Starting phenix.real_space_refine
on Thu Sep 18 02:07:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lhm_63102/09_2025/9lhm_63102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lhm_63102/09_2025/9lhm_63102.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lhm_63102/09_2025/9lhm_63102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lhm_63102/09_2025/9lhm_63102.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lhm_63102/09_2025/9lhm_63102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lhm_63102/09_2025/9lhm_63102.map"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
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
     S      30      5.16       5
     C    4158      2.51       5
     N    1053      2.21       5
     O    1137      1.98       5
     H    6390      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 12768
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4256
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 13, 'TRANS': 248}
    Chain: "B"
      Number of atoms: 4256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4256
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 13, 'TRANS': 248}
    Chain: "C"
      Number of atoms: 4256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4256
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 13, 'TRANS': 248}
  Time building chain proxies: 2.72, per 1000 atoms: 0.21
  Number of scatterers: 12768
  At special positions: 0
  Unit cell: (77.19, 80.91, 124.62, 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      30     16.00
     O    1137      8.00
     N    1053      7.00
     C    4158      6.00
     H    6390      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 149 " 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: 0.98
  Conformation dependent library (CDL) restraints added in 371.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1512

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 9 sheets defined
      31.7% alpha, 34.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 98
      removed outlier: 3.545A  pdb=" N   LYS A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 162
      removed outlier: 3.667A  pdb=" N   ASN A 162 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 159 through 162'
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.695A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 3.543A  pdb=" N   SER A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 331
    Processing helix  chain 'B' and resid 71 through 98
    Processing helix  chain 'B' and resid 158 through 162
      removed outlier: 3.669A  pdb=" N   ASN B 162 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 212
      removed outlier: 3.706A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 227
      removed outlier: 3.557A  pdb=" N   SER B 225 " --> pdb=" O   GLN B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 331
    Processing helix  chain 'C' and resid 71 through 98
      removed outlier: 3.824A  pdb=" N   LYS C  97 " --> pdb=" O   ARG C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 162
      removed outlier: 3.705A  pdb=" N   ASN C 162 " --> pdb=" O   PRO C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 212
      removed outlier: 3.696A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 227
      removed outlier: 3.538A  pdb=" N   SER C 225 " --> pdb=" O   GLN C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 331
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107
      removed outlier: 10.220A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 10.124A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   MET A 242 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   GLU A 286 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   LEU A 244 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   THR A 238 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   GLU A 286 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 131
      removed outlier: 6.740A  pdb=" N   GLN A 186 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   CYS A 128 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   PHE A 184 " --> pdb=" O   CYS A 128 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   HIS A 130 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 130 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN A 279 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   MET A 242 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   GLU A 286 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   LEU A 244 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU A 261 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 157
      removed outlier: 3.843A  pdb=" N   ILE A 154 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR A 156 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TRP A 230 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107
      removed outlier: 10.228A  pdb=" N   MET B 242 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 10.124A  pdb=" N   GLN B 293 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   LEU B 244 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   VAL B 295 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   LYS B 248 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET B 242 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   GLU B 286 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   LEU B 244 " --> pdb=" O   GLU B 286 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   THR B 238 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLU B 286 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 131
      removed outlier: 6.675A  pdb=" N   GLN B 186 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   CYS B 128 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   PHE B 184 " --> pdb=" O   CYS B 128 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   HIS B 130 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   LEU B 182 " --> pdb=" O   HIS B 130 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN B 279 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   MET B 242 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   GLU B 286 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   LEU B 244 " --> pdb=" O   GLU B 286 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLU B 261 " --> pdb=" O   LYS B 241 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 156
      removed outlier: 3.810A  pdb=" N   ILE B 154 " --> pdb=" O   ALA B 168 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR B 156 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TRP B 230 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107
      removed outlier: 10.245A  pdb=" N   MET C 242 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 10.169A  pdb=" N   GLN C 293 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   LEU C 244 " --> pdb=" O   GLN C 293 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   VAL C 295 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LYS C 246 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS C 248 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   MET C 242 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 5.684A  pdb=" N   GLU C 286 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   LEU C 244 " --> pdb=" O   GLU C 286 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   THR C 238 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   GLU C 286 " --> pdb=" O   THR C 238 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 124 through 131
      removed outlier: 6.733A  pdb=" N   GLN C 186 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   CYS C 128 " --> pdb=" O   PHE C 184 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   PHE C 184 " --> pdb=" O   CYS C 128 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   HIS C 130 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   LEU C 182 " --> pdb=" O   HIS C 130 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLN C 279 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   MET C 242 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 5.684A  pdb=" N   GLU C 286 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   LEU C 244 " --> pdb=" O   GLU C 286 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU C 261 " --> pdb=" O   LYS C 241 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 156
      removed outlier: 3.806A  pdb=" N   ILE C 154 " --> pdb=" O   ALA C 168 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   TYR C 156 " --> pdb=" O   LYS C 166 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   TRP C 230 " --> pdb=" O   TYR C 201 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    855 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: 2.73

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6378
        1.03 -     1.22: 12
        1.22 -     1.42: 2799
        1.42 -     1.61: 3699
        1.61 -     1.81: 48
  Bond restraints: 12936
  Sorted by residual:
  bond pdb=" N   PHE A 196 "
       pdb=" CA  PHE A 196 "
    ideal  model  delta    sigma   weight residual
    1.466  1.456  0.011 1.36e-02 5.41e+03 6.12e-01
  bond pdb=" N   PHE C 196 "
       pdb=" CA  PHE C 196 "
    ideal  model  delta    sigma   weight residual
    1.466  1.456  0.011 1.36e-02 5.41e+03 5.98e-01
  bond pdb=" CG  PRO A 290 "
       pdb=" CD  PRO A 290 "
    ideal  model  delta    sigma   weight residual
    1.503  1.478  0.025 3.40e-02 8.65e+02 5.38e-01
  bond pdb=" CG  PRO C 290 "
       pdb=" CD  PRO C 290 "
    ideal  model  delta    sigma   weight residual
    1.503  1.479  0.024 3.40e-02 8.65e+02 4.85e-01
  bond pdb=" CA  VAL A 284 "
       pdb=" C   VAL A 284 "
    ideal  model  delta    sigma   weight residual
    1.527  1.521  0.006 8.50e-03 1.38e+04 4.82e-01
  ... (remaining 12931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.43: 23346
        7.43 -    14.85: 0
       14.85 -    22.28: 3
       22.28 -    29.70: 15
       29.70 -    37.13: 18
  Bond angle restraints: 23382
  Sorted by residual:
  angle pdb=" N   MET A 101 "
        pdb=" CA  MET A 101 "
        pdb=" HA  MET A 101 "
      ideal   model   delta    sigma   weight residual
     110.00   72.87   37.13 3.00e+00 1.11e-01 1.53e+02
  angle pdb=" N   MET B 101 "
        pdb=" CA  MET B 101 "
        pdb=" HA  MET B 101 "
      ideal   model   delta    sigma   weight residual
     110.00   72.94   37.06 3.00e+00 1.11e-01 1.53e+02
  angle pdb=" N   MET C 101 "
        pdb=" CA  MET C 101 "
        pdb=" HA  MET C 101 "
      ideal   model   delta    sigma   weight residual
     110.00   73.42   36.58 3.00e+00 1.11e-01 1.49e+02
  angle pdb=" C   MET A 101 "
        pdb=" CA  MET A 101 "
        pdb=" HA  MET A 101 "
      ideal   model   delta    sigma   weight residual
     110.00   75.26   34.74 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" C   MET C 101 "
        pdb=" CA  MET C 101 "
        pdb=" HA  MET C 101 "
      ideal   model   delta    sigma   weight residual
     110.00   75.33   34.67 3.00e+00 1.11e-01 1.34e+02
  ... (remaining 23377 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 5510
       17.06 -    34.12: 445
       34.12 -    51.18: 137
       51.18 -    68.24: 28
       68.24 -    85.30: 12
  Dihedral angle restraints: 6132
    sinusoidal: 3255
      harmonic: 2877
  Sorted by residual:
  dihedral pdb=" CA  PHE B 204 "
           pdb=" C   PHE B 204 "
           pdb=" N   SER B 205 "
           pdb=" CA  SER B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.08  -22.92     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  PHE A 204 "
           pdb=" C   PHE A 204 "
           pdb=" N   SER A 205 "
           pdb=" CA  SER A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.17  -22.83     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  PHE C 204 "
           pdb=" C   PHE C 204 "
           pdb=" N   SER C 205 "
           pdb=" CA  SER C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.36  -22.64     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 6129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 873
       0.073 -    0.146: 87
       0.146 -    0.219: 0
       0.219 -    0.292: 0
       0.292 -    0.365: 6
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" CA  MET C 101 "
            pdb=" N   MET C 101 "
            pdb=" C   MET C 101 "
            pdb=" CB  MET C 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.37 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  MET B 101 "
            pdb=" N   MET B 101 "
            pdb=" C   MET B 101 "
            pdb=" CB  MET B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CA  MET A 101 "
            pdb=" N   MET A 101 "
            pdb=" C   MET A 101 "
            pdb=" CB  MET A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.20e+00
  ... (remaining 963 not shown)

  Planarity restraints: 1866
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 304 "    0.013 2.00e-02 2.50e+03   1.14e-02 5.22e+00
        pdb=" CG  TRP A 304 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 304 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 304 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 304 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 304 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 304 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 304 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 304 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 304 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 304 "    0.007 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 304 "    0.002 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 304 "   -0.002 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 304 "    0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 304 "    0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 304 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  83 "    0.011 2.00e-02 2.50e+03   8.92e-03 2.39e+00
        pdb=" CG  PHE C  83 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  83 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  83 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  83 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE C  83 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 PHE C  83 "    0.002 2.00e-02 2.50e+03
        pdb=" HE1 PHE C  83 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE C  83 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE C  83 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 271 "   -0.021 5.00e-02 4.00e+02   3.15e-02 1.58e+00
        pdb=" N   PRO C 272 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 272 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 272 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1863 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 493
        2.15 -     2.77: 24351
        2.77 -     3.38: 35121
        3.38 -     3.99: 44584
        3.99 -     4.60: 68900
  Nonbonded interactions: 173449
  Sorted by model distance:
  nonbonded pdb=" H   MET A 101 "
            pdb=" HA  MET A 101 "
     model   vdw
     1.542 1.816
  nonbonded pdb=" H   MET B 101 "
            pdb=" HA  MET B 101 "
     model   vdw
     1.544 1.816
  nonbonded pdb=" H   MET C 101 "
            pdb=" HA  MET C 101 "
     model   vdw
     1.547 1.816
  nonbonded pdb=" O   ALA A 113 "
            pdb=" H   PHE A 207 "
     model   vdw
     1.553 2.450
  nonbonded pdb=" O   ALA C 113 "
            pdb=" H   PHE C 207 "
     model   vdw
     1.578 2.450
  ... (remaining 173444 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.070
  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:             0.080
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.320
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
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   0.025   6549  Z= 0.125
  Angle     :  0.542   5.444   8868  Z= 0.302
  Chirality :  0.049   0.365    966
  Planarity :  0.003   0.031   1122
  Dihedral  : 14.477  75.905   2403
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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: -0.48 (0.31), residues: 780
  helix:  2.35 (0.36), residues: 216
  sheet: -0.77 (0.31), residues: 267
  loop : -1.91 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  87 
 TYR   0.007   0.001   TYR A  74 
 PHE   0.027   0.001   PHE C  83 
 TRP   0.039   0.002   TRP A 304 
 HIS   0.002   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6546)
  covalent geometry    : angle       0.54178 ( 8862)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       0.18629 (    6)
  hydrogen bonds       : bond        0.21506 (  304)
  hydrogen bonds       : angle       8.43394 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1458
  time to fit residues: 20.5197
Evaluate side-chains
  82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.220747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.189144 restraints weight = 19808.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 2.19
r_work: 0.4013 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3849 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6549  Z= 0.160
  Angle     :  0.568   5.759   8868  Z= 0.309
  Chirality :  0.051   0.381    966
  Planarity :  0.004   0.030   1122
  Dihedral  :  4.550  18.609    849
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  7.47 %
    Favored  : 91.24 %
  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: -0.64 (0.29), residues: 780
  helix:  2.01 (0.32), residues: 231
  sheet: -0.98 (0.30), residues: 261
  loop : -1.87 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  87 
 TYR   0.006   0.001   TYR C 201 
 PHE   0.020   0.001   PHE B 204 
 TRP   0.020   0.001   TRP A 304 
 HIS   0.001   0.001   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6546)
  covalent geometry    : angle       0.56784 ( 8862)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.10467 (    6)
  hydrogen bonds       : bond        0.04288 (  304)
  hydrogen bonds       : angle       5.96118 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 MET cc_start: 0.3767 (tmm) cc_final: 0.3506 (tmm)
REVERT: B  166 LYS cc_start: 0.6441 (mtpp) cc_final: 0.6230 (mtpp)
REVERT: C  262 THR cc_start: 0.8734 (m) cc_final: 0.8502 (p)
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 0.1806
  time to fit residues: 23.0792
Evaluate side-chains
  89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 60 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 43 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.219697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.188718 restraints weight = 20053.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 2.17
r_work: 0.3994 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3835 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6549  Z= 0.133
  Angle     :  0.524   5.967   8868  Z= 0.282
  Chirality :  0.050   0.375    966
  Planarity :  0.003   0.030   1122
  Dihedral  :  4.399  17.865    849
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.34 %
    Favored  : 88.51 %
  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: -0.48 (0.29), residues: 780
  helix:  2.23 (0.31), residues: 231
  sheet: -0.96 (0.30), residues: 264
  loop : -1.79 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  87 
 TYR   0.005   0.001   TYR A 111 
 PHE   0.019   0.001   PHE C  92 
 TRP   0.014   0.001   TRP A 304 
 HIS   0.007   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6546)
  covalent geometry    : angle       0.52398 ( 8862)
  SS BOND              : bond        0.00147 (    3)
  SS BOND              : angle       0.02949 (    6)
  hydrogen bonds       : bond        0.03785 (  304)
  hydrogen bonds       : angle       5.37682 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.4702 (mtp) cc_final: 0.4324 (mtp)
REVERT: A  331 MET cc_start: 0.3773 (tmm) cc_final: 0.3509 (tmm)
REVERT: B  166 LYS cc_start: 0.6538 (mtpp) cc_final: 0.6332 (mtpp)
REVERT: B  220 MET cc_start: 0.4916 (mtp) cc_final: 0.4454 (mtp)
REVERT: C  166 LYS cc_start: 0.7165 (ptmt) cc_final: 0.6905 (ptmt)
REVERT: C  262 THR cc_start: 0.8613 (m) cc_final: 0.8332 (p)
  outliers start: 8
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1954
  time to fit residues: 23.3157
Evaluate side-chains
  92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Chi-restraints excluded: chain C residue  311 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    0.0170
   chunk 61 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.4026

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.216932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.184148 restraints weight = 19995.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.27
r_work: 0.3932 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3774 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   6549  Z= 0.192
  Angle     :  0.549   6.454   8868  Z= 0.301
  Chirality :  0.051   0.387    966
  Planarity :  0.004   0.030   1122
  Dihedral  :  4.686  17.215    849
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.49 %
    Favored  : 86.78 %
  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: -0.62 (0.29), residues: 780
  helix:  2.11 (0.31), residues: 231
  sheet: -1.08 (0.30), residues: 261
  loop : -1.83 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 253 
 TYR   0.008   0.001   TYR A 111 
 PHE   0.017   0.002   PHE C  92 
 TRP   0.013   0.001   TRP B 304 
 HIS   0.005   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6546)
  covalent geometry    : angle       0.54961 ( 8862)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       0.13466 (    6)
  hydrogen bonds       : bond        0.03511 (  304)
  hydrogen bonds       : angle       5.39966 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.4754 (mtp) cc_final: 0.4397 (mtp)
REVERT: A  331 MET cc_start: 0.3853 (tmm) cc_final: 0.3596 (tmm)
REVERT: B  220 MET cc_start: 0.4928 (mtp) cc_final: 0.4436 (mtp)
REVERT: B  304 TRP cc_start: 0.6607 (m-10) cc_final: 0.6303 (m100)
REVERT: C  166 LYS cc_start: 0.7500 (ptmt) cc_final: 0.7254 (ptmt)
REVERT: C  220 MET cc_start: 0.5221 (mtp) cc_final: 0.5004 (mtp)
  outliers start: 12
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1889
  time to fit residues: 23.1035
Evaluate side-chains
  90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  204 PHE
Chi-restraints excluded: chain C residue  311 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.217934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.184504 restraints weight = 20145.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 2.38
r_work: 0.3972 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3806 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6549  Z= 0.124
  Angle     :  0.507   6.691   8868  Z= 0.273
  Chirality :  0.050   0.380    966
  Planarity :  0.003   0.031   1122
  Dihedral  :  4.441  16.751    849
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.36 %
    Favored  : 85.92 %
  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: -0.48 (0.30), residues: 780
  helix:  2.36 (0.31), residues: 231
  sheet: -1.11 (0.31), residues: 264
  loop : -1.75 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 253 
 TYR   0.004   0.001   TYR A 111 
 PHE   0.015   0.001   PHE C  92 
 TRP   0.009   0.001   TRP B 304 
 HIS   0.004   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6546)
  covalent geometry    : angle       0.50759 ( 8862)
  SS BOND              : bond        0.00131 (    3)
  SS BOND              : angle       0.11985 (    6)
  hydrogen bonds       : bond        0.03165 (  304)
  hydrogen bonds       : angle       5.01392 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 MET cc_start: 0.4857 (mtp) cc_final: 0.4502 (mtp)
REVERT: A  311 CYS cc_start: 0.6095 (t) cc_final: 0.5305 (m)
REVERT: A  331 MET cc_start: 0.3964 (tmm) cc_final: 0.3706 (tmm)
REVERT: B  220 MET cc_start: 0.4912 (mtp) cc_final: 0.4435 (mtp)
REVERT: C  220 MET cc_start: 0.5124 (mtp) cc_final: 0.4851 (mtp)
  outliers start: 12
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1780
  time to fit residues: 21.0923
Evaluate side-chains
  84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.212882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.181947 restraints weight = 20049.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 2.13
r_work: 0.3935 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3781 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   6549  Z= 0.198
  Angle     :  0.556   7.383   8868  Z= 0.304
  Chirality :  0.051   0.385    966
  Planarity :  0.004   0.032   1122
  Dihedral  :  4.774  17.326    849
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.51 %
    Favored  : 84.91 %
  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: -0.84 (0.30), residues: 780
  helix:  2.05 (0.31), residues: 231
  sheet: -1.38 (0.30), residues: 264
  loop : -1.88 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 253 
 TYR   0.008   0.001   TYR A 111 
 PHE   0.015   0.002   PHE B  83 
 TRP   0.020   0.001   TRP B 304 
 HIS   0.004   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 6546)
  covalent geometry    : angle       0.55640 ( 8862)
  SS BOND              : bond        0.00138 (    3)
  SS BOND              : angle       0.20018 (    6)
  hydrogen bonds       : bond        0.03324 (  304)
  hydrogen bonds       : angle       5.28965 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8664 (mtpt)
REVERT: A  220 MET cc_start: 0.4951 (mtp) cc_final: 0.4602 (mtp)
REVERT: A  311 CYS cc_start: 0.6388 (t) cc_final: 0.5785 (m)
REVERT: A  331 MET cc_start: 0.3763 (tmm) cc_final: 0.3544 (tmm)
REVERT: B  220 MET cc_start: 0.5025 (mtp) cc_final: 0.4575 (mtp)
REVERT: C  220 MET cc_start: 0.5095 (mtp) cc_final: 0.4859 (mtp)
REVERT: C  311 CYS cc_start: 0.6353 (t) cc_final: 0.5461 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 87
  average time/residue: 0.1831
  time to fit residues: 21.5272
Evaluate side-chains
  83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 17 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.215342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.184546 restraints weight = 20057.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.4093 rms_B_bonded: 2.16
r_work: 0.3961 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3803 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6549  Z= 0.141
  Angle     :  0.523   8.480   8868  Z= 0.281
  Chirality :  0.050   0.379    966
  Planarity :  0.003   0.033   1122
  Dihedral  :  4.595  16.790    849
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.37 %
    Favored  : 84.20 %
  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: -0.74 (0.30), residues: 780
  helix:  2.23 (0.31), residues: 231
  sheet: -1.40 (0.31), residues: 264
  loop : -1.83 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 253 
 TYR   0.006   0.001   TYR A 111 
 PHE   0.014   0.001   PHE B  83 
 TRP   0.013   0.001   TRP B 304 
 HIS   0.003   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6546)
  covalent geometry    : angle       0.52275 ( 8862)
  SS BOND              : bond        0.00084 (    3)
  SS BOND              : angle       0.17854 (    6)
  hydrogen bonds       : bond        0.03052 (  304)
  hydrogen bonds       : angle       5.02823 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8598 (mtpt)
REVERT: A  220 MET cc_start: 0.4914 (mtp) cc_final: 0.4580 (mtp)
REVERT: A  311 CYS cc_start: 0.6291 (t) cc_final: 0.5891 (m)
REVERT: A  331 MET cc_start: 0.3751 (tmm) cc_final: 0.3526 (tmm)
REVERT: B  220 MET cc_start: 0.5028 (mtp) cc_final: 0.4591 (mtp)
REVERT: B  311 CYS cc_start: 0.6346 (t) cc_final: 0.5509 (m)
REVERT: C  220 MET cc_start: 0.5087 (mtp) cc_final: 0.4849 (mtp)
REVERT: C  311 CYS cc_start: 0.6365 (t) cc_final: 0.5737 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 83
  average time/residue: 0.1705
  time to fit residues: 19.2488
Evaluate side-chains
  83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.3188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.213120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.180132 restraints weight = 20219.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 2.30
r_work: 0.3927 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6549  Z= 0.174
  Angle     :  0.549   8.742   8868  Z= 0.298
  Chirality :  0.050   0.381    966
  Planarity :  0.004   0.033   1122
  Dihedral  :  4.725  17.280    849
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.37 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.30), residues: 780
  helix:  2.16 (0.31), residues: 231
  sheet: -1.51 (0.30), residues: 264
  loop : -1.88 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 253 
 TYR   0.008   0.001   TYR A 111 
 PHE   0.015   0.001   PHE B  83 
 TRP   0.012   0.001   TRP B 304 
 HIS   0.003   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 6546)
  covalent geometry    : angle       0.54883 ( 8862)
  SS BOND              : bond        0.00100 (    3)
  SS BOND              : angle       0.23365 (    6)
  hydrogen bonds       : bond        0.03078 (  304)
  hydrogen bonds       : angle       5.15436 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8580 (mtpt)
REVERT: A  220 MET cc_start: 0.4842 (mtp) cc_final: 0.4513 (mtp)
REVERT: A  311 CYS cc_start: 0.6231 (t) cc_final: 0.5768 (m)
REVERT: A  331 MET cc_start: 0.3943 (tmm) cc_final: 0.3708 (tmm)
REVERT: B  220 MET cc_start: 0.5044 (mtp) cc_final: 0.4577 (mtp)
REVERT: B  311 CYS cc_start: 0.6279 (t) cc_final: 0.5557 (m)
REVERT: C  220 MET cc_start: 0.5119 (mtp) cc_final: 0.4854 (mtp)
REVERT: C  311 CYS cc_start: 0.6373 (t) cc_final: 0.5797 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 82
  average time/residue: 0.1762
  time to fit residues: 19.7185
Evaluate side-chains
  82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 14 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.216200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.183506 restraints weight = 20251.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 2.31
r_work: 0.3958 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6549  Z= 0.126
  Angle     :  0.534  10.259   8868  Z= 0.288
  Chirality :  0.050   0.380    966
  Planarity :  0.003   0.034   1122
  Dihedral  :  4.486  16.551    849
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.66 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.68 (0.30), residues: 780
  helix:  2.36 (0.31), residues: 231
  sheet: -1.45 (0.31), residues: 264
  loop : -1.75 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 253 
 TYR   0.009   0.001   TYR C  74 
 PHE   0.015   0.001   PHE B  83 
 TRP   0.012   0.001   TRP B 304 
 HIS   0.003   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6546)
  covalent geometry    : angle       0.53451 ( 8862)
  SS BOND              : bond        0.00062 (    3)
  SS BOND              : angle       0.21441 (    6)
  hydrogen bonds       : bond        0.02849 (  304)
  hydrogen bonds       : angle       4.86001 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8561 (mtpt)
REVERT: A  220 MET cc_start: 0.4832 (mtp) cc_final: 0.4369 (mtp)
REVERT: A  311 CYS cc_start: 0.6060 (t) cc_final: 0.5678 (m)
REVERT: B  220 MET cc_start: 0.5252 (mtp) cc_final: 0.4733 (mtp)
REVERT: B  311 CYS cc_start: 0.6091 (t) cc_final: 0.5417 (m)
REVERT: C  220 MET cc_start: 0.5123 (mtp) cc_final: 0.4910 (mtp)
REVERT: C  311 CYS cc_start: 0.6279 (t) cc_final: 0.5703 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 83
  average time/residue: 0.1763
  time to fit residues: 19.8923
Evaluate side-chains
  83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 74 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.216112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.182504 restraints weight = 20102.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.40
r_work: 0.3962 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3798 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6549  Z= 0.128
  Angle     :  0.534  10.290   8868  Z= 0.289
  Chirality :  0.050   0.380    966
  Planarity :  0.004   0.034   1122
  Dihedral  :  4.407  16.427    849
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.95 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.65 (0.30), residues: 780
  helix:  2.40 (0.31), residues: 231
  sheet: -1.46 (0.31), residues: 264
  loop : -1.74 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 253 
 TYR   0.010   0.001   TYR B  74 
 PHE   0.015   0.001   PHE B  83 
 TRP   0.011   0.001   TRP C 304 
 HIS   0.003   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6546)
  covalent geometry    : angle       0.53438 ( 8862)
  SS BOND              : bond        0.00073 (    3)
  SS BOND              : angle       0.20612 (    6)
  hydrogen bonds       : bond        0.02815 (  304)
  hydrogen bonds       : angle       4.78591 (  855)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8480 (mtpt)
REVERT: A  220 MET cc_start: 0.4867 (mtp) cc_final: 0.4407 (mtp)
REVERT: A  311 CYS cc_start: 0.5953 (t) cc_final: 0.5549 (m)
REVERT: B  220 MET cc_start: 0.5197 (mtp) cc_final: 0.4687 (mtp)
REVERT: B  311 CYS cc_start: 0.5975 (t) cc_final: 0.5295 (m)
REVERT: C  311 CYS cc_start: 0.6194 (t) cc_final: 0.5622 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 81
  average time/residue: 0.1932
  time to fit residues: 21.1201
Evaluate side-chains
  81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  204 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.216504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.183931 restraints weight = 20176.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 2.31
r_work: 0.3964 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3804 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6549  Z= 0.129
  Angle     :  0.536  11.396   8868  Z= 0.290
  Chirality :  0.050   0.381    966
  Planarity :  0.004   0.041   1122
  Dihedral  :  4.394  16.361    849
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 16.09 %
    Favored  : 82.76 %
  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: -0.62 (0.30), residues: 780
  helix:  2.41 (0.31), residues: 231
  sheet: -1.51 (0.31), residues: 267
  loop : -1.63 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 253 
 TYR   0.005   0.001   TYR B  74 
 PHE   0.019   0.001   PHE B  83 
 TRP   0.013   0.001   TRP C 304 
 HIS   0.003   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6546)
  covalent geometry    : angle       0.53619 ( 8862)
  SS BOND              : bond        0.00079 (    3)
  SS BOND              : angle       0.20437 (    6)
  hydrogen bonds       : bond        0.02748 (  304)
  hydrogen bonds       : angle       4.74110 (  855)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3646.81 seconds
wall clock time: 62 minutes 31.22 seconds (3751.22 seconds total)