Starting phenix.real_space_refine
on Wed Sep 17 10:10:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o6q_12740/09_2025/7o6q_12740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o6q_12740/09_2025/7o6q_12740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o6q_12740/09_2025/7o6q_12740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o6q_12740/09_2025/7o6q_12740.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o6q_12740/09_2025/7o6q_12740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o6q_12740/09_2025/7o6q_12740.map"
  }
  resolution = 1.88
  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=   0.005 sd=   0.042
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      40      5.16       5
     C    4777      2.51       5
     N    1323      2.21       5
     O    1859      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  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: 7999
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1902
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1813
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 4, 'TRANS': 243}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 248, 1813
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 4, 'TRANS': 243}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1736
    Chain: "B"
      Number of atoms: 1879
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1813
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 4, 'TRANS': 243}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 248, 1813
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 4, 'TRANS': 243}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1762
    Chain: "C"
      Number of atoms: 1917
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 251, 1836
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 4, 'TRANS': 246}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 251, 1836
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 4, 'TRANS': 246}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1768
    Chain: "D"
      Number of atoms: 1902
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 250, 1830
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 4, 'TRANS': 245}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 250, 1830
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 4, 'TRANS': 245}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1772
    Chain: "A"
      Number of atoms: 101
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 94, 94
          Classifications: {'water': 94}
          Link IDs: {None: 93}
      Conformer: "B"
        Number of residues, atoms: 95, 95
          Classifications: {'water': 95}
          Link IDs: {None: 94}
    Chain: "B"
      Number of atoms: 96
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 93
          Classifications: {'water': 93}
          Link IDs: {None: 92}
      Conformer: "B"
        Number of residues, atoms: 93, 93
          Classifications: {'water': 93}
          Link IDs: {None: 92}
    Chain: "C"
      Number of atoms: 103
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 101, 101
          Classifications: {'water': 101}
          Link IDs: {None: 100}
      Conformer: "B"
        Number of residues, atoms: 101, 101
          Classifications: {'water': 101}
          Link IDs: {None: 100}
    Chain: "D"
      Number of atoms: 99
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 97, 97
          Classifications: {'water': 97}
          Link IDs: {None: 96}
      Conformer: "B"
        Number of residues, atoms: 97, 97
          Classifications: {'water': 97}
          Link IDs: {None: 96}
  Residues with excluded nonbonded symmetry interactions: 61
    residue:
      pdb=" N  AARG A  58 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  58 " occ=0.50
    residue:
      pdb=" N  ASER A  61 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  61 " occ=0.50
    residue:
      pdb=" N  AASP A  71 " occ=0.50
      ... (14 atoms not shown)
      pdb=" OD2BASP A  71 " occ=0.50
    residue:
      pdb=" N  AARG A  74 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  74 " occ=0.50
    residue:
      pdb=" N  AGLU A  98 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A  98 " occ=0.50
    residue:
      pdb=" N  APHE A 104 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 104 " occ=0.50
    residue:
      pdb=" N  ALYS A 137 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 137 " occ=0.50
    residue:
      pdb=" N  ASER A 179 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A 179 " occ=0.50
    residue:
      pdb=" N  AGLU A 225 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A 225 " occ=0.50
    residue:
      pdb=" N  AGLU A 237 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A 237 " occ=0.50
    residue:
      pdb=" N  AARG B  58 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B  58 " occ=0.50
    residue:
      pdb=" N  AARG B  74 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B  74 " occ=0.50
    ... (remaining 49 not shown)
  Time building chain proxies: 3.45, per 1000 atoms: 0.43
  Number of scatterers: 7999
  At special positions: 0
  Unit cell: (75.555, 92.637, 82.782, 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      40     16.00
     O    1859      8.00
     N    1323      7.00
     C    4777      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 550.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      61.6% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 35
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 3.722A  pdb=" N   GLY A  57 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 85
    Processing helix  chain 'A' and resid 102 through 106
    Processing helix  chain 'A' and resid 107 through 119
    Processing helix  chain 'A' and resid 119 through 134
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 146 through 150
    Processing helix  chain 'A' and resid 156 through 179
      removed outlier: 3.900A  pdb=" N  ASER A 179 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 215
    Processing helix  chain 'A' and resid 223 through 236
      removed outlier: 3.514A  pdb=" N   VAL A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 240
      removed outlier: 3.551A  pdb=" N   SER A 240 " --> pdb=" O  AGLU A 237 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 237 through 240'
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.659A  pdb=" N   VAL A 256 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 267
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 45 through 57
      removed outlier: 3.733A  pdb=" N   GLY B  57 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 85
    Processing helix  chain 'B' and resid 102 through 106
    Processing helix  chain 'B' and resid 107 through 119
    Processing helix  chain 'B' and resid 119 through 134
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 146 through 150
    Processing helix  chain 'B' and resid 156 through 179
      removed outlier: 3.899A  pdb=" N  ASER B 179 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 215
    Processing helix  chain 'B' and resid 223 through 236
      removed outlier: 3.516A  pdb=" N   VAL B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 240
      removed outlier: 3.546A  pdb=" N   SER B 240 " --> pdb=" O  AGLU B 237 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 237 through 240'
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.659A  pdb=" N   VAL B 256 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 268
      removed outlier: 3.666A  pdb=" N   GLY B 267 " --> pdb=" O   VAL B 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 35
    Processing helix  chain 'C' and resid 45 through 57
      removed outlier: 3.760A  pdb=" N   GLY C  57 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 85
    Processing helix  chain 'C' and resid 102 through 106
    Processing helix  chain 'C' and resid 107 through 119
    Processing helix  chain 'C' and resid 119 through 134
    Processing helix  chain 'C' and resid 135 through 137
      No H-bonds generated for 'chain 'C' and resid 135 through 137'
    Processing helix  chain 'C' and resid 146 through 150
    Processing helix  chain 'C' and resid 156 through 179
      removed outlier: 3.900A  pdb=" N  ASER C 179 " --> pdb=" O   VAL C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 215
    Processing helix  chain 'C' and resid 223 through 236
    Processing helix  chain 'C' and resid 237 through 240
      removed outlier: 3.548A  pdb=" N   SER C 240 " --> pdb=" O  AGLU C 237 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 237 through 240'
    Processing helix  chain 'C' and resid 252 through 256
      removed outlier: 3.658A  pdb=" N   VAL C 256 " --> pdb=" O   TYR C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 267
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 45 through 57
      removed outlier: 3.717A  pdb=" N   GLY D  57 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 85
    Processing helix  chain 'D' and resid 102 through 106
    Processing helix  chain 'D' and resid 107 through 119
    Processing helix  chain 'D' and resid 119 through 134
    Processing helix  chain 'D' and resid 135 through 137
      No H-bonds generated for 'chain 'D' and resid 135 through 137'
    Processing helix  chain 'D' and resid 146 through 150
    Processing helix  chain 'D' and resid 156 through 179
      removed outlier: 3.924A  pdb=" N   SER D 179 " --> pdb=" O   VAL D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 215
      removed outlier: 3.566A  pdb=" N   GLY D 209 " --> pdb=" O   LEU D 205 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE D 210 " --> pdb=" O   MET D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 236
      removed outlier: 3.550A  pdb=" N   VAL D 227 " --> pdb=" O   THR D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 240
      removed outlier: 3.548A  pdb=" N   SER D 240 " --> pdb=" O  AGLU D 237 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 237 through 240'
    Processing helix  chain 'D' and resid 252 through 256
      removed outlier: 3.658A  pdb=" N   VAL D 256 " --> pdb=" O   TYR D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 258 through 267
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64
      removed outlier: 3.554A  pdb=" N   ASP A  43 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL A  14 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   PHE A  91 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ILE A  16 " --> pdb=" O   PHE A  91 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   MET A  90 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   THR A 144 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   SER A  92 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU A 247 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   CYS A 186 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   VAL A 249 " --> pdb=" O   CYS A 186 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   SER A 188 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 64
      removed outlier: 3.549A  pdb=" N   ASP B  43 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL B  14 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   PHE B  91 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE B  16 " --> pdb=" O   PHE B  91 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   MET B  90 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   THR B 144 " --> pdb=" O   MET B  90 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   SER B  92 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 60 through 64
      removed outlier: 6.548A  pdb=" N   VAL C  39 " --> pdb=" O   SER C  61 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   THR C  63 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   ILE C  41 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   VAL C  14 " --> pdb=" O   ILE C  89 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   PHE C  91 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE C  16 " --> pdb=" O   PHE C  91 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   MET C  90 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   THR C 144 " --> pdb=" O   MET C  90 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   SER C  92 " --> pdb=" O   THR C 144 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   LEU C 247 " --> pdb=" O   ALA C 184 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   CYS C 186 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   VAL C 249 " --> pdb=" O   CYS C 186 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER C 188 " --> pdb=" O   VAL C 249 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 60 through 64
      removed outlier: 3.539A  pdb=" N   ASP D  43 " --> pdb=" O   THR D  63 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL D  14 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   PHE D  91 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ILE D  16 " --> pdb=" O   PHE D  91 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   MET D  90 " --> pdb=" O   ILE D 142 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   THR D 144 " --> pdb=" O   MET D  90 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   SER D  92 " --> pdb=" O   THR D 144 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   LEU D 247 " --> pdb=" O   ALA D 184 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   CYS D 186 " --> pdb=" O   LEU D 247 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   VAL D 249 " --> pdb=" O   CYS D 186 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   SER D 188 " --> pdb=" O   VAL D 249 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1327 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: 1.32

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2501
        1.33 -     1.45: 897
        1.45 -     1.57: 4268
        1.57 -     1.69: 0
        1.69 -     1.80: 64
  Bond restraints: 7730
  Sorted by residual:
  bond pdb=" CB  CYS B 140 "
       pdb=" SG  CYS B 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.750  0.058 3.30e-02 9.18e+02 3.09e+00
  bond pdb=" CB  CYS C 140 "
       pdb=" SG  CYS C 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.753  0.055 3.30e-02 9.18e+02 2.79e+00
  bond pdb=" CB  THR A  28 "
       pdb=" CG2 THR A  28 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.02e+00
  bond pdb=" CB  CYS A 140 "
       pdb=" SG  CYS A 140 "
    ideal  model  delta    sigma   weight residual
    1.808  1.762  0.046 3.30e-02 9.18e+02 1.97e+00
  bond pdb=" CB  THR D  28 "
       pdb=" CG2 THR D  28 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.94e+00
  ... (remaining 7725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 9549
        1.13 -     2.26: 794
        2.26 -     3.39: 106
        3.39 -     4.52: 35
        4.52 -     5.65: 12
  Bond angle restraints: 10496
  Sorted by residual:
  angle pdb=" C   ALA D 136 "
        pdb=" N  BLYS D 137 "
        pdb=" CA BLYS D 137 "
      ideal   model   delta    sigma   weight residual
     122.74  127.91   -5.17 1.44e+00 4.82e-01 1.29e+01
  angle pdb=" C   ALA B 136 "
        pdb=" N   LYS B 137 "
        pdb=" CA  LYS B 137 "
      ideal   model   delta    sigma   weight residual
     122.74  127.52   -4.78 1.44e+00 4.82e-01 1.10e+01
  angle pdb=" C   ALA C 136 "
        pdb=" N   LYS C 137 "
        pdb=" CA  LYS C 137 "
      ideal   model   delta    sigma   weight residual
     122.74  126.89   -4.15 1.44e+00 4.82e-01 8.30e+00
  angle pdb=" C   MET A 133 "
        pdb=" N   VAL A 134 "
        pdb=" CA  VAL A 134 "
      ideal   model   delta    sigma   weight residual
     120.43  122.87   -2.44 9.60e-01 1.09e+00 6.46e+00
  angle pdb=" C   MET D 133 "
        pdb=" N   VAL D 134 "
        pdb=" CA  VAL D 134 "
      ideal   model   delta    sigma   weight residual
     120.43  122.77   -2.34 9.60e-01 1.09e+00 5.93e+00
  ... (remaining 10491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.61: 4246
       16.61 -    33.23: 284
       33.23 -    49.84: 49
       49.84 -    66.45: 15
       66.45 -    83.07: 10
  Dihedral angle restraints: 4604
    sinusoidal: 1693
      harmonic: 2911
  Sorted by residual:
  dihedral pdb=" CA  VAL A 256 "
           pdb=" C   VAL A 256 "
           pdb=" N   ASN A 257 "
           pdb=" CA  ASN A 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  VAL D 256 "
           pdb=" C   VAL D 256 "
           pdb=" N   ASN D 257 "
           pdb=" CA  ASN D 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  VAL C 256 "
           pdb=" C   VAL C 256 "
           pdb=" N   ASN C 257 "
           pdb=" CA  ASN C 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 4601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 482
       0.030 -    0.060: 428
       0.060 -    0.090: 200
       0.090 -    0.120: 89
       0.120 -    0.150: 39
  Chirality restraints: 1238
  Sorted by residual:
  chirality pdb=" CA BLYS D 137 "
            pdb=" N  BLYS D 137 "
            pdb=" C  BLYS D 137 "
            pdb=" CB BLYS D 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.63e-01
  chirality pdb=" CA  LYS B 137 "
            pdb=" N   LYS B 137 "
            pdb=" C   LYS B 137 "
            pdb=" CB  LYS B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  HIS B 128 "
            pdb=" N   HIS B 128 "
            pdb=" C   HIS B 128 "
            pdb=" CB  HIS B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 1235 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 128 "   -0.019 2.00e-02 2.50e+03   1.72e-02 4.46e+00
        pdb=" CG  HIS B 128 "    0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 128 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 128 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 128 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 128 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 128 "   -0.019 2.00e-02 2.50e+03   1.72e-02 4.44e+00
        pdb=" CG  HIS D 128 "    0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 128 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 128 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 128 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 128 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 128 "    0.019 2.00e-02 2.50e+03   1.70e-02 4.35e+00
        pdb=" CG  HIS A 128 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 128 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 128 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 128 "    0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 128 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 311
        2.67 -     3.23: 8219
        3.23 -     3.79: 13899
        3.79 -     4.34: 20514
        4.34 -     4.90: 31143
  Nonbonded interactions: 74086
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  43 "
            pdb=" O   HOH A 301 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OD2 ASP D  43 "
            pdb=" O   HOH D 301 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OE2 GLU C  98 "
            pdb=" O   HOH C 301 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OG BSER A  61 "
            pdb=" O   HOH A 302 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OD1 ASN C  59 "
            pdb=" O   HOH C 302 "
     model   vdw
     2.179 3.040
  ... (remaining 74081 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 8 through 57 or resid 59 through 60 or resid 62 through 70 \ 
 or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid  \ 
105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ 
hrough 178 or resid 180 through 186 or resid 188 through 224 or resid 226 throug \ 
h 236 or resid 238 through 268))
  selection = (chain 'B' and (resid 8 through 57 or resid 59 through 60 or resid 62 through 70 \ 
 or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid  \ 
105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ 
hrough 178 or resid 180 through 186 or resid 188 through 224 or resid 226 throug \ 
h 236 or resid 238 through 268))
  selection = (chain 'C' and (resid 8 through 57 or resid 59 through 60 or resid 62 through 70 \ 
 or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid  \ 
105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ 
hrough 178 or resid 180 through 186 or resid 188 through 192 or resid 206 throug \ 
h 224 or resid 226 through 236 or resid 238 through 268))
  selection = (chain 'D' and (resid 8 through 57 or resid 59 through 60 or resid 62 through 70 \ 
 or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid  \ 
105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ 
hrough 178 or resid 180 through 186 or resid 188 through 192 or resid 206 throug \ 
h 224 or resid 226 through 236 or resid 238 through 268))
}

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=0.33 max=1.00 mean=0.96
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:             4.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.500
  Find NCS groups from input model:        0.190
  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:7.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
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      :  0.010   0.061   7730  Z= 0.405
  Angle     :  0.708   5.648  10496  Z= 0.398
  Chirality :  0.055   0.150   1238
  Planarity :  0.006   0.045   1374
  Dihedral  : 12.799  83.066   2774
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  4.88 %
    Favored  : 93.87 %
  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: -1.61 (0.23), residues: 1083
  helix: -1.25 (0.19), residues: 528
  sheet: -0.75 (0.36), residues: 177
  loop : -0.58 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG A 183 
 TYR   0.018   0.004   TYR D 159 
 PHE   0.012   0.003   PHE D  32 
 HIS   0.015   0.003   HIS B 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00979 ( 7730)
  covalent geometry    : angle       0.70836 (10496)
  hydrogen bonds       : bond        0.20159 (  459)
  hydrogen bonds       : angle       8.35435 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.306 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 128
  average time/residue: 0.9091
  time to fit residues: 120.7927
Evaluate side-chains
  104 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 LYS
Chi-restraints excluded: chain D residue  179 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.106593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.090231 restraints weight = 100084.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.54
r_work: 0.3223 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7730  Z= 0.160
  Angle     :  0.521   4.593  10496  Z= 0.295
  Chirality :  0.043   0.147   1238
  Planarity :  0.004   0.029   1374
  Dihedral  :  5.029  29.715   1130
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.89 %
    Favored  : 89.49 %
  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:  1.24 (0.26), residues: 1083
  helix:  1.39 (0.22), residues: 538
  sheet: -0.08 (0.40), residues: 173
  loop :  0.68 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.008   0.001   TYR D 159 
 PHE   0.005   0.001   PHE B 207 
 HIS   0.004   0.001   HIS B 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7730)
  covalent geometry    : angle       0.52120 (10496)
  hydrogen bonds       : bond        0.05105 (  459)
  hydrogen bonds       : angle       5.26515 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.359 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 116
  average time/residue: 0.9057
  time to fit residues: 109.2761
Evaluate side-chains
  112 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain D residue  255 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 95 optimal weight:    0.4980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.107035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.091104 restraints weight = 88770.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.29
r_work: 0.3244 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7730  Z= 0.152
  Angle     :  0.480   4.603  10496  Z= 0.270
  Chirality :  0.042   0.140   1238
  Planarity :  0.003   0.025   1374
  Dihedral  :  4.613  19.211   1125
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.39 %
    Favored  : 88.36 %
  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:  2.08 (0.27), residues: 1083
  helix:  2.20 (0.22), residues: 538
  sheet: -0.13 (0.40), residues: 173
  loop :  1.12 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.008   0.002   TYR D 159 
 PHE   0.004   0.001   PHE D 207 
 HIS   0.006   0.001   HIS B 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7730)
  covalent geometry    : angle       0.48048 (10496)
  hydrogen bonds       : bond        0.04657 (  459)
  hydrogen bonds       : angle       4.92272 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.229 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 111
  average time/residue: 0.9362
  time to fit residues: 108.0097
Evaluate side-chains
  105 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  261 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.107741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.091445 restraints weight = 104415.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 3.50
r_work: 0.3216 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7730  Z= 0.179
  Angle     :  0.497   7.263  10496  Z= 0.277
  Chirality :  0.043   0.141   1238
  Planarity :  0.003   0.024   1374
  Dihedral  :  4.633  19.425   1125
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.26 %
    Favored  : 87.86 %
  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:  2.41 (0.27), residues: 1083
  helix:  2.49 (0.22), residues: 538
  sheet: -0.22 (0.40), residues: 176
  loop :  1.38 (0.38), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  55 
 TYR   0.008   0.002   TYR A 241 
 PHE   0.004   0.001   PHE D 207 
 HIS   0.008   0.002   HIS C 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 7730)
  covalent geometry    : angle       0.49663 (10496)
  hydrogen bonds       : bond        0.04820 (  459)
  hydrogen bonds       : angle       4.90863 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.289 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 105
  average time/residue: 0.9291
  time to fit residues: 101.3638
Evaluate side-chains
  102 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  261 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 93 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.106684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.090370 restraints weight = 103248.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.54
r_work: 0.3234 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8786
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7730  Z= 0.151
  Angle     :  0.473   5.213  10496  Z= 0.264
  Chirality :  0.042   0.137   1238
  Planarity :  0.003   0.024   1374
  Dihedral  :  4.488  18.997   1125
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 10.89 %
    Favored  : 87.73 %
  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:  2.65 (0.28), residues: 1083
  helix:  2.73 (0.22), residues: 538
  sheet: -0.18 (0.41), residues: 176
  loop :  1.48 (0.38), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  55 
 TYR   0.008   0.002   TYR C 159 
 PHE   0.003   0.001   PHE A  32 
 HIS   0.006   0.001   HIS A 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7730)
  covalent geometry    : angle       0.47262 (10496)
  hydrogen bonds       : bond        0.04475 (  459)
  hydrogen bonds       : angle       4.77397 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.286 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 112
  average time/residue: 0.8486
  time to fit residues: 98.8632
Evaluate side-chains
  108 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain D residue  255 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    0.2980
   chunk 84 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.107235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.091077 restraints weight = 105392.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 3.49
r_work: 0.3243 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7730  Z= 0.145
  Angle     :  0.460   5.224  10496  Z= 0.257
  Chirality :  0.042   0.136   1238
  Planarity :  0.003   0.024   1374
  Dihedral  :  4.414  18.906   1125
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.39 %
    Favored  : 87.48 %
  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:  2.81 (0.28), residues: 1083
  helix:  2.85 (0.22), residues: 539
  sheet: -0.16 (0.41), residues: 176
  loop :  1.60 (0.39), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  55 
 TYR   0.008   0.002   TYR B 159 
 PHE   0.004   0.001   PHE B 207 
 HIS   0.006   0.001   HIS C 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7730)
  covalent geometry    : angle       0.46022 (10496)
  hydrogen bonds       : bond        0.04394 (  459)
  hydrogen bonds       : angle       4.71898 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.271 
Fit side-chains
  outliers start: 4
  outliers final: 5
  residues processed: 110
  average time/residue: 0.8346
  time to fit residues: 95.5728
Evaluate side-chains
  108 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain D residue  255 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0870
   chunk 71 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.108054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.092031 restraints weight = 102429.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 3.45
r_work: 0.3260 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8767
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7730  Z= 0.129
  Angle     :  0.447   4.647  10496  Z= 0.249
  Chirality :  0.042   0.133   1238
  Planarity :  0.003   0.023   1374
  Dihedral  :  4.307  18.529   1125
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.64 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.94 (0.28), residues: 1083
  helix:  2.97 (0.22), residues: 540
  sheet: -0.09 (0.41), residues: 175
  loop :  1.62 (0.39), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.007   0.002   TYR B 159 
 PHE   0.004   0.001   PHE C 260 
 HIS   0.005   0.001   HIS C 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7730)
  covalent geometry    : angle       0.44656 (10496)
  hydrogen bonds       : bond        0.04180 (  459)
  hydrogen bonds       : angle       4.63982 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.302 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 110
  average time/residue: 0.8508
  time to fit residues: 97.3783
Evaluate side-chains
  108 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain D residue  255 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 40 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.106613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.090375 restraints weight = 105760.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.51
r_work: 0.3228 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7730  Z= 0.166
  Angle     :  0.478   4.673  10496  Z= 0.266
  Chirality :  0.043   0.137   1238
  Planarity :  0.003   0.023   1374
  Dihedral  :  4.435  19.114   1125
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.51 %
    Favored  : 87.23 %
  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:  2.89 (0.28), residues: 1083
  helix:  2.90 (0.22), residues: 541
  sheet: -0.16 (0.41), residues: 177
  loop :  1.69 (0.39), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 113 
 TYR   0.008   0.002   TYR C 241 
 PHE   0.004   0.001   PHE A 207 
 HIS   0.008   0.001   HIS C 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 7730)
  covalent geometry    : angle       0.47819 (10496)
  hydrogen bonds       : bond        0.04611 (  459)
  hydrogen bonds       : angle       4.77163 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.312 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 109
  average time/residue: 0.9028
  time to fit residues: 102.5063
Evaluate side-chains
  108 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain D residue  255 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 36 optimal weight:    0.2980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.108538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.092271 restraints weight = 101330.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 3.47
r_work: 0.3270 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7730  Z= 0.121
  Angle     :  0.442   4.644  10496  Z= 0.245
  Chirality :  0.041   0.133   1238
  Planarity :  0.002   0.023   1374
  Dihedral  :  4.253  18.394   1125
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.64 %
    Favored  : 87.23 %
  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:  3.06 (0.28), residues: 1083
  helix:  3.06 (0.22), residues: 541
  sheet: -0.05 (0.41), residues: 175
  loop :  1.70 (0.39), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.007   0.002   TYR D 241 
 PHE   0.003   0.001   PHE C 260 
 HIS   0.005   0.001   HIS B 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7730)
  covalent geometry    : angle       0.44151 (10496)
  hydrogen bonds       : bond        0.04050 (  459)
  hydrogen bonds       : angle       4.59331 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 0.308 
Fit side-chains
  outliers start: 4
  outliers final: 5
  residues processed: 113
  average time/residue: 0.9131
  time to fit residues: 107.1641
Evaluate side-chains
  112 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain D residue  255 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 97 optimal weight:    0.0570
   chunk 16 optimal weight:    0.5980
   chunk 96 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8902

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

Flipped N/Q/H residues before XYZ refinement:
C  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.106943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.090888 restraints weight = 96355.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.37
r_work: 0.3244 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7730  Z= 0.159
  Angle     :  0.467   4.678  10496  Z= 0.259
  Chirality :  0.042   0.135   1238
  Planarity :  0.003   0.023   1374
  Dihedral  :  4.365  19.108   1125
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.89 %
    Favored  : 86.98 %
  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:  3.01 (0.28), residues: 1083
  helix:  3.01 (0.22), residues: 541
  sheet: -0.13 (0.41), residues: 177
  loop :  1.74 (0.39), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.008   0.002   TYR C 241 
 PHE   0.003   0.001   PHE C  32 
 HIS   0.007   0.001   HIS C 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7730)
  covalent geometry    : angle       0.46656 (10496)
  hydrogen bonds       : bond        0.04486 (  459)
  hydrogen bonds       : angle       4.72268 ( 1327)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.218 
Fit side-chains
  outliers start: 4
  outliers final: 5
  residues processed: 111
  average time/residue: 0.9029
  time to fit residues: 104.1461
Evaluate side-chains
  113 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  261 ILE
Chi-restraints excluded: chain C residue  255 VAL
Chi-restraints excluded: chain D residue  255 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 71 optimal weight:    3.9990
   chunk 84 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0570
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.108366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.092182 restraints weight = 98660.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.43
r_work: 0.3268 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7730  Z= 0.125
  Angle     :  0.448   6.160  10496  Z= 0.248
  Chirality :  0.041   0.132   1238
  Planarity :  0.002   0.023   1374
  Dihedral  :  4.234  18.411   1125
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.02 %
    Favored  : 86.86 %
  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:  3.13 (0.28), residues: 1083
  helix:  3.12 (0.22), residues: 541
  sheet: -0.07 (0.41), residues: 176
  loop :  1.76 (0.39), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  55 
 TYR   0.007   0.002   TYR A 159 
 PHE   0.003   0.001   PHE C 260 
 HIS   0.005   0.001   HIS D 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7730)
  covalent geometry    : angle       0.44841 (10496)
  hydrogen bonds       : bond        0.04086 (  459)
  hydrogen bonds       : angle       4.59148 ( 1327)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4217.25 seconds
wall clock time: 72 minutes 28.29 seconds (4348.29 seconds total)