Starting phenix.real_space_refine
on Mon Mar 11 06:43:08 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/03_2024/7sfk_25091_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/03_2024/7sfk_25091.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/03_2024/7sfk_25091.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/03_2024/7sfk_25091.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/03_2024/7sfk_25091_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/03_2024/7sfk_25091_updated.pdb"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.202
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      48      5.16       5
     C    4971      2.51       5
     N    1098      2.21       5
     O    1299      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   50": "OE1" <-> "OE2"
    Residue "A PHE  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  126": "OD1" <-> "OD2"
    Residue "A GLU  158": "OE1" <-> "OE2"
    Residue "A ASP  241": "OD1" <-> "OD2"
    Residue "B GLU   50": "OE1" <-> "OE2"
    Residue "B PHE  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  126": "OD1" <-> "OD2"
    Residue "B GLU  158": "OE1" <-> "OE2"
    Residue "B ASP  241": "OD1" <-> "OD2"
    Residue "C GLU   50": "OE1" <-> "OE2"
    Residue "C PHE  104": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  126": "OD1" <-> "OD2"
    Residue "C GLU  158": "OE1" <-> "OE2"
    Residue "C ASP  241": "OD1" <-> "OD2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7419
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2299
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'AYA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 155
          Unusual residues: {'PEE': 7, 'RET': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 223
          Unresolved non-hydrogen angles: 255
          Unresolved non-hydrogen dihedrals: 215
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 5, 'PEE:plan-2': 3}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 146
          Unusual residues: {'PEE': 6, 'RET': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 181
          Unresolved non-hydrogen angles: 207
          Unresolved non-hydrogen dihedrals: 175
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 4, 'PEE:plan-2': 2}
          Unresolved non-hydrogen planarities: 25
    Chain: "C"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 164
          Unusual residues: {'PEE': 8, 'RET': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 265
          Unresolved non-hydrogen angles: 303
          Unresolved non-hydrogen dihedrals: 255
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 6, 'PEE:plan-2': 4}
          Unresolved non-hydrogen planarities: 41
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "C"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
  Time building chain proxies: 4.72, per 1000 atoms: 0.64
  Number of scatterers: 7419
  At special positions: 0
  Unit cell: (78.453, 79.59, 88.686, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       3     15.00
     O    1299      8.00
     N    1098      7.00
     C    4971      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  - 3.50
        Amino acid           : False - 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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      71.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 20
      No H-bonds generated for 'chain 'A' and resid 18 through 20'
    Processing helix  chain 'A' and resid 27 through 52
    Processing helix  chain 'A' and resid 64 through 67
      No H-bonds generated for 'chain 'A' and resid 64 through 67'
    Processing helix  chain 'A' and resid 69 through 94
      removed outlier: 4.477A  pdb=" N   ALA A  74 " --> pdb=" O   GLN A  71 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLY A  87 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 131
      Proline residue:  A 121  - end of helix
      removed outlier: 3.610A  pdb=" N   GLN A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 157
    Processing helix  chain 'A' and resid 161 through 199
      removed outlier: 5.166A  pdb=" N   ASN A 165 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A 166 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 232
      removed outlier: 3.736A  pdb=" N   HIS A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   VAL A 211 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   TRP A 223 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   ILE A 224 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   LEU A 225 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   PHE A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      Proline residue:  A 227  - end of helix
    Processing helix  chain 'A' and resid 242 through 268
      removed outlier: 3.601A  pdb=" N   GLU A 246 " --> pdb=" O   ASP A 242 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   CYS A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   TYR A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 284
      removed outlier: 3.705A  pdb=" N   GLY A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   HIS A 284 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 20
      No H-bonds generated for 'chain 'B' and resid 18 through 20'
    Processing helix  chain 'B' and resid 27 through 52
    Processing helix  chain 'B' and resid 64 through 67
      No H-bonds generated for 'chain 'B' and resid 64 through 67'
    Processing helix  chain 'B' and resid 69 through 94
      removed outlier: 4.477A  pdb=" N   ALA B  74 " --> pdb=" O   GLN B  71 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLY B  87 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 131
      Proline residue:  B 121  - end of helix
      removed outlier: 3.610A  pdb=" N   GLN B 130 " --> pdb=" O   ASP B 126 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LEU B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 157
    Processing helix  chain 'B' and resid 161 through 199
      removed outlier: 5.166A  pdb=" N   ASN B 165 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY B 166 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 232
      removed outlier: 3.736A  pdb=" N   HIS B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   VAL B 211 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   TRP B 223 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE B 224 " --> pdb=" O   SER B 220 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   LEU B 225 " --> pdb=" O   MET B 221 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   PHE B 226 " --> pdb=" O   LEU B 222 " (cutoff:3.500A)
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 242 through 268
      removed outlier: 3.600A  pdb=" N   GLU B 246 " --> pdb=" O   ASP B 242 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL B 247 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   CYS B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   TYR B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 284
      removed outlier: 3.706A  pdb=" N   GLY B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS B 284 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 20
      No H-bonds generated for 'chain 'C' and resid 18 through 20'
    Processing helix  chain 'C' and resid 27 through 52
    Processing helix  chain 'C' and resid 64 through 67
      No H-bonds generated for 'chain 'C' and resid 64 through 67'
    Processing helix  chain 'C' and resid 69 through 94
      removed outlier: 4.477A  pdb=" N   ALA C  74 " --> pdb=" O   GLN C  71 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLY C  87 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 131
      Proline residue:  C 121  - end of helix
      removed outlier: 3.610A  pdb=" N   GLN C 130 " --> pdb=" O   ASP C 126 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LEU C 131 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 157
    Processing helix  chain 'C' and resid 161 through 199
      removed outlier: 5.166A  pdb=" N   ASN C 165 " --> pdb=" O   ARG C 162 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY C 166 " --> pdb=" O   LEU C 163 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 232
      removed outlier: 3.736A  pdb=" N   HIS C 210 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   VAL C 211 " --> pdb=" O   HIS C 207 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   TRP C 223 " --> pdb=" O   PHE C 219 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   ILE C 224 " --> pdb=" O   SER C 220 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   LEU C 225 " --> pdb=" O   MET C 221 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   PHE C 226 " --> pdb=" O   LEU C 222 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
    Processing helix  chain 'C' and resid 242 through 268
      removed outlier: 3.600A  pdb=" N   GLU C 246 " --> pdb=" O   ASP C 242 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL C 247 " --> pdb=" O   ASN C 243 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   CYS C 259 " --> pdb=" O   VAL C 255 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   TYR C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 284
      removed outlier: 3.706A  pdb=" N   GLY C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS C 284 " --> pdb=" O   GLU C 280 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    765 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: 1.97

  Time building geometry restraints manager: 3.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2059
        1.34 -     1.45: 1517
        1.45 -     1.57: 3918
        1.57 -     1.69: 3
        1.69 -     1.81: 75
  Bond restraints: 7572
  Sorted by residual:
  bond pdb=" C30 PEE B 404 "
       pdb=" O5  PEE B 404 "
    ideal  model  delta    sigma   weight residual
    1.206  1.353 -0.147 2.00e-02 2.50e+03 5.40e+01
  bond pdb=" C30 PEE A 404 "
       pdb=" O5  PEE A 404 "
    ideal  model  delta    sigma   weight residual
    1.206  1.353 -0.147 2.00e-02 2.50e+03 5.40e+01
  bond pdb=" C30 PEE C 405 "
       pdb=" O5  PEE C 405 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" C30 PEE B 402 "
       pdb=" O5  PEE B 402 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" C30 PEE C 403 "
       pdb=" O5  PEE C 403 "
    ideal  model  delta    sigma   weight residual
    1.206  1.352 -0.146 2.00e-02 2.50e+03 5.33e+01
  ... (remaining 7567 not shown)

  Histogram of bond angle deviations from ideal:
       98.71 -   105.77: 107
      105.77 -   112.84: 3832
      112.84 -   119.91: 2642
      119.91 -   126.98: 3459
      126.98 -   134.04: 127
  Bond angle restraints: 10167
  Sorted by residual:
  angle pdb=" C11 PEE C 402 "
        pdb=" C10 PEE C 402 "
        pdb=" O2  PEE C 402 "
      ideal   model   delta    sigma   weight residual
     111.70  123.94  -12.24 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C11 PEE B 401 "
        pdb=" C10 PEE B 401 "
        pdb=" O2  PEE B 401 "
      ideal   model   delta    sigma   weight residual
     111.70  123.93  -12.23 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C11 PEE A 401 "
        pdb=" C10 PEE A 401 "
        pdb=" O2  PEE A 401 "
      ideal   model   delta    sigma   weight residual
     111.70  123.92  -12.22 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C31 PEE B 404 "
        pdb=" C30 PEE B 404 "
        pdb=" O3  PEE B 404 "
      ideal   model   delta    sigma   weight residual
     111.87  123.95  -12.08 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" C31 PEE A 404 "
        pdb=" C30 PEE A 404 "
        pdb=" O3  PEE A 404 "
      ideal   model   delta    sigma   weight residual
     111.87  123.91  -12.04 3.00e+00 1.11e-01 1.61e+01
  ... (remaining 10162 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 4197
       35.68 -    71.36: 99
       71.36 -   107.04: 12
      107.04 -   142.72: 6
      142.72 -   178.40: 6
  Dihedral angle restraints: 4320
    sinusoidal: 1845
      harmonic: 2475
  Sorted by residual:
  dihedral pdb=" C32 PEE C 404 "
           pdb=" C30 PEE C 404 "
           pdb=" C31 PEE C 404 "
           pdb=" O3  PEE C 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16  -20.44 -178.40     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C32 PEE B 403 "
           pdb=" C30 PEE B 403 "
           pdb=" C31 PEE B 403 "
           pdb=" O3  PEE B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16  -20.49 -178.35     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C32 PEE A 403 "
           pdb=" C30 PEE A 403 "
           pdb=" C31 PEE A 403 "
           pdb=" O3  PEE A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.16  -20.54 -178.30     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 4317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 633
       0.033 -    0.065: 282
       0.065 -    0.098: 78
       0.098 -    0.130: 15
       0.130 -    0.163: 3
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" C2  PEE A 406 "
            pdb=" C1  PEE A 406 "
            pdb=" C3  PEE A 406 "
            pdb=" O2  PEE A 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.49    0.16 2.00e-01 2.50e+01 6.63e-01
  chirality pdb=" C2  PEE B 406 "
            pdb=" C1  PEE B 406 "
            pdb=" C3  PEE B 406 "
            pdb=" O2  PEE B 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.49    0.16 2.00e-01 2.50e+01 6.52e-01
  chirality pdb=" C2  PEE C 408 "
            pdb=" C1  PEE C 408 "
            pdb=" C3  PEE C 408 "
            pdb=" O2  PEE C 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.48    0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 1242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 160 "    0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO B 161 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 161 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 161 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 160 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO A 161 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 161 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 161 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 160 "   -0.033 5.00e-02 4.00e+02   4.95e-02 3.93e+00
        pdb=" N   PRO C 161 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 161 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 161 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1239 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1880
        2.79 -     3.32: 6680
        3.32 -     3.85: 12450
        3.85 -     4.37: 15216
        4.37 -     4.90: 26101
  Nonbonded interactions: 62327
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 107 "
            pdb=" O   HOH C 501 "
     model   vdw
     2.265 2.440
  nonbonded pdb=" O   GLY B 107 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.273 2.440
  nonbonded pdb=" O   GLY A 107 "
            pdb=" O   HOH A 501 "
     model   vdw
     2.276 2.440
  nonbonded pdb=" OD1 ASN A 110 "
            pdb=" O   HOH A 502 "
     model   vdw
     2.321 2.440
  nonbonded pdb=" OD1 ASN B 110 "
            pdb=" O   HOH B 502 "
     model   vdw
     2.323 2.440
  ... (remaining 62322 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ 
ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37  \ 
or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 
5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ 
 or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ 
r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 
45 or name C46 or name C47))))
  selection = (chain 'B' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ 
ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37  \ 
or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 
5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ 
 or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ 
r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 
45 or name C46 or name C47))))
  selection = (chain 'C' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ 
ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37  \ 
or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 
5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ 
 or name C41 or name C42)) or resid 406))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.550
  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:          2.750
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     24.360
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.040
  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:12.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
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      :  0.008   0.147   7572  Z= 0.489
  Angle     :  0.966  12.239  10167  Z= 0.401
  Chirality :  0.039   0.163   1011
  Planarity :  0.005   0.050   1242
  Dihedral  : 18.398 178.399   2754
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.71 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.28), residues: 843
  helix:  1.80 (0.20), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.31 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 177 
 HIS   0.003   0.001   HIS B  96 
 PHE   0.016   0.001   PHE B 176 
 TYR   0.013   0.002   TYR B 271 
 ARG   0.002   0.000   ARG B 132 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A   68 GLN cc_start: 0.8415 (mp10) cc_final: 0.8188 (mp10)
REVERT: A  148 MET cc_start: 0.7947 (ttp) cc_final: 0.7508 (ttp)
REVERT: A  180 PHE cc_start: 0.8039 (t80) cc_final: 0.7823 (t80)
REVERT: B  148 MET cc_start: 0.7888 (ttp) cc_final: 0.7637 (ttp)
REVERT: C  148 MET cc_start: 0.8100 (ttp) cc_final: 0.7876 (ttp)
  outliers start: 3
  outliers final: 1
  residues processed: 101
  average time/residue: 1.0191
  time to fit residues: 109.8576
Evaluate side-chains
  81 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
C   9 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7572  Z= 0.174
  Angle     :  0.482   5.129  10167  Z= 0.274
  Chirality :  0.037   0.119   1011
  Planarity :  0.007   0.046   1242
  Dihedral  : 15.042 136.181   1301
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.70 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.27), residues: 843
  helix:  1.43 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.11 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 177 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.012   0.001   PHE C 155 
 TYR   0.015   0.001   TYR B 271 
 ARG   0.002   0.000   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7450 (mmtm)
REVERT: A   68 GLN cc_start: 0.8426 (mp10) cc_final: 0.8078 (mp10)
REVERT: A  148 MET cc_start: 0.7950 (ttp) cc_final: 0.7562 (ttp)
REVERT: A  272 ASP cc_start: 0.7223 (p0) cc_final: 0.7011 (p0)
  outliers start: 5
  outliers final: 4
  residues processed: 90
  average time/residue: 1.0907
  time to fit residues: 104.7238
Evaluate side-chains
  87 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7572  Z= 0.195
  Angle     :  0.483   5.025  10167  Z= 0.270
  Chirality :  0.038   0.118   1011
  Planarity :  0.007   0.049   1242
  Dihedral  : 12.861 114.631   1301
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.12 %
    Favored  : 91.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.27), residues: 843
  helix:  0.98 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.10 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  19 
 HIS   0.006   0.001   HIS B  96 
 PHE   0.019   0.002   PHE C 155 
 TYR   0.018   0.002   TYR C 271 
 ARG   0.001   0.000   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7584 (mmtm)
REVERT: A  148 MET cc_start: 0.7999 (ttp) cc_final: 0.7639 (ttp)
REVERT: B   50 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7629 (tt0)
  outliers start: 5
  outliers final: 2
  residues processed: 88
  average time/residue: 1.2446
  time to fit residues: 116.8914
Evaluate side-chains
  84 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  194 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 57 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 76 optimal weight:    8.9990
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7572  Z= 0.182
  Angle     :  0.464   5.285  10167  Z= 0.260
  Chirality :  0.037   0.120   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 11.956 114.605   1299
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.83 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.28), residues: 843
  helix:  0.87 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.14 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 177 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.019   0.001   PHE C 155 
 TYR   0.015   0.001   TYR B 271 
 ARG   0.001   0.000   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7660 (mmtm)
REVERT: A  148 MET cc_start: 0.8010 (ttp) cc_final: 0.7641 (ttp)
REVERT: B   50 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7479 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 87
  average time/residue: 1.1373
  time to fit residues: 105.6418
Evaluate side-chains
  85 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0170
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    2.4026

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B 192 GLN
C   9 GLN
C  68 GLN
C  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7572  Z= 0.381
  Angle     :  0.608   5.538  10167  Z= 0.328
  Chirality :  0.044   0.127   1011
  Planarity :  0.007   0.054   1242
  Dihedral  : 14.037 115.975   1299
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.68 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.27), residues: 843
  helix:  0.47 (0.20), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.88 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP B  19 
 HIS   0.009   0.001   HIS B  96 
 PHE   0.033   0.003   PHE C 155 
 TYR   0.027   0.002   TYR A 271 
 ARG   0.004   0.001   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7692 (mmtm)
REVERT: A  148 MET cc_start: 0.8017 (ttp) cc_final: 0.7609 (ttp)
REVERT: B   92 ASP cc_start: 0.7665 (m-30) cc_final: 0.7425 (m-30)
REVERT: B  272 ASP cc_start: 0.7978 (p0) cc_final: 0.7504 (p0)
REVERT: C  221 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6907 (tmm)
  outliers start: 10
  outliers final: 4
  residues processed: 99
  average time/residue: 1.2366
  time to fit residues: 129.6857
Evaluate side-chains
  93 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  221 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
C   9 GLN
C  68 GLN
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7572  Z= 0.165
  Angle     :  0.463   5.248  10167  Z= 0.260
  Chirality :  0.037   0.123   1011
  Planarity :  0.007   0.051   1242
  Dihedral  : 12.338 113.839   1299
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 13.11 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.28), residues: 843
  helix:  0.67 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.07 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  19 
 HIS   0.004   0.001   HIS B  96 
 PHE   0.010   0.001   PHE A 155 
 TYR   0.012   0.001   TYR C  85 
 ARG   0.001   0.000   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7485 (mmtm)
REVERT: A  148 MET cc_start: 0.8076 (ttp) cc_final: 0.7720 (ttp)
REVERT: A  272 ASP cc_start: 0.7376 (p0) cc_final: 0.7147 (p0)
REVERT: B   50 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7589 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 91
  average time/residue: 1.1263
  time to fit residues: 109.0969
Evaluate side-chains
  89 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7572  Z= 0.167
  Angle     :  0.457   5.270  10167  Z= 0.256
  Chirality :  0.037   0.123   1011
  Planarity :  0.006   0.050   1242
  Dihedral  : 11.866 114.476   1299
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.25 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.28), residues: 843
  helix:  0.74 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.16 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 177 
 HIS   0.004   0.001   HIS B  96 
 PHE   0.010   0.001   PHE C 219 
 TYR   0.012   0.001   TYR C 271 
 ARG   0.001   0.000   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7486 (mmtm)
REVERT: A  148 MET cc_start: 0.8063 (ttp) cc_final: 0.7769 (ttp)
REVERT: B  272 ASP cc_start: 0.7760 (p0) cc_final: 0.7300 (p0)
  outliers start: 6
  outliers final: 2
  residues processed: 90
  average time/residue: 1.1472
  time to fit residues: 109.7205
Evaluate side-chains
  86 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7572  Z= 0.191
  Angle     :  0.476   5.405  10167  Z= 0.265
  Chirality :  0.038   0.123   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 12.050 114.887   1299
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.25 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.28), residues: 843
  helix:  0.69 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.14 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  19 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.011   0.001   PHE C 219 
 TYR   0.014   0.001   TYR B 271 
 ARG   0.001   0.000   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7526 (mmtm)
REVERT: A  148 MET cc_start: 0.8079 (ttp) cc_final: 0.7748 (ttp)
REVERT: B   50 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7565 (tt0)
REVERT: B  122 MET cc_start: 0.7796 (mtm) cc_final: 0.7507 (mtm)
REVERT: B  272 ASP cc_start: 0.7785 (p0) cc_final: 0.7316 (p0)
  outliers start: 5
  outliers final: 2
  residues processed: 92
  average time/residue: 1.2020
  time to fit residues: 117.4598
Evaluate side-chains
  88 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7572  Z= 0.352
  Angle     :  0.589   5.276  10167  Z= 0.318
  Chirality :  0.043   0.127   1011
  Planarity :  0.007   0.051   1242
  Dihedral  : 13.443 115.876   1299
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.53 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 843
  helix:  0.44 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.92 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B  52 
 HIS   0.009   0.001   HIS B  96 
 PHE   0.024   0.002   PHE A 155 
 TYR   0.026   0.002   TYR B 271 
 ARG   0.003   0.001   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7688 (tm-30)
REVERT: A   59 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7552 (mmtm)
REVERT: A  148 MET cc_start: 0.8046 (ttp) cc_final: 0.7626 (ttp)
REVERT: B  272 ASP cc_start: 0.7920 (p0) cc_final: 0.7487 (p0)
REVERT: C  221 MET cc_start: 0.7102 (tmt) cc_final: 0.6891 (tmm)
  outliers start: 5
  outliers final: 2
  residues processed: 91
  average time/residue: 1.1802
  time to fit residues: 113.9888
Evaluate side-chains
  88 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7572  Z= 0.211
  Angle     :  0.497   5.111  10167  Z= 0.276
  Chirality :  0.038   0.125   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 12.682 114.837   1299
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 14.39 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 843
  helix:  0.55 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  1.00 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  52 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.012   0.001   PHE C 219 
 TYR   0.016   0.002   TYR C 271 
 ARG   0.002   0.000   ARG B 268 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7508 (mmtm)
REVERT: A  148 MET cc_start: 0.8093 (ttp) cc_final: 0.7760 (ttp)
REVERT: B  122 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7596 (mtm)
REVERT: B  272 ASP cc_start: 0.7850 (p0) cc_final: 0.7425 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 87
  average time/residue: 1.1732
  time to fit residues: 109.0405
Evaluate side-chains
  86 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain C residue  194 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 12 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
C   9 GLN
C  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.138896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.114756 restraints weight = 7112.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.13
r_work: 0.3109 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7572  Z= 0.154
  Angle     :  0.450   5.400  10167  Z= 0.255
  Chirality :  0.037   0.122   1011
  Planarity :  0.006   0.050   1242
  Dihedral  : 11.982 114.200   1299
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 14.53 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.28), residues: 843
  helix:  0.68 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.16 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  52 
 HIS   0.003   0.000   HIS B  96 
 PHE   0.009   0.001   PHE C 219 
 TYR   0.012   0.001   TYR C  85 
 ARG   0.001   0.000   ARG B 268 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2462.34 seconds
wall clock time: 44 minutes 33.46 seconds (2673.46 seconds total)