Starting phenix.real_space_refine
on Wed Sep 17 11:41:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g3d_50994/09_2025/9g3d_50994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g3d_50994/09_2025/9g3d_50994.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g3d_50994/09_2025/9g3d_50994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g3d_50994/09_2025/9g3d_50994.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g3d_50994/09_2025/9g3d_50994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g3d_50994/09_2025/9g3d_50994.map"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.011 sd=   0.124
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       2      5.49       5
     S      28      5.16       5
     C    5448      2.51       5
     N    1322      2.21       5
     O    1410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8210
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3155
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 14, 'TRANS': 373}
    Chain: "B"
      Number of atoms: 3200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3200
          Classifications: {'peptide': 393}
          Link IDs: {'PTRANS': 14, 'TRANS': 378}
    Chain: "C"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 887
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "D"
      Number of atoms: 878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 878
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 45
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 45
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
  Time building chain proxies: 1.77, per 1000 atoms: 0.22
  Number of scatterers: 8210
  At special positions: 0
  Unit cell: (69.496, 88.914, 119.574, 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      28     16.00
     P       2     15.00
     O    1410      8.00
     N    1322      7.00
     C    5448      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  28 " - pdb=" SG  CYS C 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  28 " - pdb=" SG  CYS D 102 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 394.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      68.8% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 28
      removed outlier: 3.812A  pdb=" N   LEU A  14 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 40
      removed outlier: 3.728A  pdb=" N   ASP A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 53
      removed outlier: 3.558A  pdb=" N   ARG A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   TRP A  53 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 79
      removed outlier: 4.085A  pdb=" N   PHE A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 88 through 125
      removed outlier: 4.169A  pdb=" N   ALA A 113 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
      removed outlier: 3.885A  pdb=" N   SER A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 175
      removed outlier: 3.735A  pdb=" N   GLU A 137 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ILE A 147 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER A 160 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET A 175 " --> pdb=" O   ASN A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 186 through 226
      removed outlier: 4.443A  pdb=" N   ASP A 194 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   THR A 195 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   MET A 196 " --> pdb=" O   GLN A 192 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 197 " --> pdb=" O   GLU A 193 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'A' and resid 227 through 230
      removed outlier: 3.575A  pdb=" N   VAL A 230 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 227 through 230'
    Processing helix  chain 'A' and resid 241 through 262
    Processing helix  chain 'A' and resid 263 through 288
      removed outlier: 4.456A  pdb=" N   GLY A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASP A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 345
      removed outlier: 3.678A  pdb=" N   LEU A 312 " --> pdb=" O   ASN A 308 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   MET A 317 " --> pdb=" O   TYR A 313 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   VAL A 332 " --> pdb=" O   GLN A 328 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   GLY A 334 " --> pdb=" O   ASP A 330 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   LEU A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
      Proline residue:  A 340  - end of helix
    Processing helix  chain 'A' and resid 348 through 392
      removed outlier: 4.368A  pdb=" N   LEU A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ILE A 370 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TRP A 373 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   THR A 374 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   THR A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL A 377 " --> pdb=" O   TRP A 373 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   GLU A 378 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 28
      removed outlier: 3.847A  pdb=" N   LEU B  14 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 40
    Processing helix  chain 'B' and resid 50 through 53
      removed outlier: 3.781A  pdb=" N   TRP B  53 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 50 through 53'
    Processing helix  chain 'B' and resid 54 through 79
    Processing helix  chain 'B' and resid 83 through 88
      removed outlier: 3.636A  pdb=" N   ILE B  88 " --> pdb=" O   GLN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 125
      removed outlier: 4.150A  pdb=" N   ALA B 113 " --> pdb=" O   ASN B 109 " (cutoff:3.500A)
      Proline residue:  B 114  - end of helix
      removed outlier: 3.883A  pdb=" N   SER B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 175
      removed outlier: 3.740A  pdb=" N   GLU B 137 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLY B 143 " --> pdb=" O   GLY B 139 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ILE B 147 " --> pdb=" O   GLY B 143 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER B 152 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B 160 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TYR B 173 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.535A  pdb=" N   VAL B 191 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 227
      removed outlier: 4.306A  pdb=" N   MET B 196 " --> pdb=" O   GLN B 192 " (cutoff:3.500A)
      Proline residue:  B 221  - end of helix
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 241 through 262
    Processing helix  chain 'B' and resid 263 through 290
      removed outlier: 4.375A  pdb=" N   GLY B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASP B 288 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 330
      removed outlier: 3.725A  pdb=" N   LEU B 312 " --> pdb=" O   ASN B 308 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   MET B 317 " --> pdb=" O   TYR B 313 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   TYR B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 345
      removed outlier: 3.598A  pdb=" N   LEU B 338 " --> pdb=" O   GLY B 334 " (cutoff:3.500A)
      Proline residue:  B 340  - end of helix
    Processing helix  chain 'B' and resid 348 through 392
      removed outlier: 3.723A  pdb=" N   THR B 375 " --> pdb=" O   ASN B 371 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL B 377 " --> pdb=" O   TRP B 373 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   GLU B 378 " --> pdb=" O   THR B 374 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   GLU B 392 " --> pdb=" O   SER B 388 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 11
    Processing sheet with id=AA2, first strand: chain 'C' and resid 18 through 19
      removed outlier: 7.335A  pdb=" N   VAL C  18 " --> pdb=" O   SER C 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 27
    Processing sheet with id=AA4, first strand: chain 'C' and resid 64 through 66
      removed outlier: 6.605A  pdb=" N   TRP C  42 " --> pdb=" O   VAL C  54 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ALA C  56 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   MET C  40 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 66
      removed outlier: 6.605A  pdb=" N   TRP C  42 " --> pdb=" O   VAL C  54 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ALA C  56 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   MET C  40 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 19
      removed outlier: 3.558A  pdb=" N   GLY D  16 " --> pdb=" O   GLN D 116 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR D 118 " --> pdb=" O   GLY D  16 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER D 120 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   MET D  40 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ALA D  56 " --> pdb=" O   MET D  40 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   TRP D  42 " --> pdb=" O   VAL D  54 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 19
      removed outlier: 3.558A  pdb=" N   GLY D  16 " --> pdb=" O   GLN D 116 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR D 118 " --> pdb=" O   GLY D  16 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER D 120 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 23 through 27

    570 hydrogen bonds defined for protein.
    1671 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: 1.31

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1331
        1.33 -     1.45: 2533
        1.45 -     1.57: 4536
        1.57 -     1.69: 4
        1.69 -     1.82: 50
  Bond restraints: 8454
  Sorted by residual:
  bond pdb=" CA  PHE A  52 "
       pdb=" C   PHE A  52 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.022 1.80e-02 3.09e+03 1.43e+00
  bond pdb=" CB  MET B 205 "
       pdb=" CG  MET B 205 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.16e+00
  bond pdb=" CB  THR A 195 "
       pdb=" CG2 THR A 195 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.02e+00
  bond pdb=" SD  MET B 205 "
       pdb=" CE  MET B 205 "
    ideal  model  delta    sigma   weight residual
    1.791  1.769  0.022 2.50e-02 1.60e+03 7.40e-01
  bond pdb=" CG  MET B 205 "
       pdb=" SD  MET B 205 "
    ideal  model  delta    sigma   weight residual
    1.803  1.783  0.020 2.50e-02 1.60e+03 6.66e-01
  ... (remaining 8449 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 11367
        1.74 -     3.48: 115
        3.48 -     5.21: 15
        5.21 -     6.95: 7
        6.95 -     8.69: 2
  Bond angle restraints: 11506
  Sorted by residual:
  angle pdb=" CA  PHE A  52 "
        pdb=" C   PHE A  52 "
        pdb=" N   TRP A  53 "
      ideal   model   delta    sigma   weight residual
     118.27  113.86    4.41 1.59e+00 3.96e-01 7.70e+00
  angle pdb=" CB  MET A 196 "
        pdb=" CG  MET A 196 "
        pdb=" SD  MET A 196 "
      ideal   model   delta    sigma   weight residual
     112.70  121.01   -8.31 3.00e+00 1.11e-01 7.68e+00
  angle pdb=" CA  LEU B 181 "
        pdb=" CB  LEU B 181 "
        pdb=" CG  LEU B 181 "
      ideal   model   delta    sigma   weight residual
     116.30  124.99   -8.69 3.50e+00 8.16e-02 6.16e+00
  angle pdb=" N   GLN A 273 "
        pdb=" CA  GLN A 273 "
        pdb=" CB  GLN A 273 "
      ideal   model   delta    sigma   weight residual
     110.12  113.42   -3.30 1.47e+00 4.63e-01 5.02e+00
  angle pdb=" CA  ARG A 167 "
        pdb=" CB  ARG A 167 "
        pdb=" CG  ARG A 167 "
      ideal   model   delta    sigma   weight residual
     114.10  110.22    3.88 2.00e+00 2.50e-01 3.77e+00
  ... (remaining 11501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.40: 4623
       28.40 -    56.80: 189
       56.80 -    85.21: 7
       85.21 -   113.61: 3
      113.61 -   142.01: 2
  Dihedral angle restraints: 4824
    sinusoidal: 1884
      harmonic: 2940
  Sorted by residual:
  dihedral pdb=" C3  PGT B 501 "
           pdb=" C1  PGT B 501 "
           pdb=" C2  PGT B 501 "
           pdb=" O3P PGT B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -66.13   75.88 -142.01     1      3.00e+01 1.11e-03 1.91e+01
  dihedral pdb=" C3  PGT A 501 "
           pdb=" C1  PGT A 501 "
           pdb=" C2  PGT A 501 "
           pdb=" O3P PGT A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -66.13   75.20 -141.33     1      3.00e+01 1.11e-03 1.90e+01
  dihedral pdb=" CA  SER A  54 "
           pdb=" C   SER A  54 "
           pdb=" N   LEU A  55 "
           pdb=" CA  LEU A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 4821 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 782
       0.028 -    0.056: 301
       0.056 -    0.084: 119
       0.084 -    0.113: 47
       0.113 -    0.141: 11
  Chirality restraints: 1260
  Sorted by residual:
  chirality pdb=" CA  VAL C 106 "
            pdb=" N   VAL C 106 "
            pdb=" C   VAL C 106 "
            pdb=" CB  VAL C 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CA  PRO A 234 "
            pdb=" N   PRO A 234 "
            pdb=" C   PRO A 234 "
            pdb=" CB  PRO A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CB  VAL B 261 "
            pdb=" CA  VAL B 261 "
            pdb=" CG1 VAL B 261 "
            pdb=" CG2 VAL B 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.71e-01
  ... (remaining 1257 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 295 "   -0.040 5.00e-02 4.00e+02   5.99e-02 5.74e+00
        pdb=" N   PRO A 296 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 296 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 296 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 294 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO A 295 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 295 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 295 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 162 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   TYR A 162 "    0.025 2.00e-02 2.50e+03
        pdb=" O   TYR A 162 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A 163 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2041
        2.80 -     3.32: 7812
        3.32 -     3.85: 13619
        3.85 -     4.37: 15318
        4.37 -     4.90: 27689
  Nonbonded interactions: 66479
  Sorted by model distance:
  nonbonded pdb=" O   ILE D  36 "
            pdb=" OG  SER D  59 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   TRP A  83 "
            pdb=" OG  SER A  87 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   VAL C  35 "
            pdb=" NH2 ARG C  78 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   ILE C  36 "
            pdb=" OG  SER C  59 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   TRP B  83 "
            pdb=" OG  SER B  87 "
     model   vdw
     2.296 3.040
  ... (remaining 66474 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 6 through 393 or resid 501))
}
ncs_group {
  reference = (chain 'C' and resid 8 through 121)
  selection = chain 'D'
}

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:             1.540
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.000
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
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      :  0.003   0.033   8456  Z= 0.135
  Angle     :  0.491   8.690  11510  Z= 0.260
  Chirality :  0.038   0.141   1260
  Planarity :  0.004   0.060   1416
  Dihedral  : 14.815 142.009   2946
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.27), residues: 1002
  helix:  1.50 (0.20), residues: 653
  sheet: -0.43 (0.52), residues: 98
  loop : -1.40 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 167 
 TYR   0.016   0.001   TYR B 368 
 PHE   0.015   0.001   PHE A 389 
 TRP   0.008   0.001   TRP A  53 
 HIS   0.003   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8454)
  covalent geometry    : angle       0.49060 (11506)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       1.13718 (    4)
  hydrogen bonds       : bond        0.12118 (  554)
  hydrogen bonds       : angle       6.11768 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.315 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0984
  time to fit residues: 11.7171
Evaluate side-chains
  72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0670
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 ASN
C  38 ASN
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.166798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.127065 restraints weight = 9450.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.07
r_work: 0.3289 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8456  Z= 0.123
  Angle     :  0.484   8.317  11510  Z= 0.255
  Chirality :  0.039   0.143   1260
  Planarity :  0.004   0.056   1416
  Dihedral  :  8.088 137.511   1200
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  4.88 %
    Favored  : 94.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.27), residues: 1002
  helix:  2.05 (0.20), residues: 654
  sheet: -0.13 (0.55), residues: 94
  loop : -1.48 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  78 
 TYR   0.012   0.001   TYR B 368 
 PHE   0.034   0.001   PHE A 389 
 TRP   0.007   0.001   TRP A  53 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8454)
  covalent geometry    : angle       0.48356 (11506)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       1.08331 (    4)
  hydrogen bonds       : bond        0.04661 (  554)
  hydrogen bonds       : angle       4.15440 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  273 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7586 (mp10)
  outliers start: 4
  outliers final: 2
  residues processed: 71
  average time/residue: 0.0907
  time to fit residues: 9.1332
Evaluate side-chains
  71 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  307 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 87 optimal weight:    0.1980
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0870
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0770
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.170047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.128203 restraints weight = 9284.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.21
r_work: 0.3325 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8456  Z= 0.103
  Angle     :  0.444   7.225  11510  Z= 0.234
  Chirality :  0.038   0.140   1260
  Planarity :  0.004   0.055   1416
  Dihedral  :  7.948 138.160   1200
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.55 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.27), residues: 1002
  helix:  2.26 (0.20), residues: 655
  sheet:  0.15 (0.56), residues: 93
  loop : -1.48 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 167 
 TYR   0.012   0.001   TYR A 162 
 PHE   0.026   0.001   PHE A 389 
 TRP   0.010   0.001   TRP A  53 
 HIS   0.003   0.001   HIS A 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 8454)
  covalent geometry    : angle       0.44375 (11506)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.90122 (    4)
  hydrogen bonds       : bond        0.04143 (  554)
  hydrogen bonds       : angle       3.83378 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  273 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7589 (mp10)
REVERT: B  196 MET cc_start: 0.7913 (tpp) cc_final: 0.7532 (tpp)
REVERT: B  214 MET cc_start: 0.8499 (mtt) cc_final: 0.8164 (mtt)
  outliers start: 6
  outliers final: 4
  residues processed: 74
  average time/residue: 0.0916
  time to fit residues: 9.5831
Evaluate side-chains
  72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  307 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 56 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 96 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.167597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.125510 restraints weight = 9563.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.06
r_work: 0.3276 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8456  Z= 0.124
  Angle     :  0.455   6.545  11510  Z= 0.241
  Chirality :  0.038   0.139   1260
  Planarity :  0.004   0.053   1416
  Dihedral  :  7.776 133.172   1200
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.02 %
    Favored  : 92.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.27), residues: 1002
  helix:  2.21 (0.20), residues: 655
  sheet:  0.27 (0.53), residues: 100
  loop : -1.54 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  51 
 TYR   0.014   0.001   TYR B 162 
 PHE   0.021   0.001   PHE A 389 
 TRP   0.006   0.001   TRP A  53 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8454)
  covalent geometry    : angle       0.45498 (11506)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       1.05651 (    4)
  hydrogen bonds       : bond        0.04361 (  554)
  hydrogen bonds       : angle       3.82596 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  273 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7607 (mp10)
REVERT: B  196 MET cc_start: 0.7877 (tpp) cc_final: 0.7551 (tpp)
  outliers start: 7
  outliers final: 4
  residues processed: 73
  average time/residue: 0.0894
  time to fit residues: 9.4438
Evaluate side-chains
  71 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.167467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.124125 restraints weight = 9466.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.17
r_work: 0.3283 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8456  Z= 0.125
  Angle     :  0.450   6.139  11510  Z= 0.238
  Chirality :  0.038   0.138   1260
  Planarity :  0.003   0.053   1416
  Dihedral  :  7.719 131.673   1200
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.10 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.27), residues: 1002
  helix:  2.22 (0.20), residues: 655
  sheet:  0.34 (0.53), residues: 100
  loop : -1.54 (0.38), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  51 
 TYR   0.014   0.001   TYR B 162 
 PHE   0.019   0.001   PHE A 389 
 TRP   0.007   0.001   TRP A  53 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8454)
  covalent geometry    : angle       0.44964 (11506)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       1.04203 (    4)
  hydrogen bonds       : bond        0.04367 (  554)
  hydrogen bonds       : angle       3.80055 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  273 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7575 (mp10)
REVERT: B  196 MET cc_start: 0.7776 (tpp) cc_final: 0.7505 (tpp)
REVERT: D   89 MET cc_start: 0.8178 (ptm) cc_final: 0.7889 (ptm)
  outliers start: 7
  outliers final: 4
  residues processed: 73
  average time/residue: 0.0954
  time to fit residues: 9.8533
Evaluate side-chains
  73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.167031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.123469 restraints weight = 9437.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.19
r_work: 0.3267 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8456  Z= 0.136
  Angle     :  0.466   6.141  11510  Z= 0.248
  Chirality :  0.039   0.137   1260
  Planarity :  0.004   0.052   1416
  Dihedral  :  7.653 128.964   1200
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  9.17 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.27), residues: 1002
  helix:  2.19 (0.20), residues: 655
  sheet:  0.04 (0.52), residues: 107
  loop : -1.51 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  51 
 TYR   0.015   0.001   TYR B 162 
 PHE   0.018   0.001   PHE A 389 
 TRP   0.006   0.001   TRP A  53 
 HIS   0.003   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8454)
  covalent geometry    : angle       0.46561 (11506)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       1.12980 (    4)
  hydrogen bonds       : bond        0.04506 (  554)
  hydrogen bonds       : angle       3.82803 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  193 GLU cc_start: 0.7855 (tp30) cc_final: 0.7325 (mm-30)
REVERT: A  273 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7586 (mp10)
  outliers start: 9
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0868
  time to fit residues: 10.0671
Evaluate side-chains
  81 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  370 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0970
   chunk 71 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0040
   chunk 34 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.170444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.127483 restraints weight = 9471.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.18
r_work: 0.3322 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8456  Z= 0.102
  Angle     :  0.434   6.108  11510  Z= 0.230
  Chirality :  0.037   0.138   1260
  Planarity :  0.003   0.052   1416
  Dihedral  :  7.597 131.304   1200
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.00 %
    Favored  : 89.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.27), residues: 1002
  helix:  2.37 (0.20), residues: 655
  sheet:  0.06 (0.52), residues: 107
  loop : -1.46 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.011   0.001   TYR B 162 
 PHE   0.016   0.001   PHE A 389 
 TRP   0.009   0.001   TRP A  53 
 HIS   0.002   0.001   HIS A 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 8454)
  covalent geometry    : angle       0.43375 (11506)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.87188 (    4)
  hydrogen bonds       : bond        0.03940 (  554)
  hydrogen bonds       : angle       3.66504 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7562 (mp10)
REVERT: B   82 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7966 (tmt170)
REVERT: D   89 MET cc_start: 0.8190 (ptm) cc_final: 0.7915 (ptm)
  outliers start: 7
  outliers final: 6
  residues processed: 75
  average time/residue: 0.0960
  time to fit residues: 10.0811
Evaluate side-chains
  75 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  370 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 82 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0270
   chunk 79 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 67 optimal weight:    0.2980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.171483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.128183 restraints weight = 9426.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.20
r_work: 0.3322 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8456  Z= 0.102
  Angle     :  0.436   6.110  11510  Z= 0.229
  Chirality :  0.037   0.136   1260
  Planarity :  0.003   0.052   1416
  Dihedral  :  7.447 128.230   1200
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 10.48 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.27), residues: 1002
  helix:  2.36 (0.20), residues: 660
  sheet:  0.35 (0.53), residues: 100
  loop : -1.37 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 167 
 TYR   0.013   0.001   TYR B 162 
 PHE   0.016   0.001   PHE A 389 
 TRP   0.009   0.001   TRP A  53 
 HIS   0.002   0.001   HIS A 238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8454)
  covalent geometry    : angle       0.43554 (11506)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.89684 (    4)
  hydrogen bonds       : bond        0.03920 (  554)
  hydrogen bonds       : angle       3.62618 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7544 (mp10)
REVERT: B   82 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7976 (tmt170)
REVERT: B  196 MET cc_start: 0.8086 (tpp) cc_final: 0.7617 (tpp)
REVERT: D   89 MET cc_start: 0.8161 (ptm) cc_final: 0.7813 (ptm)
  outliers start: 9
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1025
  time to fit residues: 10.4907
Evaluate side-chains
  74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  370 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0370
   chunk 82 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.170722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.127091 restraints weight = 9477.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.21
r_work: 0.3308 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8456  Z= 0.115
  Angle     :  0.460   7.973  11510  Z= 0.241
  Chirality :  0.038   0.136   1260
  Planarity :  0.003   0.052   1416
  Dihedral  :  7.417 125.826   1200
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.48 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.27), residues: 1002
  helix:  2.37 (0.20), residues: 655
  sheet:  0.32 (0.53), residues: 100
  loop : -1.41 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  51 
 TYR   0.014   0.001   TYR B 162 
 PHE   0.016   0.001   PHE A 389 
 TRP   0.007   0.001   TRP A  53 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8454)
  covalent geometry    : angle       0.45921 (11506)
  SS BOND              : bond        0.00176 (    2)
  SS BOND              : angle       0.99933 (    4)
  hydrogen bonds       : bond        0.04104 (  554)
  hydrogen bonds       : angle       3.68061 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7570 (mp10)
REVERT: B   82 ARG cc_start: 0.8291 (ttm170) cc_final: 0.7984 (tmt170)
REVERT: B  196 MET cc_start: 0.8251 (tpp) cc_final: 0.7706 (tpp)
REVERT: B  317 MET cc_start: 0.8754 (ttp) cc_final: 0.8510 (ttp)
REVERT: D   38 ASN cc_start: 0.7588 (m-40) cc_final: 0.7314 (m-40)
REVERT: D   89 MET cc_start: 0.8171 (ptm) cc_final: 0.7827 (ptm)
  outliers start: 8
  outliers final: 7
  residues processed: 72
  average time/residue: 0.1031
  time to fit residues: 10.2773
Evaluate side-chains
  74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  370 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 21 optimal weight:    0.3980
   chunk 3 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 86 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.170963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.127504 restraints weight = 9362.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.19
r_work: 0.3311 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8456  Z= 0.112
  Angle     :  0.454   7.455  11510  Z= 0.239
  Chirality :  0.038   0.136   1260
  Planarity :  0.003   0.052   1416
  Dihedral  :  7.391 125.403   1200
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.60 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.27), residues: 1002
  helix:  2.41 (0.20), residues: 653
  sheet:  0.35 (0.54), residues: 99
  loop : -1.38 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  51 
 TYR   0.013   0.001   TYR B 162 
 PHE   0.017   0.001   PHE A 389 
 TRP   0.007   0.001   TRP A  53 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8454)
  covalent geometry    : angle       0.45354 (11506)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.94324 (    4)
  hydrogen bonds       : bond        0.04067 (  554)
  hydrogen bonds       : angle       3.66391 ( 1671)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A  193 GLU cc_start: 0.7736 (tp30) cc_final: 0.7226 (mm-30)
REVERT: A  273 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7564 (mp10)
REVERT: B   82 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7990 (tmt170)
REVERT: B  196 MET cc_start: 0.8151 (tpp) cc_final: 0.7660 (tpp)
REVERT: D   38 ASN cc_start: 0.7582 (m-40) cc_final: 0.7306 (m-40)
REVERT: D   89 MET cc_start: 0.8193 (ptm) cc_final: 0.7819 (ptm)
  outliers start: 8
  outliers final: 7
  residues processed: 76
  average time/residue: 0.0993
  time to fit residues: 10.3963
Evaluate side-chains
  74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  273 GLN
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  370 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.169390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.125717 restraints weight = 9405.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.20
r_work: 0.3291 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8456  Z= 0.123
  Angle     :  0.462   7.489  11510  Z= 0.243
  Chirality :  0.038   0.146   1260
  Planarity :  0.003   0.052   1416
  Dihedral  :  7.376 123.666   1200
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.71 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.27), residues: 1002
  helix:  2.35 (0.20), residues: 653
  sheet:  0.35 (0.54), residues: 99
  loop : -1.39 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  51 
 TYR   0.016   0.001   TYR B 173 
 PHE   0.016   0.001   PHE A 389 
 TRP   0.007   0.001   TRP A  53 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8454)
  covalent geometry    : angle       0.46172 (11506)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       1.03847 (    4)
  hydrogen bonds       : bond        0.04251 (  554)
  hydrogen bonds       : angle       3.72456 ( 1671)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1621.04 seconds
wall clock time: 28 minutes 36.19 seconds (1716.19 seconds total)