (tptt) cc_final: 0.8329 (tptt)
REVERT: C  118 GLU cc_start: 0.8419 (tp30) cc_final: 0.7891 (tp30)
REVERT: C  128 GLU cc_start: 0.7668 (tp30) cc_final: 0.6829 (tt0)
REVERT: C  162 MET cc_start: 0.7676 (mtm) cc_final: 0.7355 (mtt)
REVERT: D  117 MET cc_start: 0.7891 (tpp) cc_final: 0.6962 (ttp)
REVERT: E  117 MET cc_start: 0.7434 (tpp) cc_final: 0.6953 (tpp)
REVERT: E  174 GLU cc_start: 0.7900 (mp0) cc_final: 0.7574 (pm20)
REVERT: F  178 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7512 (t80)
  outliers start: 17
  outliers final: 15
  residues processed: 162
  average time/residue: 0.2678
  time to fit residues: 54.6031
Evaluate side-chains
  162 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue   71 LYS
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain C residue  178 PHE
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Chi-restraints excluded: chain F residue  178 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 81 optimal weight:    9.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 124 GLN
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8328  Z= 0.171
  Angle     :  0.550   9.371  11214  Z= 0.284
  Chirality :  0.041   0.207   1188
  Planarity :  0.004   0.051   1446
  Dihedral  :  3.830  27.845   1098
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 21.28 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.27), residues: 972
  helix:  1.60 (0.23), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.12 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  95 
 HIS   0.010   0.001   HIS A 173 
 PHE   0.039   0.001   PHE E  39 
 TYR   0.010   0.001   TYR D 113 
 ARG   0.007   0.000   ARG F  90 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A  117 MET cc_start: 0.7819 (tpp) cc_final: 0.7081 (ttp)
REVERT: B   89 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7669 (ttm-80)
REVERT: B  117 MET cc_start: 0.7521 (tpp) cc_final: 0.7062 (tpp)
REVERT: C   67 LYS cc_start: 0.8579 (tptt) cc_final: 0.8329 (tptt)
REVERT: C  118 GLU cc_start: 0.8425 (tp30) cc_final: 0.7819 (tp30)
REVERT: C  128 GLU cc_start: 0.7845 (tp30) cc_final: 0.7036 (tt0)
REVERT: C  162 MET cc_start: 0.7921 (mtm) cc_final: 0.7666 (mtt)
REVERT: D  117 MET cc_start: 0.7941 (tpp) cc_final: 0.6908 (ttp)
REVERT: E  117 MET cc_start: 0.7404 (tpp) cc_final: 0.7031 (tpp)
REVERT: E  121 GLU cc_start: 0.8526 (tp30) cc_final: 0.8312 (tp30)
REVERT: E  174 GLU cc_start: 0.7959 (mp0) cc_final: 0.7106 (pm20)
REVERT: F   90 ARG cc_start: 0.8187 (ptt90) cc_final: 0.7806 (ptt90)
REVERT: F  128 GLU cc_start: 0.8098 (tp30) cc_final: 0.6989 (tt0)
REVERT: F  178 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7790 (t80)
  outliers start: 19
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2642
  time to fit residues: 52.0495
Evaluate side-chains
  162 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain B residue   71 LYS
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain C residue  124 GLN
Chi-restraints excluded: chain C residue  126 TYR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  161 LEU
Chi-restraints excluded: chain C residue  174 GLU
Chi-restraints excluded: chain C residue  178 PHE
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain F residue   94 THR
Chi-restraints excluded: chain F residue  126 TYR
Chi-restraints excluded: chain F residue  129 VAL
Chi-restraints excluded: chain F residue  161 LEU
Chi-restraints excluded: chain F residue  178 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0570
   chunk 21 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 78 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0040
   chunk 66 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4110

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 124 GLN
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.136127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.120115 restraints weight = 13043.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.123489 restraints weight = 7495.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.125855 restraints weight = 4915.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8328  Z= 0.153
  Angle     :  0.545   8.910  11214  Z= 0.279
  Chirality :  0.040   0.205   1188
  Planarity :  0.004   0.049   1446
  Dihedral  :  3.701  27.590   1098
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.51 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.27), residues: 972
  helix:  1.70 (0.23), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.02 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  95 
 HIS   0.010   0.001   HIS A 173 
 PHE   0.032   0.001   PHE E  39 
 TYR   0.010   0.001   TYR A 113 
 ARG   0.007   0.000   ARG C  43 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1800.30 seconds
wall clock time: 32 minutes 47.12 seconds (1967.12 seconds total)