Starting phenix.real_space_refine
on Sat Aug 23 06:23:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ds6_27684/08_2025/8ds6_27684.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ds6_27684/08_2025/8ds6_27684.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ds6_27684/08_2025/8ds6_27684.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ds6_27684/08_2025/8ds6_27684.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ds6_27684/08_2025/8ds6_27684.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ds6_27684/08_2025/8ds6_27684.cif"
  }
  resolution = 4.9
  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=   0.001
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      20      5.16       5
     C    3224      2.51       5
     N     909      2.21       5
     O     875      1.98       5
     H    5107      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10135
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 5051
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 34, 'TRANS': 299}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 5084
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 35, 'TRANS': 299}
          Chain breaks: 1
  Time building chain proxies: 1.54, per 1000 atoms: 0.15
  Number of scatterers: 10135
  At special positions: 0
  Unit cell: (72.645, 101.87, 108.55, 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      20     16.00
     O     875      8.00
     N     909      7.00
     C    3224      6.00
     H    5107      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 170.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      52.6% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 130 through 158
    Processing helix  chain 'A' and resid 215 through 222
    Processing helix  chain 'A' and resid 262 through 270
      removed outlier: 3.812A  pdb=" N   GLU A 268 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 299
      removed outlier: 3.507A  pdb=" N   LEU A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 308
      No H-bonds generated for 'chain 'A' and resid 306 through 308'
    Processing helix  chain 'A' and resid 330 through 332
      No H-bonds generated for 'chain 'A' and resid 330 through 332'
    Processing helix  chain 'A' and resid 348 through 361
    Processing helix  chain 'A' and resid 368 through 384
    Processing helix  chain 'A' and resid 387 through 400
    Processing helix  chain 'A' and resid 420 through 440
    Processing helix  chain 'A' and resid 446 through 459
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.528A  pdb=" N   LEU A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 158
    Processing helix  chain 'B' and resid 214 through 224
      removed outlier: 4.115A  pdb=" N   LEU B 218 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 270
      removed outlier: 3.758A  pdb=" N   GLU B 268 " --> pdb=" O   GLN B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 298
      removed outlier: 3.603A  pdb=" N   VAL B 281 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 309
    Processing helix  chain 'B' and resid 330 through 332
      No H-bonds generated for 'chain 'B' and resid 330 through 332'
    Processing helix  chain 'B' and resid 348 through 363
    Processing helix  chain 'B' and resid 368 through 385
      removed outlier: 3.515A  pdb=" N   ALA B 379 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 400
    Processing helix  chain 'B' and resid 415 through 418
    Processing helix  chain 'B' and resid 419 through 441
    Processing helix  chain 'B' and resid 446 through 459
    Processing helix  chain 'B' and resid 460 through 472
    Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 173
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173
      removed outlier: 4.652A  pdb=" N   ALA A 252 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLY A 235 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261
    Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 173
      removed outlier: 3.614A  pdb=" N   ALA B 180 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 173
      removed outlier: 5.096A  pdb=" N   ALA B 252 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLY B 235 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 261
    Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 302

    318 hydrogen bonds defined for protein.
    909 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: 2.15

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        0.92 -     1.09: 4677
        1.09 -     1.27: 1221
        1.27 -     1.45: 1392
        1.45 -     1.63: 2965
        1.63 -     1.81: 24
  Bond restraints: 10279
  Sorted by residual:
  bond pdb=" CD2 PHE B 294 "
       pdb=" HD2 PHE B 294 "
    ideal  model  delta    sigma   weight residual
    0.930  1.091 -0.161 2.00e-02 2.50e+03 6.51e+01
  bond pdb=" CD2 HIS B 348 "
       pdb=" HD2 HIS B 348 "
    ideal  model  delta    sigma   weight residual
    0.930  1.091 -0.161 2.00e-02 2.50e+03 6.50e+01
  bond pdb=" CD2 HIS A 227 "
       pdb=" HD2 HIS A 227 "
    ideal  model  delta    sigma   weight residual
    0.930  1.091 -0.161 2.00e-02 2.50e+03 6.49e+01
  bond pdb=" CZ2 TRP A 450 "
       pdb=" HZ2 TRP A 450 "
    ideal  model  delta    sigma   weight residual
    0.930  1.091 -0.161 2.00e-02 2.50e+03 6.49e+01
  bond pdb=" CZ3 TRP A 400 "
       pdb=" HZ3 TRP A 400 "
    ideal  model  delta    sigma   weight residual
    0.930  1.091 -0.161 2.00e-02 2.50e+03 6.48e+01
  ... (remaining 10274 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 16165
        2.61 -     5.21: 1903
        5.21 -     7.82: 620
        7.82 -    10.43: 16
       10.43 -    13.04: 17
  Bond angle restraints: 18721
  Sorted by residual:
  angle pdb=" N   ALA A 291 "
        pdb=" CA  ALA A 291 "
        pdb=" C   ALA A 291 "
      ideal   model   delta    sigma   weight residual
     111.28  103.64    7.64 1.09e+00 8.42e-01 4.91e+01
  angle pdb=" N   PRO B 338 "
        pdb=" CA  PRO B 338 "
        pdb=" C   PRO B 338 "
      ideal   model   delta    sigma   weight residual
     110.70  119.16   -8.46 1.22e+00 6.72e-01 4.81e+01
  angle pdb=" C   GLY A 322 "
        pdb=" N   PRO A 323 "
        pdb=" CA  PRO A 323 "
      ideal   model   delta    sigma   weight residual
     119.66  124.05   -4.39 7.20e-01 1.93e+00 3.72e+01
  angle pdb=" CA  PRO B 338 "
        pdb=" C   PRO B 338 "
        pdb=" N   PRO B 339 "
      ideal   model   delta    sigma   weight residual
     117.93  124.66   -6.73 1.20e+00 6.94e-01 3.14e+01
  angle pdb=" CA  GLU B 132 "
        pdb=" C   GLU B 132 "
        pdb=" O   GLU B 132 "
      ideal   model   delta    sigma   weight residual
     120.55  114.88    5.67 1.06e+00 8.90e-01 2.86e+01
  ... (remaining 18716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4554
       17.82 -    35.63: 156
       35.63 -    53.45: 106
       53.45 -    71.26: 34
       71.26 -    89.08: 4
  Dihedral angle restraints: 4854
    sinusoidal: 2698
      harmonic: 2156
  Sorted by residual:
  dihedral pdb=" CA  PRO B 273 "
           pdb=" C   PRO B 273 "
           pdb=" N   PRO B 274 "
           pdb=" CA  PRO B 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.08   20.92     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  THR B 329 "
           pdb=" C   THR B 329 "
           pdb=" N   ASP B 330 "
           pdb=" CA  ASP B 330 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.44  -19.56     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  GLY B 343 "
           pdb=" C   GLY B 343 "
           pdb=" N   SER B 344 "
           pdb=" CA  SER B 344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.66   19.34     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 4851 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 514
       0.051 -    0.102: 230
       0.102 -    0.152: 33
       0.152 -    0.203: 20
       0.203 -    0.254: 2
  Chirality restraints: 799
  Sorted by residual:
  chirality pdb=" CA  ASP A 473 "
            pdb=" N   ASP A 473 "
            pdb=" C   ASP A 473 "
            pdb=" CB  ASP A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  VAL A 237 "
            pdb=" N   VAL A 237 "
            pdb=" C   VAL A 237 "
            pdb=" CB  VAL A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  VAL B 237 "
            pdb=" N   VAL B 237 "
            pdb=" C   VAL B 237 "
            pdb=" CB  VAL B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.75e-01
  ... (remaining 796 not shown)

  Planarity restraints: 1520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 325 "    0.298 9.50e-02 1.11e+02   1.22e-01 1.21e+02
        pdb=" NE  ARG B 325 "    0.043 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 325 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 325 "    0.025 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 325 "   -0.062 2.00e-02 2.50e+03
        pdb="HH11 ARG B 325 "   -0.006 2.00e-02 2.50e+03
        pdb="HH12 ARG B 325 "   -0.080 2.00e-02 2.50e+03
        pdb="HH21 ARG B 325 "   -0.084 2.00e-02 2.50e+03
        pdb="HH22 ARG B 325 "    0.157 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 325 "   -0.413 9.50e-02 1.11e+02   1.48e-01 8.69e+01
        pdb=" NE  ARG A 325 "   -0.053 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 325 "    0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 325 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 325 "    0.049 2.00e-02 2.50e+03
        pdb="HH11 ARG A 325 "    0.051 2.00e-02 2.50e+03
        pdb="HH12 ARG A 325 "    0.018 2.00e-02 2.50e+03
        pdb="HH21 ARG A 325 "    0.080 2.00e-02 2.50e+03
        pdb="HH22 ARG A 325 "   -0.111 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 192 "    0.171 9.50e-02 1.11e+02   6.96e-02 3.91e+01
        pdb=" NE  ARG B 192 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 192 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 192 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 192 "   -0.033 2.00e-02 2.50e+03
        pdb="HH11 ARG B 192 "    0.024 2.00e-02 2.50e+03
        pdb="HH12 ARG B 192 "   -0.049 2.00e-02 2.50e+03
        pdb="HH21 ARG B 192 "   -0.034 2.00e-02 2.50e+03
        pdb="HH22 ARG B 192 "    0.092 2.00e-02 2.50e+03
  ... (remaining 1517 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 995
        2.24 -     2.83: 20752
        2.83 -     3.42: 28654
        3.42 -     4.01: 37970
        4.01 -     4.60: 55049
  Nonbonded interactions: 143420
  Sorted by model distance:
  nonbonded pdb=" O   TRP B 450 "
            pdb=" HG  CYS B 453 "
     model   vdw
     1.650 2.620
  nonbonded pdb=" O   TRP A 450 "
            pdb=" HG  CYS A 453 "
     model   vdw
     1.689 2.620
  nonbonded pdb="HG23 THR A 368 "
            pdb=" H   ALA A 371 "
     model   vdw
     1.707 2.270
  nonbonded pdb=" HD2 ARG A 156 "
            pdb="HH11 ARG A 156 "
     model   vdw
     1.716 2.270
  nonbonded pdb=" O   LEU A 266 "
            pdb=" HG  CYS A 270 "
     model   vdw
     1.728 2.620
  ... (remaining 143415 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 130 through 472)
  selection = (chain 'B' and (resid 130 through 406 or resid 419 through 472))
}

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 group one per residue
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:             2.430
  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:             0.060
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.590
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
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      :  0.012   0.075   5172  Z= 0.837
  Angle     :  1.434   8.458   7088  Z= 1.063
  Chirality :  0.062   0.254    799
  Planarity :  0.010   0.119    923
  Dihedral  : 10.651  89.081   1879
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  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:  1.06 (0.30), residues: 661
  helix:  1.33 (0.26), residues: 322
  sheet:  0.06 (0.51), residues: 62
  loop :  0.26 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 325 
 TYR   0.001   0.000   TYR A 188 
 PHE   0.014   0.001   PHE B 331 
 TRP   0.001   0.000   TRP A 400 
 HIS   0.004   0.000   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.01234 ( 5172)
  covalent geometry    : angle       1.43355 ( 7088)
  hydrogen bonds       : bond        0.20831 (  310)
  hydrogen bonds       : angle       6.85343 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  268 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8732 (mp0)
REVERT: B  398 LEU cc_start: 0.8050 (mt) cc_final: 0.7802 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1678
  time to fit residues: 18.2815
Evaluate side-chains
  65 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.050285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.038367 restraints weight = 118596.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.040196 restraints weight = 69968.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.041578 restraints weight = 47669.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.042612 restraints weight = 35505.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.043391 restraints weight = 28103.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5172  Z= 0.183
  Angle     :  0.622   6.146   7088  Z= 0.329
  Chirality :  0.038   0.133    799
  Planarity :  0.006   0.048    923
  Dihedral  :  4.323  16.354    722
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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:  1.82 (0.31), residues: 661
  helix:  2.45 (0.27), residues: 326
  sheet: -0.58 (0.49), residues: 84
  loop :  0.27 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 156 
 TYR   0.008   0.001   TYR B 187 
 PHE   0.015   0.002   PHE A 331 
 TRP   0.010   0.001   TRP A 216 
 HIS   0.005   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 5172)
  covalent geometry    : angle       0.62193 ( 7088)
  hydrogen bonds       : bond        0.06936 (  310)
  hydrogen bonds       : angle       5.34959 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  247 TRP cc_start: 0.7607 (p90) cc_final: 0.6946 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1925
  time to fit residues: 17.7894
Evaluate side-chains
  53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0040
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8194

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.051134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.038764 restraints weight = 119458.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.040725 restraints weight = 69191.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.042141 restraints weight = 46529.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.043264 restraints weight = 34290.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.044132 restraints weight = 26848.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   5172  Z= 0.128
  Angle     :  0.537   5.764   7088  Z= 0.276
  Chirality :  0.037   0.137    799
  Planarity :  0.006   0.064    923
  Dihedral  :  4.017  14.635    722
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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:  1.92 (0.32), residues: 661
  helix:  2.55 (0.27), residues: 327
  sheet: -0.79 (0.49), residues: 84
  loop :  0.38 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 156 
 TYR   0.012   0.001   TYR B 455 
 PHE   0.007   0.001   PHE A 294 
 TRP   0.007   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5172)
  covalent geometry    : angle       0.53709 ( 7088)
  hydrogen bonds       : bond        0.05871 (  310)
  hydrogen bonds       : angle       4.95866 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  464 MET cc_start: 0.7471 (mmm) cc_final: 0.7111 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1310
  time to fit residues: 10.5096
Evaluate side-chains
  52 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.050197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.038157 restraints weight = 124495.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.040044 restraints weight = 73210.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.041473 restraints weight = 49370.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.042530 restraints weight = 36214.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.043366 restraints weight = 28318.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5172  Z= 0.127
  Angle     :  0.526   5.729   7088  Z= 0.265
  Chirality :  0.036   0.140    799
  Planarity :  0.006   0.047    923
  Dihedral  :  3.849  14.301    722
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.94 (0.33), residues: 661
  helix:  2.66 (0.27), residues: 326
  sheet: -0.97 (0.47), residues: 84
  loop :  0.32 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 438 
 TYR   0.012   0.001   TYR B 455 
 PHE   0.015   0.001   PHE A 331 
 TRP   0.009   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5172)
  covalent geometry    : angle       0.52628 ( 7088)
  hydrogen bonds       : bond        0.05009 (  310)
  hydrogen bonds       : angle       4.68451 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  188 TYR cc_start: 0.8869 (m-80) cc_final: 0.8099 (m-80)
REVERT: B  219 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8964 (tm-30)
REVERT: B  464 MET cc_start: 0.7325 (mmm) cc_final: 0.6868 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1319
  time to fit residues: 10.7322
Evaluate side-chains
  49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.5924

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.049892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.038234 restraints weight = 127941.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.040081 restraints weight = 74711.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.041480 restraints weight = 50113.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.042523 restraints weight = 36623.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.043289 restraints weight = 28504.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6764
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5172  Z= 0.142
  Angle     :  0.533   5.681   7088  Z= 0.271
  Chirality :  0.036   0.140    799
  Planarity :  0.006   0.045    923
  Dihedral  :  3.837  13.907    722
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.92 (0.33), residues: 661
  helix:  2.64 (0.28), residues: 326
  sheet: -1.05 (0.46), residues: 84
  loop :  0.36 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 306 
 TYR   0.007   0.001   TYR B 187 
 PHE   0.010   0.001   PHE A 294 
 TRP   0.012   0.001   TRP A 472 
 HIS   0.007   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5172)
  covalent geometry    : angle       0.53318 ( 7088)
  hydrogen bonds       : bond        0.04858 (  310)
  hydrogen bonds       : angle       4.65926 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9052 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1327
  time to fit residues: 10.4664
Evaluate side-chains
  49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.049929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.038084 restraints weight = 128195.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.039867 restraints weight = 76538.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.041206 restraints weight = 52363.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.042225 restraints weight = 38814.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.043002 restraints weight = 30698.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5172  Z= 0.136
  Angle     :  0.529   5.649   7088  Z= 0.264
  Chirality :  0.036   0.139    799
  Planarity :  0.006   0.042    923
  Dihedral  :  3.728  13.378    722
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.86 (0.33), residues: 661
  helix:  2.58 (0.28), residues: 326
  sheet: -1.17 (0.46), residues: 84
  loop :  0.39 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 390 
 TYR   0.007   0.001   TYR B 187 
 PHE   0.014   0.001   PHE A 331 
 TRP   0.012   0.001   TRP A 472 
 HIS   0.003   0.001   HIS B 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5172)
  covalent geometry    : angle       0.52858 ( 7088)
  hydrogen bonds       : bond        0.04541 (  310)
  hydrogen bonds       : angle       4.53338 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLU cc_start: 0.9483 (mt-10) cc_final: 0.9042 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1592
  time to fit residues: 12.1727
Evaluate side-chains
  47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** 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 = 0.3520 r_free = 0.3520 target = 0.049817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.038511 restraints weight = 128201.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.040252 restraints weight = 75420.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.041601 restraints weight = 51113.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.042595 restraints weight = 37640.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.043358 restraints weight = 29598.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5172  Z= 0.119
  Angle     :  0.507   5.601   7088  Z= 0.253
  Chirality :  0.036   0.140    799
  Planarity :  0.005   0.042    923
  Dihedral  :  3.650  13.392    722
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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:  1.95 (0.34), residues: 661
  helix:  2.71 (0.28), residues: 326
  sheet: -1.26 (0.47), residues: 84
  loop :  0.40 (0.43), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.006   0.001   TYR B 187 
 PHE   0.007   0.001   PHE A 294 
 TRP   0.012   0.001   TRP A 472 
 HIS   0.007   0.001   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5172)
  covalent geometry    : angle       0.50679 ( 7088)
  hydrogen bonds       : bond        0.04311 (  310)
  hydrogen bonds       : angle       4.40999 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9016 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1572
  time to fit residues: 11.3955
Evaluate side-chains
  46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0470
   chunk 14 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7682

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

Flipped N/Q/H residues before XYZ refinement:
A 466 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.049869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.038574 restraints weight = 130716.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.040353 restraints weight = 78675.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.041694 restraints weight = 53557.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.042698 restraints weight = 39419.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.043474 restraints weight = 30827.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   5172  Z= 0.104
  Angle     :  0.499   5.547   7088  Z= 0.244
  Chirality :  0.036   0.139    799
  Planarity :  0.006   0.056    923
  Dihedral  :  3.582  13.435    722
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.34), residues: 661
  helix:  2.90 (0.28), residues: 325
  sheet: -1.28 (0.46), residues: 84
  loop :  0.41 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 192 
 TYR   0.006   0.001   TYR A 188 
 PHE   0.007   0.001   PHE A 294 
 TRP   0.012   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 5172)
  covalent geometry    : angle       0.49882 ( 7088)
  hydrogen bonds       : bond        0.04165 (  310)
  hydrogen bonds       : angle       4.31778 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  188 TYR cc_start: 0.8987 (m-80) cc_final: 0.8462 (m-80)
REVERT: B  219 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9022 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1105
  time to fit residues: 8.8375
Evaluate side-chains
  47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.1980
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.049817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.038903 restraints weight = 131878.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.040665 restraints weight = 78800.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.041960 restraints weight = 53632.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.042933 restraints weight = 39397.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.043706 restraints weight = 30792.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5172  Z= 0.119
  Angle     :  0.511   5.572   7088  Z= 0.252
  Chirality :  0.036   0.140    799
  Planarity :  0.005   0.040    923
  Dihedral  :  3.544  12.930    722
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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 (0.34), residues: 661
  helix:  2.78 (0.28), residues: 325
  sheet: -1.31 (0.47), residues: 84
  loop :  0.35 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 192 
 TYR   0.006   0.001   TYR A 188 
 PHE   0.009   0.001   PHE A 294 
 TRP   0.012   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5172)
  covalent geometry    : angle       0.51093 ( 7088)
  hydrogen bonds       : bond        0.04070 (  310)
  hydrogen bonds       : angle       4.31793 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  188 TYR cc_start: 0.8971 (m-80) cc_final: 0.8430 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1157
  time to fit residues: 8.2569
Evaluate side-chains
  44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.3980
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 HIS ** 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 = 0.3527 r_free = 0.3527 target = 0.050006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.038901 restraints weight = 130200.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.040663 restraints weight = 77819.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.041979 restraints weight = 53101.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.042953 restraints weight = 39208.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.043734 restraints weight = 30759.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5172  Z= 0.102
  Angle     :  0.502   5.540   7088  Z= 0.245
  Chirality :  0.036   0.138    799
  Planarity :  0.005   0.038    923
  Dihedral  :  3.502  12.902    722
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.34), residues: 661
  helix:  2.91 (0.29), residues: 325
  sheet: -1.33 (0.46), residues: 84
  loop :  0.36 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 192 
 TYR   0.007   0.001   TYR A 188 
 PHE   0.008   0.001   PHE A 294 
 TRP   0.014   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 5172)
  covalent geometry    : angle       0.50207 ( 7088)
  hydrogen bonds       : bond        0.04006 (  310)
  hydrogen bonds       : angle       4.26052 (  909)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
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Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
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Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  188 TYR cc_start: 0.8974 (m-80) cc_final: 0.8440 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1224
  time to fit residues: 8.4149
Evaluate side-chains
  43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
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XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 58 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 59 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
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ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.050274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.038605 restraints weight = 129480.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.040395 restraints weight = 78134.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.041754 restraints weight = 53763.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.042785 restraints weight = 39990.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.043565 restraints weight = 31486.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.4250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5172  Z= 0.095
  Angle     :  0.493   5.500   7088  Z= 0.238
  Chirality :  0.036   0.137    799
  Planarity :  0.005   0.039    923
  Dihedral  :  3.413  12.841    722
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.34), residues: 661
  helix:  3.05 (0.28), residues: 325
  sheet: -1.36 (0.46), residues: 84
  loop :  0.41 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 192 
 TYR   0.007   0.001   TYR A 188 
 PHE   0.008   0.001   PHE A 294 
 TRP   0.012   0.001   TRP A 472 
 HIS   0.001   0.000   HIS B 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 5172)
  covalent geometry    : angle       0.49268 ( 7088)
  hydrogen bonds       : bond        0.03884 (  310)
  hydrogen bonds       : angle       4.18473 (  909)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1703.43 seconds
wall clock time: 29 minutes 33.84 seconds (1773.84 seconds total)