Starting phenix.real_space_refine
on Wed Sep 17 16:43:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r22_53520/09_2025/9r22_53520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r22_53520/09_2025/9r22_53520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r22_53520/09_2025/9r22_53520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r22_53520/09_2025/9r22_53520.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r22_53520/09_2025/9r22_53520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r22_53520/09_2025/9r22_53520.map"
  }
  resolution = 2.48
  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=   0.000 sd=   0.024
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      55      5.16       5
     C    6573      2.51       5
     N    1350      2.21       5
     O    1665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9643
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "A"
      Number of atoms: 1779
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1812
    Chain: "B"
      Number of atoms: 1779
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1812
    Chain: "C"
      Number of atoms: 1779
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1812
    Chain: "D"
      Number of atoms: 1779
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1812
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 230, 1772
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 1812
    Chain: "A"
      Number of atoms: 123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 123
          Unusual residues: {'LFA': 6, 'LMT': 1, 'RET': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 53
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 131
          Unusual residues: {'LFA': 6, 'LMT': 1, 'RET': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 116
          Unusual residues: {'LFA': 8, 'RET': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 65
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 154
          Unusual residues: {'LFA': 5, 'LMT': 2, 'RET': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 119
          Unusual residues: {'LFA': 5, 'LMT': 1, 'RET': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "B"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "C"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 20
          Classifications: {'water': 20}
          Link IDs: {None: 19}
    Chain: "D"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "E"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  AVAL A  17 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL A  17 " occ=0.50
    residue:
      pdb=" N  AVAL B  17 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL B  17 " occ=0.50
    residue:
      pdb=" N  AVAL C  17 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL C  17 " occ=0.50
    residue:
      pdb=" N  AVAL D  17 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL D  17 " occ=0.50
    residue:
      pdb=" N  AVAL E  17 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL E  17 " occ=0.50
  Time building chain proxies: 4.82, per 1000 atoms: 0.50
  Number of scatterers: 9643
  At special positions: 0
  Unit cell: (96.976, 96.14, 69.388, 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      55     16.00
     O    1665      8.00
     N    1350      7.00
     C    6573      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=5, symmetry=0
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 687.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2090

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      87.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.509A  pdb=" N   MET A  31 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 68
      removed outlier: 4.565A  pdb=" N   LEU A  39 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   SER A  40 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP A  60 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 77
    Processing helix  chain 'A' and resid 78 through 100
      removed outlier: 4.483A  pdb=" N   ILE A  84 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      Proline residue:  A  87  - end of helix
      removed outlier: 4.249A  pdb=" N   PHE A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   PHE A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU A  97 " --> pdb=" O   PHE A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 128
      removed outlier: 4.059A  pdb=" N   PHE A 109 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 153
    Processing helix  chain 'A' and resid 154 through 163
    Processing helix  chain 'A' and resid 166 through 179
    Processing helix  chain 'A' and resid 182 through 191
    Processing helix  chain 'A' and resid 198 through 214
      removed outlier: 4.451A  pdb=" N   PHE A 211 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 229
    Processing helix  chain 'B' and resid 6 through 31
      removed outlier: 3.508A  pdb=" N   MET B  31 " --> pdb=" O   PHE B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 68
      removed outlier: 4.561A  pdb=" N   LEU B  39 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   SER B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASP B  60 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 77
    Processing helix  chain 'B' and resid 78 through 100
      removed outlier: 4.484A  pdb=" N   ILE B  84 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      Proline residue:  B  87  - end of helix
      removed outlier: 4.251A  pdb=" N   PHE B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   PHE B  94 " --> pdb=" O   MET B  90 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU B  97 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 127
      removed outlier: 4.060A  pdb=" N   PHE B 109 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 130
      No H-bonds generated for 'chain 'B' and resid 128 through 130'
    Processing helix  chain 'B' and resid 132 through 153
    Processing helix  chain 'B' and resid 154 through 163
    Processing helix  chain 'B' and resid 166 through 179
    Processing helix  chain 'B' and resid 182 through 191
    Processing helix  chain 'B' and resid 198 through 214
      removed outlier: 4.452A  pdb=" N   PHE B 211 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   VAL B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 229
    Processing helix  chain 'C' and resid 6 through 31
      removed outlier: 3.509A  pdb=" N   MET C  31 " --> pdb=" O   PHE C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 68
      removed outlier: 4.570A  pdb=" N   LEU C  39 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   SER C  40 " --> pdb=" O   GLU C  36 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASP C  60 " --> pdb=" O   TYR C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 77
    Processing helix  chain 'C' and resid 78 through 100
      removed outlier: 4.486A  pdb=" N   ILE C  84 " --> pdb=" O   ILE C  80 " (cutoff:3.500A)
      Proline residue:  C  87  - end of helix
      removed outlier: 4.248A  pdb=" N   PHE C  93 " --> pdb=" O   LEU C  89 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   PHE C  94 " --> pdb=" O   MET C  90 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU C  97 " --> pdb=" O   PHE C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 128
      removed outlier: 4.070A  pdb=" N   PHE C 109 " --> pdb=" O   SER C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 153
    Processing helix  chain 'C' and resid 154 through 163
    Processing helix  chain 'C' and resid 166 through 179
    Processing helix  chain 'C' and resid 182 through 191
    Processing helix  chain 'C' and resid 198 through 214
      removed outlier: 4.454A  pdb=" N   PHE C 211 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   VAL C 212 " --> pdb=" O   LEU C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 229
    Processing helix  chain 'D' and resid 6 through 31
      removed outlier: 3.509A  pdb=" N   MET D  31 " --> pdb=" O   PHE D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 68
      removed outlier: 4.560A  pdb=" N   LEU D  39 " --> pdb=" O   LYS D  35 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   SER D  40 " --> pdb=" O   GLU D  36 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASP D  60 " --> pdb=" O   TYR D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 77
    Processing helix  chain 'D' and resid 78 through 100
      removed outlier: 4.477A  pdb=" N   ILE D  84 " --> pdb=" O   ILE D  80 " (cutoff:3.500A)
      Proline residue:  D  87  - end of helix
      removed outlier: 4.248A  pdb=" N   PHE D  93 " --> pdb=" O   LEU D  89 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE D  94 " --> pdb=" O   MET D  90 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU D  97 " --> pdb=" O   PHE D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 128
      removed outlier: 4.073A  pdb=" N   PHE D 109 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 153
    Processing helix  chain 'D' and resid 154 through 163
    Processing helix  chain 'D' and resid 166 through 179
    Processing helix  chain 'D' and resid 182 through 191
    Processing helix  chain 'D' and resid 198 through 214
      removed outlier: 4.456A  pdb=" N   PHE D 211 " --> pdb=" O   ASN D 207 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL D 212 " --> pdb=" O   LEU D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 229
    Processing helix  chain 'E' and resid 6 through 31
      removed outlier: 3.510A  pdb=" N   MET E  31 " --> pdb=" O   PHE E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 34 through 68
      removed outlier: 4.562A  pdb=" N   LEU E  39 " --> pdb=" O   LYS E  35 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   SER E  40 " --> pdb=" O   GLU E  36 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASP E  60 " --> pdb=" O   TYR E  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 77
    Processing helix  chain 'E' and resid 78 through 100
      removed outlier: 4.482A  pdb=" N   ILE E  84 " --> pdb=" O   ILE E  80 " (cutoff:3.500A)
      Proline residue:  E  87  - end of helix
      removed outlier: 4.248A  pdb=" N   PHE E  93 " --> pdb=" O   LEU E  89 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   PHE E  94 " --> pdb=" O   MET E  90 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU E  97 " --> pdb=" O   PHE E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 105 through 128
      removed outlier: 4.071A  pdb=" N   PHE E 109 " --> pdb=" O   SER E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 132 through 153
    Processing helix  chain 'E' and resid 154 through 163
    Processing helix  chain 'E' and resid 166 through 179
    Processing helix  chain 'E' and resid 182 through 191
    Processing helix  chain 'E' and resid 198 through 214
      removed outlier: 4.454A  pdb=" N   PHE E 211 " --> pdb=" O   ASN E 207 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   VAL E 212 " --> pdb=" O   LEU E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 229

    729 hydrogen bonds defined for protein.
    2177 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: 1.70

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1574
        1.32 -     1.45: 2976
        1.45 -     1.57: 5098
        1.57 -     1.70: 0
        1.70 -     1.83: 110
  Bond restraints: 9758
  Sorted by residual:
  bond pdb=" C10 RET C 309 "
       pdb=" C11 RET C 309 "
    ideal  model  delta    sigma   weight residual
    1.433  1.330  0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" C10 RET A 306 "
       pdb=" C11 RET A 306 "
    ideal  model  delta    sigma   weight residual
    1.433  1.330  0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" C10 RET B 307 "
       pdb=" C11 RET B 307 "
    ideal  model  delta    sigma   weight residual
    1.433  1.331  0.102 2.00e-02 2.50e+03 2.62e+01
  bond pdb=" C10 RET E 307 "
       pdb=" C11 RET E 307 "
    ideal  model  delta    sigma   weight residual
    1.433  1.331  0.102 2.00e-02 2.50e+03 2.62e+01
  bond pdb=" C10 RET D 307 "
       pdb=" C11 RET D 307 "
    ideal  model  delta    sigma   weight residual
    1.433  1.331  0.102 2.00e-02 2.50e+03 2.59e+01
  ... (remaining 9753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 12467
        3.82 -     7.63: 621
        7.63 -    11.45: 46
       11.45 -    15.26: 3
       15.26 -    19.08: 1
  Bond angle restraints: 13138
  Sorted by residual:
  angle pdb=" N   GLU B 127 "
        pdb=" CA  GLU B 127 "
        pdb=" C   GLU B 127 "
      ideal   model   delta    sigma   weight residual
     110.55   91.47   19.08 1.35e+00 5.49e-01 2.00e+02
  angle pdb=" CA  ASP C  81 "
        pdb=" CB  ASP C  81 "
        pdb=" CG  ASP C  81 "
      ideal   model   delta    sigma   weight residual
     112.60  120.46   -7.86 1.00e+00 1.00e+00 6.17e+01
  angle pdb=" CA  ASP D  81 "
        pdb=" CB  ASP D  81 "
        pdb=" CG  ASP D  81 "
      ideal   model   delta    sigma   weight residual
     112.60  120.43   -7.83 1.00e+00 1.00e+00 6.13e+01
  angle pdb=" CA  ASP E  81 "
        pdb=" CB  ASP E  81 "
        pdb=" CG  ASP E  81 "
      ideal   model   delta    sigma   weight residual
     112.60  120.42   -7.82 1.00e+00 1.00e+00 6.12e+01
  angle pdb=" CA  ASP A  81 "
        pdb=" CB  ASP A  81 "
        pdb=" CG  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     112.60  120.40   -7.80 1.00e+00 1.00e+00 6.09e+01
  ... (remaining 13133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.30: 5371
       22.30 -    44.61: 311
       44.61 -    66.91: 62
       66.91 -    89.22: 0
       89.22 -   111.52: 4
  Dihedral angle restraints: 5748
    sinusoidal: 2448
      harmonic: 3300
  Sorted by residual:
  dihedral pdb=" C   GLU B 127 "
           pdb=" N   GLU B 127 "
           pdb=" CA  GLU B 127 "
           pdb=" CB  GLU B 127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.82  -17.78     0      2.50e+00 1.60e-01 5.06e+01
  dihedral pdb=" C   MET D 193 "
           pdb=" N   MET D 193 "
           pdb=" CA  MET D 193 "
           pdb=" CB  MET D 193 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.82   17.22     0      2.50e+00 1.60e-01 4.74e+01
  dihedral pdb=" N   MET D 193 "
           pdb=" C   MET D 193 "
           pdb=" CA  MET D 193 "
           pdb=" CB  MET D 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.95  -13.15     0      2.50e+00 1.60e-01 2.77e+01
  ... (remaining 5745 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 1233
       0.129 -    0.257: 230
       0.257 -    0.386: 27
       0.386 -    0.514: 4
       0.514 -    0.643: 1
  Chirality restraints: 1495
  Sorted by residual:
  chirality pdb=" CA  MET D 193 "
            pdb=" N   MET D 193 "
            pdb=" C   MET D 193 "
            pdb=" CB  MET D 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.87    0.64 2.00e-01 2.50e+01 1.03e+01
  chirality pdb=" CA  GLU B 127 "
            pdb=" N   GLU B 127 "
            pdb=" C   GLU B 127 "
            pdb=" CB  GLU B 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.98   -0.47 2.00e-01 2.50e+01 5.59e+00
  chirality pdb=" CA  ASP A  60 "
            pdb=" N   ASP A  60 "
            pdb=" C   ASP A  60 "
            pdb=" CB  ASP A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  ... (remaining 1492 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 RET E 307 "    0.065 2.00e-02 2.50e+03   6.68e-02 5.58e+01
        pdb=" C13 RET E 307 "   -0.027 2.00e-02 2.50e+03
        pdb=" C14 RET E 307 "   -0.104 2.00e-02 2.50e+03
        pdb=" C15 RET E 307 "    0.079 2.00e-02 2.50e+03
        pdb=" C20 RET E 307 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 RET A 306 "    0.065 2.00e-02 2.50e+03   6.66e-02 5.55e+01
        pdb=" C13 RET A 306 "   -0.027 2.00e-02 2.50e+03
        pdb=" C14 RET A 306 "   -0.104 2.00e-02 2.50e+03
        pdb=" C15 RET A 306 "    0.079 2.00e-02 2.50e+03
        pdb=" C20 RET A 306 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 RET D 307 "   -0.065 2.00e-02 2.50e+03   6.63e-02 5.49e+01
        pdb=" C13 RET D 307 "    0.027 2.00e-02 2.50e+03
        pdb=" C14 RET D 307 "    0.104 2.00e-02 2.50e+03
        pdb=" C15 RET D 307 "   -0.078 2.00e-02 2.50e+03
        pdb=" C20 RET D 307 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 69
        2.53 -     3.12: 8052
        3.12 -     3.72: 16150
        3.72 -     4.31: 25365
        4.31 -     4.90: 39578
  Nonbonded interactions: 89214
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 124 "
            pdb=" O   GLU B 127 "
     model   vdw
     1.941 3.040
  nonbonded pdb=" N   GLU B 127 "
            pdb=" O   GLU B 127 "
     model   vdw
     2.144 2.496
  nonbonded pdb=" OD2 ASP E   6 "
            pdb=" O   HOH E 401 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OD2 ASP D   6 "
            pdb=" O   HOH D 401 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OD2 ASP C   6 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.170 3.040
  ... (remaining 89209 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 1 through 16 or resid 18 through 230 or (resid 303 and (na \ 
me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18)) \ 
 or (resid 304 and (name C1 or name C10 or name C11 or name C2 or name C3 or nam \ 
e C4 or name C5 or name C6 or name C7 or name C8 or name C9 ))))
  selection = (chain 'B' and (resid 1 through 16 or resid 18 through 230 or (resid 303 and (na \ 
me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18)) \ 
 or resid 304))
  selection = (chain 'C' and (resid 1 through 16 or resid 18 through 230 or (resid 303 and (na \ 
me C10 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or ( \ 
resid 304 and (name C1 or name C10 or name C11 or name C2 or name C3 or name C4  \ 
or name C5 or name C6 or name C7 or name C8 or name C9 ))))
  selection = (chain 'D' and (resid 1 through 16 or resid 18 through 230 or (resid 303 and (na \ 
me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18)) \ 
 or (resid 304 and (name C1 or name C10 or name C11 or name C2 or name C3 or nam \ 
e C4 or name C5 or name C6 or name C7 or name C8 or name C9 ))))
  selection = (chain 'E' and (resid 1 through 16 or resid 18 through 230 or (resid 303 and (na \ 
me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18)) \ 
 or (resid 304 and (name C1 or name C10 or name C11 or name C2 or name C3 or nam \ 
e C4 or name C5 or name C6 or name C7 or name C8 or name C9 ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.060
  Find NCS groups from input model:        0.260
  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:7.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
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      :  0.014   0.103   9763  Z= 0.914
  Angle     :  1.878  19.076  13138  Z= 1.166
  Chirality :  0.106   0.643   1495
  Planarity :  0.020   0.278   1505
  Dihedral  : 14.565 111.520   3658
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  4.86 %
    Favored  : 93.15 %
  Cbeta Deviations :  1.63 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -2.26 (0.21), residues: 1155
  helix: -1.54 (0.13), residues: 915
  sheet:  None (None), residues: 0
  loop : -0.35 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.044   0.006   ARG B  59 
 TYR   0.045   0.013   TYR E  28 
 PHE   0.055   0.013   PHE B 170 
 TRP   0.056   0.016   TRP D  13 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.01449 ( 9758)
  covalent geometry    : angle       1.87812 (13138)
  hydrogen bonds       : bond        0.18418 (  729)
  hydrogen bonds       : angle       7.40227 ( 2177)
  Misc. bond           : bond        0.01069 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7567 (mt0) cc_final: 0.6558 (pt0)
REVERT: A   41 MET cc_start: 0.9091 (mmm) cc_final: 0.8767 (mmp)
REVERT: A  167 LYS cc_start: 0.8276 (tttt) cc_final: 0.8068 (tttt)
REVERT: B    3 GLN cc_start: 0.7612 (mt0) cc_final: 0.6686 (pt0)
REVERT: B  193 MET cc_start: 0.8961 (mtp) cc_final: 0.8410 (mtp)
REVERT: C    3 GLN cc_start: 0.7634 (mt0) cc_final: 0.6598 (pt0)
REVERT: C   41 MET cc_start: 0.9087 (mmm) cc_final: 0.8831 (mmm)
REVERT: C  193 MET cc_start: 0.8940 (mtp) cc_final: 0.8727 (mtm)
REVERT: D    3 GLN cc_start: 0.7685 (mt0) cc_final: 0.6791 (pt0)
REVERT: E  141 MET cc_start: 0.8539 (mmm) cc_final: 0.8249 (mmm)
REVERT: E  167 LYS cc_start: 0.8318 (tttt) cc_final: 0.8043 (tttm)
  outliers start: 18
  outliers final: 13
  residues processed: 129
  average time/residue: 0.6051
  time to fit residues: 83.7804
Evaluate side-chains
  110 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  208 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.6518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.113866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.079722 restraints weight = 38637.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 2.56
r_work: 0.2619 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2479 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2487 r_free = 0.2487    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9763  Z= 0.142
  Angle     :  0.548   8.585  13138  Z= 0.292
  Chirality :  0.040   0.194   1495
  Planarity :  0.004   0.043   1505
  Dihedral  : 11.182  83.465   1890
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  6.96 %
    Favored  : 91.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.77 (0.25), residues: 1155
  helix:  1.47 (0.16), residues: 910
  sheet:  None (None), residues: 0
  loop :  0.30 (0.47), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 227 
 TYR   0.014   0.002   TYR B 184 
 PHE   0.013   0.002   PHE A  26 
 TRP   0.011   0.002   TRP B  82 
 HIS   0.004   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9758)
  covalent geometry    : angle       0.54773 (13138)
  hydrogen bonds       : bond        0.05912 (  729)
  hydrogen bonds       : angle       4.01085 ( 2177)
  Misc. bond           : bond        0.00044 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7490 (mt0) cc_final: 0.6492 (pt0)
REVERT: A   41 MET cc_start: 0.9120 (mmm) cc_final: 0.8761 (mmp)
REVERT: A  167 LYS cc_start: 0.8185 (tttt) cc_final: 0.7878 (tttt)
REVERT: B    3 GLN cc_start: 0.7465 (mt0) cc_final: 0.6459 (pt0)
REVERT: C    3 GLN cc_start: 0.7603 (mt0) cc_final: 0.6516 (pt0)
REVERT: D    3 GLN cc_start: 0.7519 (mt0) cc_final: 0.6620 (pt0)
REVERT: D  104 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7518 (tp)
REVERT: E  189 ILE cc_start: 0.8400 (mt) cc_final: 0.8175 (mt)
REVERT: E  194 MET cc_start: 0.8250 (ttm) cc_final: 0.8046 (mtp)
REVERT: E  196 SER cc_start: 0.8700 (m) cc_final: 0.8477 (p)
  outliers start: 17
  outliers final: 10
  residues processed: 141
  average time/residue: 0.5383
  time to fit residues: 82.1448
Evaluate side-chains
  118 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  210 ASP
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  210 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    0.0470
   chunk 13 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 108 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 114 optimal weight:    0.5980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.114695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.081323 restraints weight = 31811.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 2.35
r_work: 0.2657 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2518 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2526 r_free = 0.2526    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2526 r_free = 0.2526    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9763  Z= 0.128
  Angle     :  0.498  10.964  13138  Z= 0.261
  Chirality :  0.039   0.264   1495
  Planarity :  0.003   0.035   1505
  Dihedral  :  9.762  59.291   1884
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  8.40 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.43 (0.25), residues: 1155
  helix:  1.96 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.36 (0.48), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 227 
 TYR   0.012   0.001   TYR D  56 
 PHE   0.013   0.002   PHE E 217 
 TRP   0.010   0.001   TRP E  82 
 HIS   0.004   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9758)
  covalent geometry    : angle       0.49795 (13138)
  hydrogen bonds       : bond        0.05451 (  729)
  hydrogen bonds       : angle       3.76760 ( 2177)
  Misc. bond           : bond        0.00066 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7505 (mt0) cc_final: 0.6538 (pt0)
REVERT: A   41 MET cc_start: 0.9128 (mmm) cc_final: 0.8743 (mmp)
REVERT: A  167 LYS cc_start: 0.8297 (tttt) cc_final: 0.8030 (tttt)
REVERT: B    3 GLN cc_start: 0.7520 (mt0) cc_final: 0.6492 (pt0)
REVERT: B  210 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7927 (t0)
REVERT: C    3 GLN cc_start: 0.7653 (mt0) cc_final: 0.6612 (pt0)
REVERT: D    3 GLN cc_start: 0.7550 (mt0) cc_final: 0.6633 (pt0)
REVERT: D  104 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7522 (tp)
REVERT: E  189 ILE cc_start: 0.8454 (mt) cc_final: 0.8217 (mt)
REVERT: E  196 SER cc_start: 0.8716 (m) cc_final: 0.8516 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 126
  average time/residue: 0.5652
  time to fit residues: 76.8896
Evaluate side-chains
  125 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  210 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.113215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.080083 restraints weight = 32245.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 2.34
r_work: 0.2637 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2500 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2513 r_free = 0.2513    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2513 r_free = 0.2513    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9763  Z= 0.126
  Angle     :  0.480   8.108  13138  Z= 0.253
  Chirality :  0.039   0.170   1495
  Planarity :  0.003   0.033   1505
  Dihedral  :  9.082  59.888   1880
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  :  8.51 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.57 (0.25), residues: 1155
  helix:  2.07 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.35 (0.47), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 227 
 TYR   0.011   0.001   TYR C  56 
 PHE   0.012   0.002   PHE D 217 
 TRP   0.009   0.001   TRP D 149 
 HIS   0.004   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9758)
  covalent geometry    : angle       0.48029 (13138)
  hydrogen bonds       : bond        0.05359 (  729)
  hydrogen bonds       : angle       3.69470 ( 2177)
  Misc. bond           : bond        0.00067 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7382 (mt0) cc_final: 0.6370 (pt0)
REVERT: A  167 LYS cc_start: 0.8127 (tttt) cc_final: 0.7866 (tttt)
REVERT: B    3 GLN cc_start: 0.7455 (mt0) cc_final: 0.6424 (pt0)
REVERT: B  210 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7898 (t0)
REVERT: C    3 GLN cc_start: 0.7534 (mt0) cc_final: 0.6458 (pt0)
REVERT: D    3 GLN cc_start: 0.7433 (mt0) cc_final: 0.6499 (pt0)
REVERT: D  104 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7469 (tp)
REVERT: E  189 ILE cc_start: 0.8357 (mt) cc_final: 0.8106 (mm)
REVERT: E  196 SER cc_start: 0.8679 (m) cc_final: 0.8448 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 123
  average time/residue: 0.5635
  time to fit residues: 75.0113
Evaluate side-chains
  131 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  210 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 111 optimal weight:    0.3980
   chunk 14 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.114298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.080195 restraints weight = 42038.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 2.66
r_work: 0.2632 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9763  Z= 0.120
  Angle     :  0.460   5.893  13138  Z= 0.244
  Chirality :  0.038   0.138   1495
  Planarity :  0.003   0.027   1505
  Dihedral  :  8.479  56.283   1878
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  :  8.95 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.71 (0.25), residues: 1155
  helix:  2.17 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.43 (0.47), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 227 
 TYR   0.010   0.001   TYR B  56 
 PHE   0.012   0.002   PHE D 217 
 TRP   0.010   0.001   TRP D 149 
 HIS   0.004   0.002   HIS D  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9758)
  covalent geometry    : angle       0.46027 (13138)
  hydrogen bonds       : bond        0.05153 (  729)
  hydrogen bonds       : angle       3.62096 ( 2177)
  Misc. bond           : bond        0.00062 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7342 (mt0) cc_final: 0.6361 (pt0)
REVERT: A  167 LYS cc_start: 0.8063 (tttt) cc_final: 0.7810 (tttt)
REVERT: B    3 GLN cc_start: 0.7376 (mt0) cc_final: 0.6379 (pt0)
REVERT: C    3 GLN cc_start: 0.7471 (mt0) cc_final: 0.6456 (pt0)
REVERT: D    3 GLN cc_start: 0.7375 (mt0) cc_final: 0.6489 (pt0)
REVERT: D  104 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7509 (tp)
REVERT: E  141 MET cc_start: 0.8516 (mmm) cc_final: 0.8309 (mmp)
REVERT: E  189 ILE cc_start: 0.8260 (mt) cc_final: 0.8011 (mm)
REVERT: E  194 MET cc_start: 0.8178 (mtp) cc_final: 0.7896 (mtm)
REVERT: E  196 SER cc_start: 0.8660 (m) cc_final: 0.8448 (p)
  outliers start: 21
  outliers final: 17
  residues processed: 127
  average time/residue: 0.5525
  time to fit residues: 76.0451
Evaluate side-chains
  129 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  157 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  199 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 112 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0370
   chunk 86 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   overall best weight:    0.7060

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.115629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.081878 restraints weight = 34221.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.41
r_work: 0.2683 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2545 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2543
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2543 r_free = 0.2543    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2543 r_free = 0.2543    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2543
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9763  Z= 0.120
  Angle     :  0.458   5.615  13138  Z= 0.243
  Chirality :  0.038   0.133   1495
  Planarity :  0.003   0.025   1505
  Dihedral  :  8.138  56.497   1878
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  9.17 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.74 (0.25), residues: 1155
  helix:  2.18 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.45 (0.47), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 227 
 TYR   0.010   0.001   TYR B  56 
 PHE   0.012   0.002   PHE D 217 
 TRP   0.009   0.001   TRP B 149 
 HIS   0.004   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9758)
  covalent geometry    : angle       0.45785 (13138)
  hydrogen bonds       : bond        0.05169 (  729)
  hydrogen bonds       : angle       3.61645 ( 2177)
  Misc. bond           : bond        0.00059 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7465 (mt0) cc_final: 0.6485 (pt0)
REVERT: A  167 LYS cc_start: 0.8250 (tttt) cc_final: 0.8013 (tttt)
REVERT: B    3 GLN cc_start: 0.7503 (mt0) cc_final: 0.6499 (pt0)
REVERT: C    3 GLN cc_start: 0.7606 (mt0) cc_final: 0.6560 (pt0)
REVERT: D    3 GLN cc_start: 0.7464 (mt0) cc_final: 0.6524 (pt0)
REVERT: D   19 MET cc_start: 0.9260 (mmt) cc_final: 0.9032 (mmt)
REVERT: E   36 GLU cc_start: 0.8309 (mp0) cc_final: 0.8064 (mp0)
REVERT: E  141 MET cc_start: 0.8681 (mmm) cc_final: 0.8397 (mmm)
REVERT: E  189 ILE cc_start: 0.8434 (mt) cc_final: 0.8213 (mm)
REVERT: E  194 MET cc_start: 0.8253 (mtp) cc_final: 0.7991 (mtm)
REVERT: E  196 SER cc_start: 0.8695 (m) cc_final: 0.8481 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 126
  average time/residue: 0.5471
  time to fit residues: 74.6070
Evaluate side-chains
  133 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  199 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 108 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.114590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.081117 restraints weight = 31092.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 2.30
r_work: 0.2671 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2532 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2529 r_free = 0.2529    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2529 r_free = 0.2529    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9763  Z= 0.128
  Angle     :  0.471   5.618  13138  Z= 0.250
  Chirality :  0.039   0.137   1495
  Planarity :  0.003   0.026   1505
  Dihedral  :  8.116  57.965   1878
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.28 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.68 (0.25), residues: 1155
  helix:  2.13 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.48 (0.47), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 227 
 TYR   0.011   0.001   TYR B  56 
 PHE   0.012   0.002   PHE D 217 
 TRP   0.009   0.001   TRP A 149 
 HIS   0.004   0.002   HIS E  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9758)
  covalent geometry    : angle       0.47069 (13138)
  hydrogen bonds       : bond        0.05373 (  729)
  hydrogen bonds       : angle       3.66389 ( 2177)
  Misc. bond           : bond        0.00069 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7466 (mt0) cc_final: 0.6485 (pt0)
REVERT: A  167 LYS cc_start: 0.8252 (tttt) cc_final: 0.8012 (tttt)
REVERT: B    3 GLN cc_start: 0.7484 (mt0) cc_final: 0.6463 (pt0)
REVERT: C    3 GLN cc_start: 0.7598 (mt0) cc_final: 0.6564 (pt0)
REVERT: D    3 GLN cc_start: 0.7447 (mt0) cc_final: 0.6506 (pt0)
REVERT: D  104 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7737 (tp)
REVERT: E   36 GLU cc_start: 0.8331 (mp0) cc_final: 0.7997 (mp0)
REVERT: E  189 ILE cc_start: 0.8448 (mt) cc_final: 0.8221 (mm)
REVERT: E  196 SER cc_start: 0.8665 (m) cc_final: 0.8452 (p)
  outliers start: 19
  outliers final: 17
  residues processed: 125
  average time/residue: 0.5573
  time to fit residues: 75.3867
Evaluate side-chains
  134 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  157 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  199 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.114360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.080999 restraints weight = 38286.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 2.63
r_work: 0.2623 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2485 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9763  Z= 0.127
  Angle     :  0.468   5.540  13138  Z= 0.249
  Chirality :  0.039   0.133   1495
  Planarity :  0.003   0.026   1505
  Dihedral  :  8.035  58.342   1878
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  9.39 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.69 (0.25), residues: 1155
  helix:  2.14 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.51 (0.47), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  59 
 TYR   0.012   0.001   TYR C  56 
 PHE   0.012   0.002   PHE D 217 
 TRP   0.008   0.001   TRP D 149 
 HIS   0.004   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9758)
  covalent geometry    : angle       0.46784 (13138)
  hydrogen bonds       : bond        0.05324 (  729)
  hydrogen bonds       : angle       3.65333 ( 2177)
  Misc. bond           : bond        0.00066 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7424 (mt0) cc_final: 0.6407 (pt0)
REVERT: A  167 LYS cc_start: 0.8241 (tttt) cc_final: 0.7991 (tttt)
REVERT: B    3 GLN cc_start: 0.7359 (mt0) cc_final: 0.6318 (pt0)
REVERT: B   36 GLU cc_start: 0.8234 (mp0) cc_final: 0.7988 (pm20)
REVERT: C    3 GLN cc_start: 0.7559 (mt0) cc_final: 0.6507 (pt0)
REVERT: D    3 GLN cc_start: 0.7351 (mt0) cc_final: 0.6350 (pt0)
REVERT: D  104 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7810 (tp)
REVERT: E   36 GLU cc_start: 0.8392 (mp0) cc_final: 0.8065 (mp0)
REVERT: E  189 ILE cc_start: 0.8478 (mt) cc_final: 0.8253 (mm)
  outliers start: 18
  outliers final: 16
  residues processed: 125
  average time/residue: 0.5488
  time to fit residues: 74.2856
Evaluate side-chains
  132 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  157 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  199 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.113881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.080694 restraints weight = 38152.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 2.65
r_work: 0.2624 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2486 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2470
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2470 r_free = 0.2470    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2470 r_free = 0.2470    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2470
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9763  Z= 0.127
  Angle     :  0.467   5.646  13138  Z= 0.248
  Chirality :  0.039   0.134   1495
  Planarity :  0.003   0.025   1505
  Dihedral  :  7.981  56.182   1878
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  9.83 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.70 (0.25), residues: 1155
  helix:  2.14 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.53 (0.46), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 227 
 TYR   0.010   0.001   TYR C  56 
 PHE   0.012   0.002   PHE D 217 
 TRP   0.008   0.001   TRP D 149 
 HIS   0.004   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9758)
  covalent geometry    : angle       0.46743 (13138)
  hydrogen bonds       : bond        0.05326 (  729)
  hydrogen bonds       : angle       3.65397 ( 2177)
  Misc. bond           : bond        0.00067 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7427 (mt0) cc_final: 0.6422 (pt0)
REVERT: A  167 LYS cc_start: 0.8228 (tttt) cc_final: 0.7979 (tttt)
REVERT: B    3 GLN cc_start: 0.7368 (mt0) cc_final: 0.6330 (pt0)
REVERT: C    3 GLN cc_start: 0.7564 (mt0) cc_final: 0.6519 (pt0)
REVERT: D    3 GLN cc_start: 0.7327 (mt0) cc_final: 0.6320 (pt0)
REVERT: D  104 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7809 (tp)
REVERT: E   36 GLU cc_start: 0.8386 (mp0) cc_final: 0.8060 (mp0)
REVERT: E  189 ILE cc_start: 0.8476 (mt) cc_final: 0.8256 (mm)
  outliers start: 17
  outliers final: 16
  residues processed: 126
  average time/residue: 0.5731
  time to fit residues: 77.9307
Evaluate side-chains
  134 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  157 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  199 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 110 optimal weight:    0.1980
   chunk 31 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0040
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.116387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.083123 restraints weight = 40821.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 2.59
r_work: 0.2671 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9763  Z= 0.110
  Angle     :  0.438   5.463  13138  Z= 0.233
  Chirality :  0.037   0.123   1495
  Planarity :  0.003   0.022   1505
  Dihedral  :  7.544  56.363   1878
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.94 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.87 (0.25), residues: 1155
  helix:  2.28 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.50 (0.46), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 227 
 TYR   0.008   0.001   TYR E 184 
 PHE   0.011   0.001   PHE D 217 
 TRP   0.008   0.001   TRP B 149 
 HIS   0.004   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 9758)
  covalent geometry    : angle       0.43775 (13138)
  hydrogen bonds       : bond        0.04840 (  729)
  hydrogen bonds       : angle       3.53019 ( 2177)
  Misc. bond           : bond        0.00046 (    5)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A    3 GLN cc_start: 0.7400 (mt0) cc_final: 0.6467 (pt0)
REVERT: A  167 LYS cc_start: 0.8214 (tttt) cc_final: 0.7968 (tttt)
REVERT: B    3 GLN cc_start: 0.7356 (mt0) cc_final: 0.6413 (pt0)
REVERT: C    3 GLN cc_start: 0.7500 (mt0) cc_final: 0.6534 (pt0)
REVERT: D    3 GLN cc_start: 0.7357 (mt0) cc_final: 0.6456 (pt0)
REVERT: E   36 GLU cc_start: 0.8171 (mp0) cc_final: 0.7910 (mp0)
REVERT: E  189 ILE cc_start: 0.8420 (mt) cc_final: 0.8203 (mm)
REVERT: E  210 ASP cc_start: 0.7739 (m-30) cc_final: 0.7314 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 129
  average time/residue: 0.5351
  time to fit residues: 75.2108
Evaluate side-chains
  130 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  157 SER
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   81 ASP
Chi-restraints excluded: chain D residue  157 SER
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  199 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 38 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0040
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 61 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.116090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.083501 restraints weight = 32543.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 2.27
r_work: 0.2676 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2538 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2521
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2521 r_free = 0.2521    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2521 r_free = 0.2521    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2521
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9763  Z= 0.114
  Angle     :  0.445   5.481  13138  Z= 0.238
  Chirality :  0.038   0.122   1495
  Planarity :  0.003   0.023   1505
  Dihedral  :  7.483  56.937   1876
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.28 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.88 (0.25), residues: 1155
  helix:  2.28 (0.17), residues: 915
  sheet:  None (None), residues: 0
  loop :  0.51 (0.46), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 227 
 TYR   0.009   0.001   TYR A  56 
 PHE   0.012   0.001   PHE D 217 
 TRP   0.007   0.001   TRP A 149 
 HIS   0.004   0.002   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9758)
  covalent geometry    : angle       0.44521 (13138)
  hydrogen bonds       : bond        0.04963 (  729)
  hydrogen bonds       : angle       3.53632 ( 2177)
  Misc. bond           : bond        0.00054 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4034.39 seconds
wall clock time: 69 minutes 44.72 seconds (4184.72 seconds total)