Starting phenix.real_space_refine
on Tue Feb  3 20:41:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gqn_51507/02_2026/9gqn_51507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gqn_51507/02_2026/9gqn_51507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gqn_51507/02_2026/9gqn_51507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gqn_51507/02_2026/9gqn_51507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gqn_51507/02_2026/9gqn_51507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gqn_51507/02_2026/9gqn_51507.cif"
  }
  resolution = 3.1
  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=   0.150
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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    4330      2.51       5
     N    1100      2.21       5
     O    1268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6718
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 408, 3359
          Classifications: {'peptide': 408}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 395}
          Chain breaks: 3
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.22, per 1000 atoms: 0.33
  Number of scatterers: 6718
  At special positions: 0
  Unit cell: (128.438, 76.718, 84.476, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1268      8.00
     N    1100      7.00
     C    4330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 0.38
  Conformation dependent library (CDL) restraints added in 346.2 milliseconds
  

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      72.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 151 through 155
    Processing helix  chain 'A' and resid 178 through 198
      removed outlier: 3.535A  pdb=" N   LEU A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 222
    Processing helix  chain 'A' and resid 226 through 240
      removed outlier: 3.514A  pdb=" N   LYS A 236 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 273
      removed outlier: 3.511A  pdb=" N   GLN A 254 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLN A 260 " --> pdb=" O   ASN A 256 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 264 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 286
    Processing helix  chain 'A' and resid 287 through 314
      removed outlier: 3.592A  pdb=" N   PHE A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   ASP A 308 " --> pdb=" O   MET A 304 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   SER A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 319
    Processing helix  chain 'A' and resid 320 through 324
      removed outlier: 3.527A  pdb=" N   MET A 324 " --> pdb=" O   THR A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 329
      No H-bonds generated for 'chain 'A' and resid 327 through 329'
    Processing helix  chain 'A' and resid 330 through 344
      removed outlier: 3.806A  pdb=" N   LYS A 334 " --> pdb=" O   PHE A 330 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 336 " --> pdb=" O   HIS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 362
      removed outlier: 3.946A  pdb=" N   SER A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 388
    Processing helix  chain 'A' and resid 400 through 416
      removed outlier: 4.396A  pdb=" N   LEU A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ALA A 405 " --> pdb=" O   LYS A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 438
    Processing helix  chain 'A' and resid 453 through 478
    Processing helix  chain 'A' and resid 495 through 499
    Processing helix  chain 'A' and resid 507 through 525
      removed outlier: 3.533A  pdb=" N   HIS A 524 " --> pdb=" O   TYR A 520 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 556
      Proline residue:  A 553  - end of helix
    Processing helix  chain 'B' and resid 139 through 149
    Processing helix  chain 'B' and resid 151 through 155
    Processing helix  chain 'B' and resid 178 through 198
      removed outlier: 3.535A  pdb=" N   LEU B 196 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 222
    Processing helix  chain 'B' and resid 226 through 240
      removed outlier: 3.514A  pdb=" N   LYS B 236 " --> pdb=" O   GLU B 232 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B 237 " --> pdb=" O   GLU B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 273
      removed outlier: 3.510A  pdb=" N   GLN B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLN B 260 " --> pdb=" O   ASN B 256 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B 264 " --> pdb=" O   GLN B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 286
    Processing helix  chain 'B' and resid 287 through 314
      removed outlier: 3.592A  pdb=" N   PHE B 307 " --> pdb=" O   LYS B 303 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ASP B 308 " --> pdb=" O   MET B 304 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   SER B 309 " --> pdb=" O   LYS B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 319
    Processing helix  chain 'B' and resid 320 through 324
      removed outlier: 3.529A  pdb=" N   MET B 324 " --> pdb=" O   THR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 329
      No H-bonds generated for 'chain 'B' and resid 327 through 329'
    Processing helix  chain 'B' and resid 330 through 344
      removed outlier: 3.807A  pdb=" N   LYS B 334 " --> pdb=" O   PHE B 330 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE B 336 " --> pdb=" O   HIS B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 362
      removed outlier: 3.946A  pdb=" N   SER B 348 " --> pdb=" O   LYS B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 388
    Processing helix  chain 'B' and resid 400 through 416
      removed outlier: 4.396A  pdb=" N   LEU B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ALA B 405 " --> pdb=" O   LYS B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 438
    Processing helix  chain 'B' and resid 453 through 478
    Processing helix  chain 'B' and resid 495 through 499
    Processing helix  chain 'B' and resid 507 through 525
      removed outlier: 3.532A  pdb=" N   HIS B 524 " --> pdb=" O   TYR B 520 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLU B 525 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 556
      Proline residue:  B 553  - end of helix

    402 hydrogen bonds defined for protein.
    1164 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: 0.98

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2098
        1.34 -     1.46: 1189
        1.46 -     1.57: 3535
        1.57 -     1.69: 0
        1.69 -     1.80: 36
  Bond restraints: 6858
  Sorted by residual:
  bond pdb=" CA  PHE A 445 "
       pdb=" C   PHE A 445 "
    ideal  model  delta    sigma   weight residual
    1.523  1.539 -0.016 1.34e-02 5.57e+03 1.34e+00
  bond pdb=" CA  PHE B 445 "
       pdb=" C   PHE B 445 "
    ideal  model  delta    sigma   weight residual
    1.523  1.538 -0.015 1.34e-02 5.57e+03 1.19e+00
  bond pdb=" CA  ASP B 447 "
       pdb=" CB  ASP B 447 "
    ideal  model  delta    sigma   weight residual
    1.528  1.541 -0.012 1.37e-02 5.33e+03 8.21e-01
  bond pdb=" CA  ASP A 447 "
       pdb=" CB  ASP A 447 "
    ideal  model  delta    sigma   weight residual
    1.528  1.540 -0.012 1.37e-02 5.33e+03 7.91e-01
  bond pdb=" C   GLN A 465 "
       pdb=" O   GLN A 465 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.010 1.15e-02 7.56e+03 7.64e-01
  ... (remaining 6853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 8470
        1.46 -     2.91: 625
        2.91 -     4.37: 109
        4.37 -     5.83: 16
        5.83 -     7.28: 4
  Bond angle restraints: 9224
  Sorted by residual:
  angle pdb=" N   GLN A 535 "
        pdb=" CA  GLN A 535 "
        pdb=" C   GLN A 535 "
      ideal   model   delta    sigma   weight residual
     114.62  110.09    4.53 1.14e+00 7.69e-01 1.58e+01
  angle pdb=" N   GLN B 535 "
        pdb=" CA  GLN B 535 "
        pdb=" C   GLN B 535 "
      ideal   model   delta    sigma   weight residual
     114.62  110.12    4.50 1.14e+00 7.69e-01 1.56e+01
  angle pdb=" N   LEU B 238 "
        pdb=" CA  LEU B 238 "
        pdb=" C   LEU B 238 "
      ideal   model   delta    sigma   weight residual
     111.28  114.88   -3.60 1.09e+00 8.42e-01 1.09e+01
  angle pdb=" N   LEU A 238 "
        pdb=" CA  LEU A 238 "
        pdb=" C   LEU A 238 "
      ideal   model   delta    sigma   weight residual
     111.28  114.87   -3.59 1.09e+00 8.42e-01 1.09e+01
  angle pdb=" C   PHE B 445 "
        pdb=" N   THR B 446 "
        pdb=" CA  THR B 446 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  ... (remaining 9219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 3776
       17.30 -    34.61: 322
       34.61 -    51.91: 50
       51.91 -    69.21: 26
       69.21 -    86.51: 6
  Dihedral angle restraints: 4180
    sinusoidal: 1746
      harmonic: 2434
  Sorted by residual:
  dihedral pdb=" CG  ARG B 547 "
           pdb=" CD  ARG B 547 "
           pdb=" NE  ARG B 547 "
           pdb=" CZ  ARG B 547 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  129.72  -39.72     2      1.50e+01 4.44e-03 8.71e+00
  dihedral pdb=" CG  ARG A 547 "
           pdb=" CD  ARG A 547 "
           pdb=" NE  ARG A 547 "
           pdb=" CZ  ARG A 547 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  129.71  -39.71     2      1.50e+01 4.44e-03 8.71e+00
  dihedral pdb=" CA  LYS B 131 "
           pdb=" C   LYS B 131 "
           pdb=" N   LYS B 132 "
           pdb=" CA  LYS B 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -166.00  -14.00     0      5.00e+00 4.00e-02 7.83e+00
  ... (remaining 4177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 587
       0.036 -    0.072: 308
       0.072 -    0.108: 95
       0.108 -    0.143: 16
       0.143 -    0.179: 8
  Chirality restraints: 1014
  Sorted by residual:
  chirality pdb=" CB  THR A 223 "
            pdb=" CA  THR A 223 "
            pdb=" OG1 THR A 223 "
            pdb=" CG2 THR A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" CB  THR B 223 "
            pdb=" CA  THR B 223 "
            pdb=" OG1 THR B 223 "
            pdb=" CG2 THR B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.63e-01
  chirality pdb=" CA  ILE B 276 "
            pdb=" N   ILE B 276 "
            pdb=" C   ILE B 276 "
            pdb=" CB  ILE B 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.81e-01
  ... (remaining 1011 not shown)

  Planarity restraints: 1158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 183 "   -0.114 9.50e-02 1.11e+02   5.15e-02 2.18e+00
        pdb=" NE  ARG A 183 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 183 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 183 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 183 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 183 "    0.114 9.50e-02 1.11e+02   5.14e-02 2.17e+00
        pdb=" NE  ARG B 183 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 183 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 183 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 183 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 292 "    0.007 2.00e-02 2.50e+03   1.38e-02 1.89e+00
        pdb=" C   LYS A 292 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   LYS A 292 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE A 293 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1155 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 418
        2.74 -     3.28: 6814
        3.28 -     3.82: 10013
        3.82 -     4.36: 11838
        4.36 -     4.90: 20632
  Nonbonded interactions: 49715
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 530 "
            pdb=" ND2 ASN B 534 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   ASP A 530 "
            pdb=" ND2 ASN A 534 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   MET B 372 "
            pdb=" NZ  LYS B 406 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   MET A 372 "
            pdb=" NZ  LYS A 406 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   ILE A 533 "
            pdb=" N   GLN A 535 "
     model   vdw
     2.230 3.120
  ... (remaining 49710 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'
}

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:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
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   0.023   6858  Z= 0.174
  Angle     :  0.851   7.283   9224  Z= 0.580
  Chirality :  0.046   0.179   1014
  Planarity :  0.004   0.052   1158
  Dihedral  : 13.829  86.512   2596
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.50 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  0.08 (0.28), residues: 800
  helix:  0.99 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.02 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 183 
 TYR   0.015   0.003   TYR B 350 
 PHE   0.013   0.002   PHE B 492 
 TRP   0.015   0.002   TRP A 328 
 HIS   0.005   0.002   HIS B 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6858)
  covalent geometry    : angle       0.85069 ( 9224)
  hydrogen bonds       : bond        0.24252 (  402)
  hydrogen bonds       : angle       4.75873 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 LYS cc_start: 0.7336 (tttt) cc_final: 0.6913 (tptt)
REVERT: A  276 ILE cc_start: 0.7666 (mt) cc_final: 0.7224 (pt)
REVERT: A  312 LYS cc_start: 0.7767 (ttmm) cc_final: 0.7445 (tttm)
REVERT: A  342 LYS cc_start: 0.8119 (tttt) cc_final: 0.7633 (mptt)
REVERT: A  388 LYS cc_start: 0.7187 (mtpt) cc_final: 0.6890 (mmtt)
REVERT: B  140 LYS cc_start: 0.7740 (tmmt) cc_final: 0.7108 (mptt)
REVERT: B  216 LYS cc_start: 0.7375 (tttt) cc_final: 0.7151 (tptt)
REVERT: B  276 ILE cc_start: 0.7647 (mt) cc_final: 0.7266 (pt)
REVERT: B  341 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7797 (tttm)
REVERT: B  342 LYS cc_start: 0.7954 (tttt) cc_final: 0.7415 (mptt)
REVERT: B  388 LYS cc_start: 0.6561 (mtpt) cc_final: 0.6283 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1047
  time to fit residues: 20.7664
Evaluate side-chains
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0870
   chunk 61 optimal weight:    0.0050
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0040
   overall best weight:    0.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 268 HIS
A 329 GLN
A 399 HIS
** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 GLN
B 268 HIS
B 329 GLN
B 399 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.176373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.133776 restraints weight = 6788.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.05
r_work: 0.3260 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6858  Z= 0.142
  Angle     :  0.539   5.484   9224  Z= 0.296
  Chirality :  0.039   0.142   1014
  Planarity :  0.003   0.025   1158
  Dihedral  :  3.631  14.313    870
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  7.46 %
    Favored  : 91.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  2.09 (0.31), residues: 800
  helix:  2.60 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -1.61 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 143 
 TYR   0.015   0.002   TYR A 453 
 PHE   0.026   0.002   PHE A 445 
 TRP   0.012   0.002   TRP A 207 
 HIS   0.005   0.002   HIS B 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6858)
  covalent geometry    : angle       0.53903 ( 9224)
  hydrogen bonds       : bond        0.05995 (  402)
  hydrogen bonds       : angle       3.48646 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.7154 (ttmm) cc_final: 0.6894 (tptt)
REVERT: A  388 LYS cc_start: 0.5899 (mtpt) cc_final: 0.5624 (mmtt)
REVERT: A  409 LYS cc_start: 0.7412 (tttm) cc_final: 0.7199 (ttmt)
REVERT: B  409 LYS cc_start: 0.7562 (tttm) cc_final: 0.7305 (ttmt)
  outliers start: 10
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0997
  time to fit residues: 11.9431
Evaluate side-chains
  85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  532 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 GLN
** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.165001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.121065 restraints weight = 6817.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.04
r_work: 0.3089 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6858  Z= 0.154
  Angle     :  0.555   8.132   9224  Z= 0.300
  Chirality :  0.039   0.136   1014
  Planarity :  0.003   0.028   1158
  Dihedral  :  3.640  15.948    870
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  :  8.77 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  2.02 (0.31), residues: 800
  helix:  2.57 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.72 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 454 
 TYR   0.015   0.002   TYR B 350 
 PHE   0.018   0.002   PHE A 182 
 TRP   0.009   0.002   TRP B 353 
 HIS   0.004   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6858)
  covalent geometry    : angle       0.55504 ( 9224)
  hydrogen bonds       : bond        0.07028 (  402)
  hydrogen bonds       : angle       3.38558 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.7177 (ttmm) cc_final: 0.6939 (tptt)
REVERT: A  342 LYS cc_start: 0.7661 (tttt) cc_final: 0.7324 (tttm)
REVERT: A  388 LYS cc_start: 0.5518 (mtpt) cc_final: 0.5309 (mmtt)
REVERT: B  290 MET cc_start: 0.7602 (mmt) cc_final: 0.7320 (mmm)
REVERT: B  312 LYS cc_start: 0.7402 (tttm) cc_final: 0.6930 (tptt)
REVERT: B  342 LYS cc_start: 0.7513 (tttt) cc_final: 0.6456 (mptt)
  outliers start: 20
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0991
  time to fit residues: 11.7929
Evaluate side-chains
  79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  532 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0170
   chunk 71 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 GLN
B 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.165792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.121983 restraints weight = 6957.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.08
r_work: 0.3099 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6858  Z= 0.122
  Angle     :  0.471   5.232   9224  Z= 0.258
  Chirality :  0.037   0.137   1014
  Planarity :  0.003   0.018   1158
  Dihedral  :  3.639  15.458    870
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.69 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  2.15 (0.32), residues: 800
  helix:  2.69 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.73 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 183 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.015   0.001   PHE B 182 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.004   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6858)
  covalent geometry    : angle       0.47150 ( 9224)
  hydrogen bonds       : bond        0.05545 (  402)
  hydrogen bonds       : angle       3.19470 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  233 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7187 (mm-30)
REVERT: A  312 LYS cc_start: 0.7123 (ttmm) cc_final: 0.6922 (tptt)
REVERT: A  543 GLU cc_start: 0.6922 (tt0) cc_final: 0.6618 (mt-10)
REVERT: B  290 MET cc_start: 0.7544 (mmt) cc_final: 0.7247 (mmm)
REVERT: B  312 LYS cc_start: 0.7297 (tttm) cc_final: 0.6894 (tptt)
REVERT: B  543 GLU cc_start: 0.6816 (tt0) cc_final: 0.6478 (mt-10)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1058
  time to fit residues: 11.8670
Evaluate side-chains
  78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  532 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0070
   overall best weight:    0.9002

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

Flipped N/Q/H residues before XYZ refinement:
A 215 ASN
A 465 GLN
A 524 HIS
A 535 GLN
B 235 GLN
B 524 HIS
B 535 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.163531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.117065 restraints weight = 7001.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.34
r_work: 0.3094 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6858  Z= 0.150
  Angle     :  0.517   6.335   9224  Z= 0.281
  Chirality :  0.038   0.135   1014
  Planarity :  0.003   0.022   1158
  Dihedral  :  3.693  15.620    870
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.13 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  1.94 (0.31), residues: 800
  helix:  2.50 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.73 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 454 
 TYR   0.013   0.002   TYR A 350 
 PHE   0.017   0.002   PHE A 182 
 TRP   0.009   0.002   TRP A 353 
 HIS   0.005   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6858)
  covalent geometry    : angle       0.51682 ( 9224)
  hydrogen bonds       : bond        0.06725 (  402)
  hydrogen bonds       : angle       3.29527 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  196 LEU cc_start: 0.7248 (tp) cc_final: 0.6517 (mt)
REVERT: A  342 LYS cc_start: 0.7665 (tttt) cc_final: 0.7406 (tttm)
REVERT: A  382 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6819 (tp30)
REVERT: A  543 GLU cc_start: 0.6978 (tt0) cc_final: 0.6662 (mt-10)
REVERT: B  312 LYS cc_start: 0.7419 (tttm) cc_final: 0.7089 (tptt)
REVERT: B  342 LYS cc_start: 0.7526 (tttt) cc_final: 0.7262 (tttm)
REVERT: B  382 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6844 (tp30)
REVERT: B  543 GLU cc_start: 0.6921 (tt0) cc_final: 0.6657 (mt-10)
  outliers start: 14
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1032
  time to fit residues: 11.1323
Evaluate side-chains
  79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  532 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0170
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.9620

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
B 256 ASN
B 535 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.161620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.114590 restraints weight = 7037.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.37
r_work: 0.3053 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6858  Z= 0.153
  Angle     :  0.510   5.731   9224  Z= 0.277
  Chirality :  0.038   0.135   1014
  Planarity :  0.003   0.025   1158
  Dihedral  :  3.741  15.808    870
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.65 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  1.85 (0.31), residues: 800
  helix:  2.41 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.73 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 454 
 TYR   0.011   0.002   TYR A 350 
 PHE   0.016   0.002   PHE B 182 
 TRP   0.009   0.002   TRP A 353 
 HIS   0.005   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6858)
  covalent geometry    : angle       0.50964 ( 9224)
  hydrogen bonds       : bond        0.06591 (  402)
  hydrogen bonds       : angle       3.28474 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  382 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6853 (tp30)
REVERT: A  543 GLU cc_start: 0.7054 (tt0) cc_final: 0.6696 (mt-10)
REVERT: B  312 LYS cc_start: 0.7432 (tttm) cc_final: 0.7114 (tptt)
REVERT: B  342 LYS cc_start: 0.7522 (tttt) cc_final: 0.7275 (tttm)
REVERT: B  382 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6852 (tp30)
REVERT: B  543 GLU cc_start: 0.7081 (tt0) cc_final: 0.6722 (mt-10)
  outliers start: 16
  outliers final: 15
  residues processed: 80
  average time/residue: 0.1055
  time to fit residues: 11.0122
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain B residue  181 LYS
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  552 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0170
   chunk 0 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0870
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 511 ASN
A 535 GLN
B 535 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.162705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.116269 restraints weight = 6945.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.33
r_work: 0.3087 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.4236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6858  Z= 0.135
  Angle     :  0.480   5.423   9224  Z= 0.262
  Chirality :  0.037   0.133   1014
  Planarity :  0.002   0.018   1158
  Dihedral  :  3.700  15.287    870
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.65 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  1.98 (0.31), residues: 800
  helix:  2.49 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.60 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 475 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.014   0.001   PHE B 182 
 TRP   0.010   0.002   TRP A 353 
 HIS   0.005   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6858)
  covalent geometry    : angle       0.47987 ( 9224)
  hydrogen bonds       : bond        0.06006 (  402)
  hydrogen bonds       : angle       3.22426 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  382 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6828 (tp30)
REVERT: A  543 GLU cc_start: 0.7071 (tt0) cc_final: 0.6706 (mt-10)
REVERT: B  312 LYS cc_start: 0.7392 (tttm) cc_final: 0.7104 (tptt)
REVERT: B  382 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6830 (tp30)
REVERT: B  543 GLU cc_start: 0.7016 (tt0) cc_final: 0.6677 (mt-10)
  outliers start: 17
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0984
  time to fit residues: 10.3513
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  552 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
B 215 ASN
B 535 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.161857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.115435 restraints weight = 7055.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.34
r_work: 0.3075 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6858  Z= 0.141
  Angle     :  0.491   5.358   9224  Z= 0.267
  Chirality :  0.037   0.134   1014
  Planarity :  0.002   0.021   1158
  Dihedral  :  3.723  15.137    870
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.04 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  1.94 (0.31), residues: 800
  helix:  2.44 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.56 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.014   0.001   PHE B 182 
 TRP   0.010   0.002   TRP A 353 
 HIS   0.005   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6858)
  covalent geometry    : angle       0.49059 ( 9224)
  hydrogen bonds       : bond        0.06276 (  402)
  hydrogen bonds       : angle       3.24130 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  382 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6833 (tp30)
REVERT: A  543 GLU cc_start: 0.7020 (tt0) cc_final: 0.6662 (mt-10)
REVERT: B  312 LYS cc_start: 0.7369 (tttm) cc_final: 0.7108 (tptt)
REVERT: B  382 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6834 (tp30)
REVERT: B  543 GLU cc_start: 0.7045 (tt0) cc_final: 0.6688 (mt-10)
  outliers start: 18
  outliers final: 15
  residues processed: 79
  average time/residue: 0.1092
  time to fit residues: 11.2206
Evaluate side-chains
  77 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  552 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 78 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
B 511 ASN
B 535 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.162877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.116556 restraints weight = 7026.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.34
r_work: 0.3072 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6858  Z= 0.130
  Angle     :  0.474   6.215   9224  Z= 0.258
  Chirality :  0.037   0.134   1014
  Planarity :  0.002   0.018   1158
  Dihedral  :  3.671  14.845    870
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.70 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  2.03 (0.31), residues: 800
  helix:  2.51 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.55 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.013   0.001   PHE B 182 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.004   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6858)
  covalent geometry    : angle       0.47448 ( 9224)
  hydrogen bonds       : bond        0.05857 (  402)
  hydrogen bonds       : angle       3.20662 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  382 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6849 (tp30)
REVERT: A  543 GLU cc_start: 0.7087 (tt0) cc_final: 0.6721 (mt-10)
REVERT: B  312 LYS cc_start: 0.7359 (tttm) cc_final: 0.7119 (tptt)
REVERT: B  382 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6851 (tp30)
REVERT: B  543 GLU cc_start: 0.7046 (tt0) cc_final: 0.6690 (mt-10)
  outliers start: 15
  outliers final: 15
  residues processed: 79
  average time/residue: 0.1099
  time to fit residues: 11.1087
Evaluate side-chains
  82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  552 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 25 optimal weight:    0.3980
   chunk 52 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
B 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.165075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.118757 restraints weight = 7004.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.35
r_work: 0.3119 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6858  Z= 0.118
  Angle     :  0.462   7.107   9224  Z= 0.250
  Chirality :  0.036   0.135   1014
  Planarity :  0.002   0.018   1158
  Dihedral  :  3.623  14.588    870
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.96 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  2.12 (0.31), residues: 800
  helix:  2.58 (0.23), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.53 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 475 
 TYR   0.013   0.001   TYR A 453 
 PHE   0.013   0.001   PHE B 182 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.004   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6858)
  covalent geometry    : angle       0.46168 ( 9224)
  hydrogen bonds       : bond        0.05442 (  402)
  hydrogen bonds       : angle       3.15713 ( 1164)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  382 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6810 (tp30)
REVERT: A  543 GLU cc_start: 0.7061 (tt0) cc_final: 0.6691 (mt-10)
REVERT: B  312 LYS cc_start: 0.7320 (tttm) cc_final: 0.7072 (tptt)
REVERT: B  382 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6811 (tp30)
REVERT: B  543 GLU cc_start: 0.7015 (tt0) cc_final: 0.6658 (mt-10)
  outliers start: 14
  outliers final: 13
  residues processed: 76
  average time/residue: 0.1119
  time to fit residues: 11.0477
Evaluate side-chains
  78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  477 ILE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  552 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0370
   chunk 13 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
B 535 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.164986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.118694 restraints weight = 7005.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.35
r_work: 0.3139 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6858  Z= 0.119
  Angle     :  0.457   4.944   9224  Z= 0.249
  Chirality :  0.036   0.135   1014
  Planarity :  0.002   0.018   1158
  Dihedral  :  3.588  14.580    870
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.96 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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 are not related in a simple way.
  whole:  2.13 (0.31), residues: 800
  helix:  2.59 (0.23), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.51 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 475 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.013   0.001   PHE B 182 
 TRP   0.010   0.001   TRP A 353 
 HIS   0.004   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6858)
  covalent geometry    : angle       0.45697 ( 9224)
  hydrogen bonds       : bond        0.05449 (  402)
  hydrogen bonds       : angle       3.14600 ( 1164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1722.24 seconds
wall clock time: 30 minutes 18.38 seconds (1818.38 seconds total)