Starting phenix.real_space_refine
on Tue Mar  3 14:37:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7voj_32050/03_2026/7voj_32050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7voj_32050/03_2026/7voj_32050.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7voj_32050/03_2026/7voj_32050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7voj_32050/03_2026/7voj_32050.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7voj_32050/03_2026/7voj_32050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7voj_32050/03_2026/7voj_32050.cif"
  }
  resolution = 3.0
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic.
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
     Al      2      5.89       5
     S      32      5.16       5
     C    4074      2.51       5
     N    1052      2.21       5
     O    1158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6318
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3150
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 12, 'TRANS': 387}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 9
          Unusual residues: {' AL': 1, 'ACY': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.27, per 1000 atoms: 0.36
  Number of scatterers: 6318
  At special positions: 0
  Unit cell: (84.162, 84.162, 113.568, 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      32     16.00
     Al      2     13.00
     O    1158      8.00
     N    1052      7.00
     C    4074      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: 0.68
  Conformation dependent library (CDL) restraints added in 246.3 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      84.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
      removed outlier: 3.753A  pdb=" N   ASP A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 42
      removed outlier: 3.723A  pdb=" N   GLY A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 66
      removed outlier: 3.879A  pdb=" N   VAL A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 102
      removed outlier: 3.844A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 125
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 134 through 150
    Processing helix  chain 'A' and resid 156 through 183
    Processing helix  chain 'A' and resid 187 through 214
    Processing helix  chain 'A' and resid 223 through 241
      removed outlier: 4.754A  pdb=" N   ARG A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   TYR A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP A 241 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 254
      removed outlier: 3.716A  pdb=" N   GLU A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 294
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 3.750A  pdb=" N   LYS A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 330
      removed outlier: 3.727A  pdb=" N   LEU A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 356
      removed outlier: 3.914A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER A 344 " --> pdb=" O   HIS A 340 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 399
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 3.753A  pdb=" N   ASP B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 42
      removed outlier: 3.723A  pdb=" N   GLY B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 66
      removed outlier: 3.879A  pdb=" N   VAL B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 102
      removed outlier: 3.844A  pdb=" N   GLY B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 125
    Processing helix  chain 'B' and resid 127 through 133
    Processing helix  chain 'B' and resid 134 through 150
    Processing helix  chain 'B' and resid 156 through 183
    Processing helix  chain 'B' and resid 187 through 214
    Processing helix  chain 'B' and resid 223 through 241
      removed outlier: 4.754A  pdb=" N   ARG B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   TYR B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP B 241 " --> pdb=" O   LYS B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 254
      removed outlier: 3.716A  pdb=" N   GLU B 246 " --> pdb=" O   SER B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 294
    Processing helix  chain 'B' and resid 299 through 305
      removed outlier: 3.750A  pdb=" N   LYS B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 330
      removed outlier: 3.727A  pdb=" N   LEU B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 356
      removed outlier: 3.914A  pdb=" N   ILE B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER B 344 " --> pdb=" O   HIS B 340 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS B 356 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 399

    521 hydrogen bonds defined for protein.
    1563 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: 0.94

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1610
        1.33 -     1.45: 1186
        1.45 -     1.57: 3588
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 6440
  Sorted by residual:
  bond pdb=" C   CYS A 184 "
       pdb=" O   CYS A 184 "
    ideal  model  delta    sigma   weight residual
    1.249  1.229  0.020 8.50e-03 1.38e+04 5.39e+00
  bond pdb=" C   CYS B 184 "
       pdb=" O   CYS B 184 "
    ideal  model  delta    sigma   weight residual
    1.249  1.229  0.020 8.50e-03 1.38e+04 5.39e+00
  bond pdb=" C   GLY A 102 "
       pdb=" N   ALA A 103 "
    ideal  model  delta    sigma   weight residual
    1.333  1.301  0.032 1.52e-02 4.33e+03 4.40e+00
  bond pdb=" C   GLY B 102 "
       pdb=" N   ALA B 103 "
    ideal  model  delta    sigma   weight residual
    1.333  1.301  0.032 1.52e-02 4.33e+03 4.40e+00
  bond pdb=" CA  TYR B  50 "
       pdb=" C   TYR B  50 "
    ideal  model  delta    sigma   weight residual
    1.522  1.548 -0.026 1.37e-02 5.33e+03 3.59e+00
  ... (remaining 6435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 8322
        2.18 -     4.36: 328
        4.36 -     6.54: 24
        6.54 -     8.72: 18
        8.72 -    10.90: 6
  Bond angle restraints: 8698
  Sorted by residual:
  angle pdb=" N   PHE B  51 "
        pdb=" CA  PHE B  51 "
        pdb=" C   PHE B  51 "
      ideal   model   delta    sigma   weight residual
     111.28  122.18  -10.90 1.09e+00 8.42e-01 1.00e+02
  angle pdb=" N   PHE A  51 "
        pdb=" CA  PHE A  51 "
        pdb=" C   PHE A  51 "
      ideal   model   delta    sigma   weight residual
     111.28  122.18  -10.90 1.09e+00 8.42e-01 1.00e+02
  angle pdb=" N   PHE B 182 "
        pdb=" CA  PHE B 182 "
        pdb=" C   PHE B 182 "
      ideal   model   delta    sigma   weight residual
     113.17  122.72   -9.55 1.26e+00 6.30e-01 5.75e+01
  angle pdb=" N   PHE A 182 "
        pdb=" CA  PHE A 182 "
        pdb=" C   PHE A 182 "
      ideal   model   delta    sigma   weight residual
     113.17  122.72   -9.55 1.26e+00 6.30e-01 5.75e+01
  angle pdb=" N   VAL B  65 "
        pdb=" CA  VAL B  65 "
        pdb=" C   VAL B  65 "
      ideal   model   delta    sigma   weight residual
     110.62  117.44   -6.82 1.02e+00 9.61e-01 4.48e+01
  ... (remaining 8693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.31: 3354
       14.31 -    28.62: 372
       28.62 -    42.93: 88
       42.93 -    57.24: 30
       57.24 -    71.55: 6
  Dihedral angle restraints: 3850
    sinusoidal: 1526
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CA  ARG B 154 "
           pdb=" C   ARG B 154 "
           pdb=" N   ASP B 155 "
           pdb=" CA  ASP B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.71  -26.29     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ARG A 154 "
           pdb=" C   ARG A 154 "
           pdb=" N   ASP A 155 "
           pdb=" CA  ASP A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.71  -26.29     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  PRO A 299 "
           pdb=" C   PRO A 299 "
           pdb=" N   VAL A 300 "
           pdb=" CA  VAL A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.47  -21.53     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 3847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 866
       0.081 -    0.162: 110
       0.162 -    0.243: 14
       0.243 -    0.324: 2
       0.324 -    0.404: 4
  Chirality restraints: 996
  Sorted by residual:
  chirality pdb=" CA  PHE B 182 "
            pdb=" N   PHE B 182 "
            pdb=" C   PHE B 182 "
            pdb=" CB  PHE B 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.09e+00
  chirality pdb=" CA  PHE A 182 "
            pdb=" N   PHE A 182 "
            pdb=" C   PHE A 182 "
            pdb=" CB  PHE A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.09e+00
  chirality pdb=" CA  PHE A  51 "
            pdb=" N   PHE A  51 "
            pdb=" C   PHE A  51 "
            pdb=" CB  PHE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.05e+00
  ... (remaining 993 not shown)

  Planarity restraints: 1094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 180 "    0.019 2.00e-02 2.50e+03   3.94e-02 1.55e+01
        pdb=" C   SER B 180 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   SER B 180 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ILE B 181 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 180 "   -0.019 2.00e-02 2.50e+03   3.94e-02 1.55e+01
        pdb=" C   SER A 180 "    0.068 2.00e-02 2.50e+03
        pdb=" O   SER A 180 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ILE A 181 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 184 "    0.047 5.00e-02 4.00e+02   7.11e-02 8.09e+00
        pdb=" N   PRO B 185 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 185 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 185 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1091 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 96
        2.63 -     3.20: 5470
        3.20 -     3.76: 9637
        3.76 -     4.33: 12737
        4.33 -     4.90: 21603
  Nonbonded interactions: 49543
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 160 "
            pdb="AL    AL A 603 "
     model   vdw
     2.061 2.020
  nonbonded pdb=" OD1 ASP B 160 "
            pdb="AL    AL B 603 "
     model   vdw
     2.061 2.020
  nonbonded pdb=" OD2 ASP B 160 "
            pdb="AL    AL B 603 "
     model   vdw
     2.113 2.020
  nonbonded pdb=" OD2 ASP A 160 "
            pdb="AL    AL A 603 "
     model   vdw
     2.113 2.020
  nonbonded pdb=" O   ACY B 601 "
            pdb="AL    AL B 603 "
     model   vdw
     2.116 2.020
  ... (remaining 49538 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.150
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057   6440  Z= 0.371
  Angle     :  1.008  10.902   8698  Z= 0.626
  Chirality :  0.062   0.404    996
  Planarity :  0.007   0.071   1094
  Dihedral  : 13.588  71.548   2346
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.28 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.39 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.46 (0.26), residues: 792
  helix: -1.27 (0.17), residues: 664
  sheet:  None (None), residues: 0
  loop : -2.54 (0.60), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 154 
 TYR   0.015   0.002   TYR A 236 
 PHE   0.016   0.002   PHE B 134 
 TRP   0.019   0.003   TRP B 129 
 HIS   0.003   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00829 ( 6440)
  covalent geometry    : angle       1.00782 ( 8698)
  hydrogen bonds       : bond        0.18289 (  521)
  hydrogen bonds       : angle       6.32160 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.5751 (mmp-170)
REVERT: A   96 GLN cc_start: 0.7767 (mm110) cc_final: 0.7501 (mm-40)
REVERT: A  201 ASP cc_start: 0.7737 (t0) cc_final: 0.7447 (t70)
REVERT: A  209 ASP cc_start: 0.7532 (m-30) cc_final: 0.7159 (m-30)
REVERT: A  226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p)
REVERT: A  370 SER cc_start: 0.9002 (m) cc_final: 0.8750 (p)
REVERT: B    5 ARG cc_start: 0.6463 (mtt-85) cc_final: 0.5741 (mmp-170)
REVERT: B   96 GLN cc_start: 0.7757 (mm110) cc_final: 0.7491 (mm-40)
REVERT: B  201 ASP cc_start: 0.7734 (t0) cc_final: 0.7445 (t70)
REVERT: B  209 ASP cc_start: 0.7539 (m-30) cc_final: 0.7166 (m-30)
REVERT: B  226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p)
  outliers start: 12
  outliers final: 10
  residues processed: 149
  average time/residue: 0.4891
  time to fit residues: 76.8042
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A  24 HIS
A  96 GLN
A 266 HIS
A 289 ASN
A 293 ASN
A 330 GLN
A 340 HIS
A 403 ASN
B  24 HIS
B  96 GLN
B 266 HIS
B 289 ASN
B 293 ASN
B 330 GLN
B 340 HIS
B 403 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.156077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.105584 restraints weight = 7467.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.23
r_work: 0.3175 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6440  Z= 0.132
  Angle     :  0.532   5.671   8698  Z= 0.294
  Chirality :  0.037   0.137    996
  Planarity :  0.004   0.042   1094
  Dihedral  :  5.590  56.592    874
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.60 %
    Favored  : 77.52 %
  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 are not related in a simple way.
  whole:  0.96 (0.30), residues: 792
  helix:  1.26 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.69 (0.52), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 235 
 TYR   0.010   0.001   TYR B  50 
 PHE   0.020   0.001   PHE B 206 
 TRP   0.014   0.001   TRP A 129 
 HIS   0.004   0.001   HIS B 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6440)
  covalent geometry    : angle       0.53191 ( 8698)
  hydrogen bonds       : bond        0.05281 (  521)
  hydrogen bonds       : angle       3.85903 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.6561 (mtt-85) cc_final: 0.5948 (mmp-170)
REVERT: A  201 ASP cc_start: 0.8132 (t0) cc_final: 0.7862 (t70)
REVERT: A  209 ASP cc_start: 0.7331 (m-30) cc_final: 0.6915 (m-30)
REVERT: B    5 ARG cc_start: 0.6506 (mtt-85) cc_final: 0.5593 (mmp-170)
REVERT: B  201 ASP cc_start: 0.8138 (t0) cc_final: 0.7877 (t70)
REVERT: B  209 ASP cc_start: 0.7337 (m-30) cc_final: 0.6921 (m-30)
  outliers start: 20
  outliers final: 8
  residues processed: 121
  average time/residue: 0.4333
  time to fit residues: 55.5254
Evaluate side-chains
  93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 62 optimal weight:   10.0000
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 293 ASN
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.156358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.106990 restraints weight = 7520.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.15
r_work: 0.3142 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6440  Z= 0.140
  Angle     :  0.524   7.211   8698  Z= 0.281
  Chirality :  0.036   0.142    996
  Planarity :  0.004   0.043   1094
  Dihedral  :  4.772  50.399    862
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 20.75 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.31), residues: 792
  helix:  2.10 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.57 (0.51), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A   9 
 TYR   0.010   0.001   TYR B  50 
 PHE   0.018   0.001   PHE A 206 
 TRP   0.015   0.002   TRP A 129 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6440)
  covalent geometry    : angle       0.52394 ( 8698)
  hydrogen bonds       : bond        0.05358 (  521)
  hydrogen bonds       : angle       3.66111 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.6964 (mtt-85) cc_final: 0.6135 (mmp-170)
REVERT: A   95 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.8073 (m-70)
REVERT: A  129 TRP cc_start: 0.7439 (OUTLIER) cc_final: 0.7181 (t-100)
REVERT: A  201 ASP cc_start: 0.8186 (t0) cc_final: 0.7882 (t70)
REVERT: A  209 ASP cc_start: 0.7443 (m-30) cc_final: 0.6996 (m-30)
REVERT: B    5 ARG cc_start: 0.6629 (mtt-85) cc_final: 0.6093 (mmp-170)
REVERT: B  129 TRP cc_start: 0.7437 (OUTLIER) cc_final: 0.7178 (t-100)
REVERT: B  201 ASP cc_start: 0.8190 (t0) cc_final: 0.7889 (t70)
REVERT: B  209 ASP cc_start: 0.7441 (m-30) cc_final: 0.6997 (m-30)
  outliers start: 29
  outliers final: 8
  residues processed: 111
  average time/residue: 0.3824
  time to fit residues: 45.2163
Evaluate side-chains
  99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  129 TRP
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  129 TRP
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0070
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.6006

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

Flipped N/Q/H residues before XYZ refinement:
A 293 ASN
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.151013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.099897 restraints weight = 7723.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.23
r_work: 0.3097 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6440  Z= 0.148
  Angle     :  0.510   5.456   8698  Z= 0.279
  Chirality :  0.036   0.141    996
  Planarity :  0.003   0.042   1094
  Dihedral  :  4.269  27.508    862
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.19 %
    Favored  : 74.50 %
  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 are not related in a simple way.
  whole:  2.55 (0.30), residues: 792
  helix:  2.52 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.70 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B   9 
 TYR   0.014   0.001   TYR A  50 
 PHE   0.017   0.001   PHE B 206 
 TRP   0.014   0.002   TRP A 129 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6440)
  covalent geometry    : angle       0.51031 ( 8698)
  hydrogen bonds       : bond        0.05331 (  521)
  hydrogen bonds       : angle       3.63737 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7073 (mtt-85) cc_final: 0.6288 (mmp-170)
REVERT: A   95 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.8016 (m-70)
REVERT: A  201 ASP cc_start: 0.8171 (t0) cc_final: 0.7867 (t70)
REVERT: A  209 ASP cc_start: 0.7424 (m-30) cc_final: 0.6977 (m-30)
REVERT: A  334 SER cc_start: 0.8610 (m) cc_final: 0.8312 (p)
REVERT: B    5 ARG cc_start: 0.7022 (mtt-85) cc_final: 0.6224 (mmp-170)
REVERT: B  201 ASP cc_start: 0.8183 (t0) cc_final: 0.7881 (t70)
REVERT: B  209 ASP cc_start: 0.7429 (m-30) cc_final: 0.6987 (m-30)
REVERT: B  334 SER cc_start: 0.8609 (m) cc_final: 0.8313 (p)
  outliers start: 23
  outliers final: 12
  residues processed: 113
  average time/residue: 0.3803
  time to fit residues: 45.8435
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  281 CYS
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 293 ASN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.154320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.105337 restraints weight = 7654.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.17
r_work: 0.3101 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6440  Z= 0.128
  Angle     :  0.505   7.278   8698  Z= 0.267
  Chirality :  0.036   0.138    996
  Planarity :  0.003   0.042   1094
  Dihedral  :  3.965  18.329    858
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.78 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.89 (0.30), residues: 792
  helix:  2.72 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.49 (0.48), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A   9 
 TYR   0.015   0.001   TYR A  50 
 PHE   0.008   0.001   PHE A 206 
 TRP   0.012   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6440)
  covalent geometry    : angle       0.50525 ( 8698)
  hydrogen bonds       : bond        0.04762 (  521)
  hydrogen bonds       : angle       3.52529 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7086 (mtt-85) cc_final: 0.6403 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8118 (tt) cc_final: 0.7814 (mt)
REVERT: A   95 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.8072 (m-70)
REVERT: A  129 TRP cc_start: 0.6827 (t-100) cc_final: 0.6615 (t60)
REVERT: A  201 ASP cc_start: 0.8172 (t0) cc_final: 0.7858 (t70)
REVERT: A  209 ASP cc_start: 0.7396 (m-30) cc_final: 0.6898 (m-30)
REVERT: A  291 TYR cc_start: 0.8174 (t80) cc_final: 0.7947 (t80)
REVERT: A  334 SER cc_start: 0.8605 (m) cc_final: 0.8348 (p)
REVERT: B    5 ARG cc_start: 0.7062 (mtt-85) cc_final: 0.6268 (mmp-170)
REVERT: B  129 TRP cc_start: 0.6828 (t-100) cc_final: 0.6613 (t60)
REVERT: B  201 ASP cc_start: 0.8183 (t0) cc_final: 0.7870 (t70)
REVERT: B  209 ASP cc_start: 0.7403 (m-30) cc_final: 0.6906 (m-30)
REVERT: B  291 TYR cc_start: 0.8177 (t80) cc_final: 0.7950 (t80)
REVERT: B  334 SER cc_start: 0.8598 (m) cc_final: 0.8345 (p)
  outliers start: 23
  outliers final: 18
  residues processed: 115
  average time/residue: 0.3883
  time to fit residues: 47.6166
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   51 PHE
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   51 PHE
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  281 CYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0170
   chunk 64 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.4026

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

Flipped N/Q/H residues before XYZ refinement:
A 266 HIS
A 293 ASN
B 266 HIS
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.103081 restraints weight = 7597.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.12
r_work: 0.3022 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6440  Z= 0.190
  Angle     :  0.572   7.382   8698  Z= 0.304
  Chirality :  0.038   0.134    996
  Planarity :  0.004   0.039   1094
  Dihedral  :  4.136  18.960    858
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 24.93 %
    Favored  : 71.18 %
  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 are not related in a simple way.
  whole:  2.61 (0.30), residues: 792
  helix:  2.58 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.85 (0.47), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B   9 
 TYR   0.012   0.001   TYR B  39 
 PHE   0.019   0.002   PHE B 206 
 TRP   0.012   0.002   TRP A 129 
 HIS   0.005   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6440)
  covalent geometry    : angle       0.57180 ( 8698)
  hydrogen bonds       : bond        0.05986 (  521)
  hydrogen bonds       : angle       3.76139 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7191 (mtt-85) cc_final: 0.6373 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8114 (tt) cc_final: 0.7802 (mt)
REVERT: A  201 ASP cc_start: 0.8115 (t0) cc_final: 0.7805 (t70)
REVERT: A  209 ASP cc_start: 0.7511 (m-30) cc_final: 0.7055 (m-30)
REVERT: A  291 TYR cc_start: 0.8285 (t80) cc_final: 0.8079 (t80)
REVERT: B    5 ARG cc_start: 0.7120 (mtt-85) cc_final: 0.6363 (mmp-170)
REVERT: B  201 ASP cc_start: 0.8125 (t0) cc_final: 0.7818 (t70)
REVERT: B  209 ASP cc_start: 0.7497 (m-30) cc_final: 0.7038 (m-30)
REVERT: B  291 TYR cc_start: 0.8287 (t80) cc_final: 0.8081 (t80)
  outliers start: 27
  outliers final: 16
  residues processed: 123
  average time/residue: 0.4150
  time to fit residues: 54.3311
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0770
   chunk 24 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 21 optimal weight:    0.3980
   chunk 36 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
A 266 HIS
A 293 ASN
B 266 HIS
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.157473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.109070 restraints weight = 7508.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.14
r_work: 0.3153 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6440  Z= 0.114
  Angle     :  0.509   8.398   8698  Z= 0.268
  Chirality :  0.035   0.125    996
  Planarity :  0.003   0.038   1094
  Dihedral  :  3.907  18.776    858
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 26.51 %
    Favored  : 71.18 %
  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 are not related in a simple way.
  whole:  3.05 (0.30), residues: 792
  helix:  2.89 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.80 (0.47), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A   9 
 TYR   0.014   0.001   TYR B  50 
 PHE   0.010   0.001   PHE A 206 
 TRP   0.019   0.002   TRP B 129 
 HIS   0.002   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6440)
  covalent geometry    : angle       0.50887 ( 8698)
  hydrogen bonds       : bond        0.04356 (  521)
  hydrogen bonds       : angle       3.44130 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7104 (mtt-85) cc_final: 0.6374 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8181 (tt) cc_final: 0.7834 (mt)
REVERT: A   95 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.8127 (m-70)
REVERT: A  201 ASP cc_start: 0.8133 (t0) cc_final: 0.7810 (t70)
REVERT: A  209 ASP cc_start: 0.7398 (m-30) cc_final: 0.6852 (m-30)
REVERT: A  291 TYR cc_start: 0.8100 (t80) cc_final: 0.7858 (t80)
REVERT: B    5 ARG cc_start: 0.7016 (mtt-85) cc_final: 0.6310 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8180 (tt) cc_final: 0.7870 (mt)
REVERT: B  201 ASP cc_start: 0.8152 (t0) cc_final: 0.7839 (t70)
REVERT: B  209 ASP cc_start: 0.7399 (m-30) cc_final: 0.6852 (m-30)
REVERT: B  291 TYR cc_start: 0.8098 (t80) cc_final: 0.7858 (t80)
  outliers start: 16
  outliers final: 15
  residues processed: 107
  average time/residue: 0.4149
  time to fit residues: 47.2909
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 PHE
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   51 PHE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 55 optimal weight:    0.0020
   chunk 62 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.3594

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.151054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.100038 restraints weight = 7624.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.21
r_work: 0.3127 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6440  Z= 0.137
  Angle     :  0.518   6.735   8698  Z= 0.278
  Chirality :  0.036   0.128    996
  Planarity :  0.004   0.039   1094
  Dihedral  :  3.938  18.559    858
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 26.22 %
    Favored  : 70.61 %
  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 are not related in a simple way.
  whole:  3.02 (0.30), residues: 792
  helix:  2.87 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.83 (0.47), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A   9 
 TYR   0.009   0.001   TYR B 283 
 PHE   0.012   0.001   PHE B 264 
 TRP   0.018   0.002   TRP A 129 
 HIS   0.003   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6440)
  covalent geometry    : angle       0.51829 ( 8698)
  hydrogen bonds       : bond        0.04911 (  521)
  hydrogen bonds       : angle       3.50806 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6398 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8164 (tt) cc_final: 0.7844 (mt)
REVERT: A  201 ASP cc_start: 0.8125 (t0) cc_final: 0.7909 (t0)
REVERT: A  209 ASP cc_start: 0.7408 (m-30) cc_final: 0.6873 (m-30)
REVERT: A  291 TYR cc_start: 0.8111 (t80) cc_final: 0.7850 (t80)
REVERT: B    5 ARG cc_start: 0.7058 (mtt-85) cc_final: 0.6375 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8156 (tt) cc_final: 0.7859 (mt)
REVERT: B  201 ASP cc_start: 0.8137 (t0) cc_final: 0.7823 (t70)
REVERT: B  209 ASP cc_start: 0.7412 (m-30) cc_final: 0.6878 (m-30)
REVERT: B  291 TYR cc_start: 0.8124 (t80) cc_final: 0.7856 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 113
  average time/residue: 0.4120
  time to fit residues: 49.5109
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 71 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.156485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107672 restraints weight = 7599.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.16
r_work: 0.3096 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6440  Z= 0.119
  Angle     :  0.520   9.405   8698  Z= 0.271
  Chirality :  0.035   0.123    996
  Planarity :  0.003   0.038   1094
  Dihedral  :  3.832  18.086    858
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 27.23 %
    Favored  : 70.46 %
  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 are not related in a simple way.
  whole:  3.29 (0.30), residues: 792
  helix:  3.05 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.76 (0.47), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A   9 
 TYR   0.015   0.001   TYR B  50 
 PHE   0.010   0.001   PHE A 206 
 TRP   0.021   0.002   TRP B 129 
 HIS   0.002   0.001   HIS B 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6440)
  covalent geometry    : angle       0.52011 ( 8698)
  hydrogen bonds       : bond        0.04336 (  521)
  hydrogen bonds       : angle       3.40057 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7094 (mtt-85) cc_final: 0.6366 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8090 (tt) cc_final: 0.7748 (mt)
REVERT: A  201 ASP cc_start: 0.8062 (t0) cc_final: 0.7737 (t70)
REVERT: A  209 ASP cc_start: 0.7337 (m-30) cc_final: 0.6792 (m-30)
REVERT: A  291 TYR cc_start: 0.7955 (t80) cc_final: 0.7697 (t80)
REVERT: B    5 ARG cc_start: 0.7007 (mtt-85) cc_final: 0.6340 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8088 (tt) cc_final: 0.7792 (mt)
REVERT: B  201 ASP cc_start: 0.8081 (t0) cc_final: 0.7761 (t70)
REVERT: B  209 ASP cc_start: 0.7333 (m-30) cc_final: 0.6790 (m-30)
REVERT: B  291 TYR cc_start: 0.7965 (t80) cc_final: 0.7713 (t80)
  outliers start: 16
  outliers final: 14
  residues processed: 106
  average time/residue: 0.3855
  time to fit residues: 43.4180
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0970
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.158982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.110467 restraints weight = 7462.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.15
r_work: 0.3096 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   6440  Z= 0.113
  Angle     :  0.515   6.417   8698  Z= 0.272
  Chirality :  0.035   0.122    996
  Planarity :  0.004   0.067   1094
  Dihedral  :  3.791  17.204    858
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 28.39 %
    Favored  : 70.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.42 (0.30), residues: 792
  helix:  3.12 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.68 (0.47), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B   9 
 TYR   0.007   0.001   TYR A 236 
 PHE   0.009   0.001   PHE A 206 
 TRP   0.020   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6440)
  covalent geometry    : angle       0.51517 ( 8698)
  hydrogen bonds       : bond        0.04044 (  521)
  hydrogen bonds       : angle       3.33377 ( 1563)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7123 (mtt-85) cc_final: 0.6351 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8106 (tt) cc_final: 0.7795 (mt)
REVERT: A    9 ARG cc_start: 0.7466 (ptp-110) cc_final: 0.6976 (mtm110)
REVERT: A  201 ASP cc_start: 0.8049 (t0) cc_final: 0.7840 (t0)
REVERT: A  209 ASP cc_start: 0.7318 (m-30) cc_final: 0.6729 (m-30)
REVERT: A  376 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.7944 (p)
REVERT: B    5 ARG cc_start: 0.7003 (mtt-85) cc_final: 0.6430 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8101 (tt) cc_final: 0.7820 (mt)
REVERT: B  201 ASP cc_start: 0.8074 (t0) cc_final: 0.7868 (t0)
REVERT: B  209 ASP cc_start: 0.7312 (m-30) cc_final: 0.6725 (m-30)
REVERT: B  376 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.7951 (p)
  outliers start: 10
  outliers final: 7
  residues processed: 109
  average time/residue: 0.4039
  time to fit residues: 46.8835
Evaluate side-chains
  98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3824 r_free = 0.3824 target = 0.152408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.102362 restraints weight = 7609.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.18
r_work: 0.3019 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6440  Z= 0.139
  Angle     :  0.551   9.924   8698  Z= 0.289
  Chirality :  0.036   0.125    996
  Planarity :  0.004   0.067   1094
  Dihedral  :  3.906  17.281    858
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 29.11 %
    Favored  : 69.16 %
  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 are not related in a simple way.
  whole:  3.25 (0.30), residues: 792
  helix:  3.06 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.92 (0.46), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B   9 
 TYR   0.015   0.001   TYR A  50 
 PHE   0.017   0.001   PHE A 264 
 TRP   0.019   0.002   TRP B 129 
 HIS   0.004   0.001   HIS B 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6440)
  covalent geometry    : angle       0.55147 ( 8698)
  hydrogen bonds       : bond        0.04818 (  521)
  hydrogen bonds       : angle       3.45628 ( 1563)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2289.18 seconds
wall clock time: 39 minutes 38.11 seconds (2378.11 seconds total)