Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 13:30:05 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/04_2023/7sfk_25091_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/04_2023/7sfk_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_25091/04_2023/7sfk_25091.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/04_2023/7sfk_25091.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/04_2023/7sfk_25091_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfk_25091/04_2023/7sfk_25091_updated.pdb"
  }
  resolution = 2.74
  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
-------------------------------------------------------------------------------
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-1.21rc1-4938/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: 155
          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: 125
          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: 185
          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: 4.59, per 1000 atoms: 0.62
  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: 3.27
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.47
  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: 1.87

  Time building geometry restraints manager: 3.51 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: 4176
       35.68 -    71.36: 90
       71.36 -   107.04: 12
      107.04 -   142.72: 6
      142.72 -   178.40: 6
  Dihedral angle restraints: 4290
    sinusoidal: 1815
      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 4287 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:             0.660
  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:          3.020
  Check model and map are aligned:         0.110
  Set scattering table:                    0.060
  Process input model:                     22.390
  Find NCS groups from input model:        0.470
  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:11.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.920
-------------------------------------------------------------------------------
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  : 18.019 178.399   2724
  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 %
  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

*********************** 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  : 0.779 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 101
  average time/residue: 0.9962
  time to fit residues: 107.6896
Evaluate side-chains
  79 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.813 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 0
  time to fit residues: 1.0043
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   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:    0.7780

-------------------------------------------------------------------------------
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: 0.8114
moved from start:          0.1277

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= 0.173
  Angle     :  0.474   4.638  10167  Z= 0.271
  Chirality :  0.037   0.118   1011
  Planarity :  0.007   0.046   1242
  Dihedral  : 14.969 134.517   1269
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer Outliers :  0.71 %
  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:  1.84 (0.27), residues: 843
  helix:  1.40 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.11 (0.35), residues: 267

*********************** 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  : 0.841 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 90
  average time/residue: 1.0719
  time to fit residues: 102.9838
Evaluate side-chains
  88 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.751 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.0565
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   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:    0.9980
   chunk 61 optimal weight:    6.9990
   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   9 GLN
C  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7572  Z= 0.163
  Angle     :  0.455   5.409  10167  Z= 0.256
  Chirality :  0.037   0.120   1011
  Planarity :  0.007   0.048   1242
  Dihedral  : 12.263 114.135   1269
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer Outliers :  0.71 %
  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:  1.45 (0.28), residues: 843
  helix:  1.03 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.13 (0.35), residues: 267

*********************** 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
  89 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.830 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 88
  average time/residue: 1.1257
  time to fit residues: 106.0244
Evaluate side-chains
  85 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.856 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.1276
  time to fit residues: 1.4523
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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: 0.8191
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7572  Z= 0.226
  Angle     :  0.501   5.280  10167  Z= 0.278
  Chirality :  0.039   0.122   1011
  Planarity :  0.007   0.051   1242
  Dihedral  : 12.615 114.959   1269
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer Outliers :  0.85 %
  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:  1.19 (0.27), residues: 843
  helix:  0.82 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  1.07 (0.35), residues: 270

*********************** 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
  97 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.837 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 94
  average time/residue: 1.0652
  time to fit residues: 106.9809
Evaluate side-chains
  90 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.747 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 3
  residues processed: 2
  average time/residue: 0.1070
  time to fit residues: 1.3367
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0570
   overall best weight:    1.5902

-------------------------------------------------------------------------------
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: 0.8218
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7572  Z= 0.269
  Angle     :  0.530   5.264  10167  Z= 0.291
  Chirality :  0.040   0.124   1011
  Planarity :  0.007   0.052   1242
  Dihedral  : 13.126 115.213   1269
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer Outliers :  0.71 %
  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:  0.95 (0.27), residues: 843
  helix:  0.64 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.98 (0.34), residues: 270

*********************** 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
  96 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.741 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 94
  average time/residue: 1.0612
  time to fit residues: 106.6699
Evaluate side-chains
  91 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.811 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 3
  residues processed: 2
  average time/residue: 0.1208
  time to fit residues: 1.4798
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  78 ASN
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: 0.8229
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7572  Z= 0.288
  Angle     :  0.541   5.160  10167  Z= 0.297
  Chirality :  0.041   0.127   1011
  Planarity :  0.007   0.053   1242
  Dihedral  : 13.354 115.068   1269
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer Outliers :  1.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 843
  helix:  0.51 (0.21), residues: 573
  sheet:  None (None), residues: 0
  loop :  0.90 (0.35), residues: 270

*********************** 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
  101 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.799 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 99
  average time/residue: 1.0881
  time to fit residues: 114.8303
Evaluate side-chains
  91 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.814 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 1
  average time/residue: 0.1079
  time to fit residues: 1.2819
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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
C  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7572  Z= 0.178
  Angle     :  0.468   5.259  10167  Z= 0.263
  Chirality :  0.037   0.123   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 12.215 114.187   1269
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer Outliers :  0.71 %
  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:  0.99 (0.28), residues: 843
  helix:  0.63 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.09 (0.36), residues: 267

*********************** 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
  97 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.803 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 96
  average time/residue: 1.0916
  time to fit residues: 111.8142
Evaluate side-chains
  93 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.845 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 2
  residues processed: 0
  time to fit residues: 1.1472
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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: 0.8190
moved from start:          0.2240

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= 0.194
  Angle     :  0.480   5.306  10167  Z= 0.268
  Chirality :  0.038   0.124   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 12.251 114.792   1269
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer Outliers :  0.57 %
  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:  0.99 (0.28), residues: 843
  helix:  0.62 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.13 (0.36), residues: 267

*********************** 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
  95 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.799 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 94
  average time/residue: 1.0917
  time to fit residues: 109.5855
Evaluate side-chains
  90 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.810 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 2
  residues processed: 1
  average time/residue: 0.1125
  time to fit residues: 1.2511
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 48 optimal weight:    8.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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: 0.8176
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7572  Z= 0.178
  Angle     :  0.466   5.368  10167  Z= 0.261
  Chirality :  0.037   0.123   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 12.041 114.932   1269
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer Outliers :  0.57 %
  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:  1.06 (0.28), residues: 843
  helix:  0.67 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.15 (0.36), residues: 267

*********************** 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
  94 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.699 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 92
  average time/residue: 1.1616
  time to fit residues: 113.7113
Evaluate side-chains
  90 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.808 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 2
  residues processed: 0
  time to fit residues: 1.1608
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.1388

-------------------------------------------------------------------------------
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: 0.8197
moved from start:          0.2273

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= 0.210
  Angle     :  0.490   5.374  10167  Z= 0.272
  Chirality :  0.038   0.125   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 12.319 115.091   1269
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer Outliers :  0.43 %
  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:  0.97 (0.28), residues: 843
  helix:  0.61 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.12 (0.36), residues: 267

********************** 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
  91 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.759 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 90
  average time/residue: 1.1282
  time to fit residues: 108.1477
Evaluate side-chains
  89 residues out of total 702 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.827 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 2
  residues processed: 1
  average time/residue: 0.1152
  time to fit residues: 1.3131
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.141120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120234 restraints weight = 6979.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.11
r_work: 0.3098 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7572  Z= 0.173
  Angle     :  0.463   5.414  10167  Z= 0.260
  Chirality :  0.037   0.123   1011
  Planarity :  0.007   0.050   1242
  Dihedral  : 11.992 115.008   1269
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer Outliers :  0.43 %
  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:  1.08 (0.28), residues: 843
  helix:  0.69 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop :  1.16 (0.36), residues: 267

===============================================================================
Job complete
usr+sys time: 2338.08 seconds
wall clock time: 42 minutes 25.75 seconds (2545.75 seconds total)