Starting phenix.real_space_refine
on Tue Mar 11 15:24:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7voj_32050/03_2025/7voj_32050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7voj_32050/03_2025/7voj_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_2025/7voj_32050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7voj_32050/03_2025/7voj_32050.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7voj_32050/03_2025/7voj_32050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7voj_32050/03_2025/7voj_32050.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.49, per 1000 atoms: 0.87
  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: 1.69
  Conformation dependent library (CDL) restraints added in 959.1 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: 0.48
  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: 1.75

  Time building geometry restraints manager: 1.93 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: 0.03
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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.610
  Find NCS groups from input model:        0.110
  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:12.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.990
-------------------------------------------------------------------------------
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= 0.529
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.019   0.003   TRP B 129 
 HIS   0.003   0.001   HIS A 340 
 PHE   0.016   0.002   PHE B 134 
 TYR   0.015   0.002   TYR A 236 
 ARG   0.003   0.001   ARG A 154 

*********************** 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  : 0.678 
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: 0.7736 (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: 0.7758 (mm110) cc_final: 0.7491 (mm-40)
REVERT: B  201 ASP cc_start: 0.7733 (t0) cc_final: 0.7444 (t70)
REVERT: B  209 ASP cc_start: 0.7539 (m-30) cc_final: 0.7165 (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: 1.0262
  time to fit residues: 161.4594
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  : 0.750 
-------------------------------------------------------------------------------
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 67 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 403 ASN
B  24 HIS
B  96 GLN
B 266 HIS
B 289 ASN
B 293 ASN
B 330 GLN
B 403 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.160895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.111670 restraints weight = 7431.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.20
r_work: 0.3180 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6440  Z= 0.174
  Angle     :  0.533   5.751   8698  Z= 0.295
  Chirality :  0.037   0.137    996
  Planarity :  0.004   0.042   1094
  Dihedral  :  5.670  55.937    874
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.88 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.30), residues: 792
  helix:  1.27 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.65 (0.53), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 129 
 HIS   0.004   0.001   HIS B 193 
 PHE   0.020   0.001   PHE A 206 
 TYR   0.011   0.001   TYR B  50 
 ARG   0.002   0.000   ARG B 235 

*********************** 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  : 0.751 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.6550 (mtt-85) cc_final: 0.5965 (mmp-170)
REVERT: A  201 ASP cc_start: 0.8109 (t0) cc_final: 0.7849 (t70)
REVERT: A  209 ASP cc_start: 0.7348 (m-30) cc_final: 0.6947 (m-30)
REVERT: A  265 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6988 (tpp80)
REVERT: B    5 ARG cc_start: 0.6489 (mtt-85) cc_final: 0.5600 (mmp-170)
REVERT: B  201 ASP cc_start: 0.8115 (t0) cc_final: 0.7855 (t70)
REVERT: B  209 ASP cc_start: 0.7358 (m-30) cc_final: 0.6954 (m-30)
REVERT: B  265 ARG cc_start: 0.7192 (mmt180) cc_final: 0.6955 (tpp80)
  outliers start: 20
  outliers final: 8
  residues processed: 121
  average time/residue: 0.9724
  time to fit residues: 124.9735
Evaluate side-chains
  96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
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 47 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.159362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.108337 restraints weight = 7448.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.29
r_work: 0.3107 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6440  Z= 0.159
  Angle     :  0.491   6.159   8698  Z= 0.262
  Chirality :  0.035   0.141    996
  Planarity :  0.003   0.043   1094
  Dihedral  :  4.690  53.464    862
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.75 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.31), residues: 792
  helix:  2.35 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.53 (0.50), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 129 
 HIS   0.002   0.000   HIS A 193 
 PHE   0.016   0.001   PHE A 206 
 TYR   0.010   0.001   TYR B  50 
 ARG   0.006   0.000   ARG A   9 

*********************** 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
  127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.6815 (mtt-85) cc_final: 0.5886 (mmp-170)
REVERT: A   34 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8160 (mp)
REVERT: A   95 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7860 (m-70)
REVERT: A  129 TRP cc_start: 0.7240 (t-100) cc_final: 0.7026 (t60)
REVERT: A  201 ASP cc_start: 0.8037 (t0) cc_final: 0.7740 (t70)
REVERT: A  206 PHE cc_start: 0.8279 (t80) cc_final: 0.8065 (t80)
REVERT: A  209 ASP cc_start: 0.7292 (m-30) cc_final: 0.6832 (m-30)
REVERT: A  265 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6822 (tpp80)
REVERT: B    5 ARG cc_start: 0.6539 (mtt-85) cc_final: 0.6007 (mmp-170)
REVERT: B   34 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8151 (mp)
REVERT: B   95 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7874 (m-70)
REVERT: B  129 TRP cc_start: 0.7237 (t-100) cc_final: 0.7018 (t60)
REVERT: B  201 ASP cc_start: 0.8032 (t0) cc_final: 0.7736 (t70)
REVERT: B  206 PHE cc_start: 0.8277 (t80) cc_final: 0.8062 (t80)
REVERT: B  209 ASP cc_start: 0.7296 (m-30) cc_final: 0.6841 (m-30)
REVERT: B  265 ARG cc_start: 0.7142 (mmt180) cc_final: 0.6828 (tpp80)
  outliers start: 23
  outliers final: 6
  residues processed: 117
  average time/residue: 0.9524
  time to fit residues: 118.2565
Evaluate side-chains
  100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
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  332 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.7386

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.151158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.100351 restraints weight = 7722.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.21
r_work: 0.3036 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6440  Z= 0.229
  Angle     :  0.520   5.436   8698  Z= 0.283
  Chirality :  0.037   0.142    996
  Planarity :  0.003   0.042   1094
  Dihedral  :  4.341  34.822    862
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.77 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.31), residues: 792
  helix:  2.53 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.80 (0.48), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 129 
 HIS   0.004   0.001   HIS B 193 
 PHE   0.017   0.002   PHE A 206 
 TYR   0.008   0.001   TYR B  50 
 ARG   0.007   0.000   ARG B   9 

*********************** 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
  124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.6991 (mtt-85) cc_final: 0.6176 (mmp-170)
REVERT: A  201 ASP cc_start: 0.8151 (t0) cc_final: 0.7851 (t70)
REVERT: A  209 ASP cc_start: 0.7395 (m-30) cc_final: 0.6946 (m-30)
REVERT: A  265 ARG cc_start: 0.7236 (mmt180) cc_final: 0.6908 (tpp80)
REVERT: A  291 TYR cc_start: 0.7970 (t80) cc_final: 0.7768 (t80)
REVERT: A  334 SER cc_start: 0.8611 (m) cc_final: 0.8277 (p)
REVERT: B    5 ARG cc_start: 0.6994 (mtt-85) cc_final: 0.6197 (mmp-170)
REVERT: B  201 ASP cc_start: 0.8150 (t0) cc_final: 0.7852 (t70)
REVERT: B  209 ASP cc_start: 0.7391 (m-30) cc_final: 0.6944 (m-30)
REVERT: B  265 ARG cc_start: 0.7241 (mmt180) cc_final: 0.6903 (tpp80)
REVERT: B  334 SER cc_start: 0.8659 (m) cc_final: 0.8303 (p)
  outliers start: 20
  outliers final: 9
  residues processed: 114
  average time/residue: 0.9508
  time to fit residues: 115.3029
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  281 CYS
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   34 LEU
Chi-restraints excluded: chain B residue  281 CYS
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.153947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.104425 restraints weight = 7558.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.18
r_work: 0.3126 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6440  Z= 0.178
  Angle     :  0.501   6.560   8698  Z= 0.265
  Chirality :  0.036   0.140    996
  Planarity :  0.003   0.042   1094
  Dihedral  :  4.024  18.260    862
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.20 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.30), residues: 792
  helix:  2.72 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.61 (0.48), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A 193 
 PHE   0.009   0.001   PHE B 264 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.006   0.000   ARG B   9 

*********************** 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
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7004 (mtt-85) cc_final: 0.6211 (mmp-170)
REVERT: A   95 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.8010 (m-70)
REVERT: A  129 TRP cc_start: 0.6812 (t-100) cc_final: 0.6598 (t60)
REVERT: A  201 ASP cc_start: 0.8173 (t0) cc_final: 0.7870 (t70)
REVERT: A  209 ASP cc_start: 0.7397 (m-30) cc_final: 0.6901 (m-30)
REVERT: A  265 ARG cc_start: 0.7277 (mmt180) cc_final: 0.6962 (tpp80)
REVERT: A  291 TYR cc_start: 0.8191 (t80) cc_final: 0.7959 (t80)
REVERT: A  334 SER cc_start: 0.8597 (m) cc_final: 0.8328 (p)
REVERT: B    5 ARG cc_start: 0.7062 (mtt-85) cc_final: 0.6241 (mmp-170)
REVERT: B   95 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7993 (m-70)
REVERT: B  129 TRP cc_start: 0.6825 (t-100) cc_final: 0.6608 (t60)
REVERT: B  201 ASP cc_start: 0.8180 (t0) cc_final: 0.7872 (t70)
REVERT: B  209 ASP cc_start: 0.7403 (m-30) cc_final: 0.6909 (m-30)
REVERT: B  265 ARG cc_start: 0.7275 (mmt180) cc_final: 0.6965 (tpp80)
REVERT: B  291 TYR cc_start: 0.8244 (t80) cc_final: 0.7991 (t80)
REVERT: B  334 SER cc_start: 0.8631 (m) cc_final: 0.8350 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 114
  average time/residue: 0.9240
  time to fit residues: 112.2915
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  : 0.680 
-------------------------------------------------------------------------------
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  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   95 HIS
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  290 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.152219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.103262 restraints weight = 7538.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.13
r_work: 0.3022 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6440  Z= 0.248
  Angle     :  0.538   6.467   8698  Z= 0.288
  Chirality :  0.037   0.134    996
  Planarity :  0.003   0.040   1094
  Dihedral  :  4.048  18.725    858
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.76 (0.30), residues: 792
  helix:  2.69 (0.20), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.87 (0.46), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 129 
 HIS   0.004   0.001   HIS A 193 
 PHE   0.016   0.001   PHE A 206 
 TYR   0.014   0.002   TYR B  50 
 ARG   0.007   0.000   ARG A   9 

*********************** 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: 26
    poor density    : 106
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7115 (mtt-85) cc_final: 0.6347 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8081 (tt) cc_final: 0.7780 (mt)
REVERT: A   95 HIS cc_start: 0.8329 (OUTLIER) cc_final: 0.8020 (m-70)
REVERT: A  129 TRP cc_start: 0.7007 (t-100) cc_final: 0.6784 (t60)
REVERT: A  201 ASP cc_start: 0.8107 (t0) cc_final: 0.7794 (t70)
REVERT: A  209 ASP cc_start: 0.7454 (m-30) cc_final: 0.6956 (m-30)
REVERT: A  265 ARG cc_start: 0.7326 (mmt180) cc_final: 0.7024 (tpp80)
REVERT: A  291 TYR cc_start: 0.8188 (t80) cc_final: 0.7956 (t80)
REVERT: A  334 SER cc_start: 0.8594 (m) cc_final: 0.8383 (p)
REVERT: B    5 ARG cc_start: 0.7101 (mtt-85) cc_final: 0.6315 (mmp-170)
REVERT: B   95 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.8001 (m-70)
REVERT: B  129 TRP cc_start: 0.7021 (t-100) cc_final: 0.6759 (t60)
REVERT: B  201 ASP cc_start: 0.8109 (t0) cc_final: 0.7797 (t70)
REVERT: B  209 ASP cc_start: 0.7440 (m-30) cc_final: 0.6939 (m-30)
REVERT: B  265 ARG cc_start: 0.7342 (mmt180) cc_final: 0.6989 (tpp80)
REVERT: B  291 TYR cc_start: 0.8271 (t80) cc_final: 0.8071 (t80)
REVERT: B  334 SER cc_start: 0.8620 (m) cc_final: 0.8398 (p)
  outliers start: 26
  outliers final: 15
  residues processed: 124
  average time/residue: 0.8852
  time to fit residues: 117.3229
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  111 VAL
Chi-restraints excluded: chain A residue  290 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   95 HIS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  290 SER
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 77 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.154422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.104419 restraints weight = 7621.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.20
r_work: 0.3064 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3982

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= 0.182
  Angle     :  0.506   7.866   8698  Z= 0.270
  Chirality :  0.036   0.131    996
  Planarity :  0.003   0.039   1094
  Dihedral  :  3.945  18.973    858
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 25.65 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.30), residues: 792
  helix:  2.84 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.86 (0.46), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A 193 
 PHE   0.011   0.001   PHE A 206 
 TYR   0.015   0.001   TYR A  50 
 ARG   0.007   0.000   ARG A   9 

*********************** 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
  127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7070 (mtt-85) cc_final: 0.6308 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8101 (tt) cc_final: 0.7782 (mt)
REVERT: A   95 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7965 (m-70)
REVERT: A  129 TRP cc_start: 0.6870 (t-100) cc_final: 0.6643 (t60)
REVERT: A  201 ASP cc_start: 0.8093 (t0) cc_final: 0.7780 (t70)
REVERT: A  209 ASP cc_start: 0.7368 (m-30) cc_final: 0.6871 (m-30)
REVERT: A  265 ARG cc_start: 0.7354 (mmt180) cc_final: 0.7077 (tpp80)
REVERT: A  291 TYR cc_start: 0.8116 (t80) cc_final: 0.7872 (t80)
REVERT: A  334 SER cc_start: 0.8656 (m) cc_final: 0.8452 (p)
REVERT: B    5 ARG cc_start: 0.7036 (mtt-85) cc_final: 0.6278 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8107 (tt) cc_final: 0.7797 (mt)
REVERT: B   95 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7945 (m-70)
REVERT: B  129 TRP cc_start: 0.6911 (t-100) cc_final: 0.6644 (t60)
REVERT: B  201 ASP cc_start: 0.8096 (t0) cc_final: 0.7783 (t70)
REVERT: B  209 ASP cc_start: 0.7369 (m-30) cc_final: 0.6871 (m-30)
REVERT: B  265 ARG cc_start: 0.7356 (mmt180) cc_final: 0.7033 (tpp80)
REVERT: B  291 TYR cc_start: 0.8204 (t80) cc_final: 0.7979 (t80)
REVERT: B  334 SER cc_start: 0.8674 (m) cc_final: 0.8434 (p)
  outliers start: 24
  outliers final: 15
  residues processed: 119
  average time/residue: 0.9199
  time to fit residues: 116.5280
Evaluate side-chains
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
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  159 MET
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  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   95 HIS
Chi-restraints excluded: chain B residue  159 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 55 optimal weight:    0.2980
   chunk 33 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.150543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.101645 restraints weight = 7503.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.13
r_work: 0.3089 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6440  Z= 0.222
  Angle     :  0.538   8.595   8698  Z= 0.286
  Chirality :  0.036   0.132    996
  Planarity :  0.003   0.039   1094
  Dihedral  :  3.996  19.017    858
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 25.50 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.30), residues: 792
  helix:  2.82 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.85 (0.46), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 129 
 HIS   0.004   0.001   HIS A 193 
 PHE   0.016   0.001   PHE A 206 
 TYR   0.015   0.001   TYR B  50 
 ARG   0.008   0.000   ARG B   9 

*********************** 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
  130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7148 (mtt-85) cc_final: 0.6396 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8187 (tt) cc_final: 0.7861 (mt)
REVERT: A   95 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.8022 (m-70)
REVERT: A  129 TRP cc_start: 0.6957 (t-100) cc_final: 0.6739 (t60)
REVERT: A  201 ASP cc_start: 0.8127 (t0) cc_final: 0.7810 (t70)
REVERT: A  209 ASP cc_start: 0.7438 (m-30) cc_final: 0.6939 (m-30)
REVERT: A  265 ARG cc_start: 0.7405 (mmt180) cc_final: 0.7148 (tpp80)
REVERT: A  291 TYR cc_start: 0.8154 (t80) cc_final: 0.7917 (t80)
REVERT: B    5 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6371 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8175 (tt) cc_final: 0.7865 (mt)
REVERT: B   95 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.8025 (m-70)
REVERT: B  129 TRP cc_start: 0.6974 (t-100) cc_final: 0.6729 (t60)
REVERT: B  201 ASP cc_start: 0.8133 (t0) cc_final: 0.7816 (t70)
REVERT: B  209 ASP cc_start: 0.7423 (m-30) cc_final: 0.6922 (m-30)
REVERT: B  265 ARG cc_start: 0.7412 (mmt180) cc_final: 0.7118 (tpp80)
REVERT: B  291 TYR cc_start: 0.8208 (t80) cc_final: 0.7992 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 123
  average time/residue: 0.9043
  time to fit residues: 118.4648
Evaluate side-chains
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
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  111 VAL
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  290 SER
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   95 HIS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  281 CYS
Chi-restraints excluded: chain B residue  290 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 7 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    0.3980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.155202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.105887 restraints weight = 7585.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.18
r_work: 0.3165 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6440  Z= 0.162
  Angle     :  0.513   9.514   8698  Z= 0.271
  Chirality :  0.035   0.128    996
  Planarity :  0.003   0.040   1094
  Dihedral  :  3.888  18.780    858
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 25.50 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.23 (0.30), residues: 792
  helix:  3.00 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.74 (0.47), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 129 
 HIS   0.002   0.001   HIS A 193 
 PHE   0.010   0.001   PHE B 206 
 TYR   0.016   0.001   TYR A  50 
 ARG   0.009   0.000   ARG B   9 

*********************** 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
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7122 (mtt-85) cc_final: 0.6394 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8200 (tt) cc_final: 0.7844 (mt)
REVERT: A   95 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.8103 (m-70)
REVERT: A  201 ASP cc_start: 0.8147 (t0) cc_final: 0.7818 (t70)
REVERT: A  209 ASP cc_start: 0.7312 (m-30) cc_final: 0.6782 (m-30)
REVERT: A  291 TYR cc_start: 0.8059 (t80) cc_final: 0.7834 (t80)
REVERT: B    5 ARG cc_start: 0.7065 (mtt-85) cc_final: 0.6514 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8202 (tt) cc_final: 0.7893 (mt)
REVERT: B   95 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.8094 (m-70)
REVERT: B  129 TRP cc_start: 0.6758 (t-100) cc_final: 0.6503 (t60)
REVERT: B  201 ASP cc_start: 0.8176 (t0) cc_final: 0.7858 (t70)
REVERT: B  209 ASP cc_start: 0.7310 (m-30) cc_final: 0.6780 (m-30)
REVERT: B  291 TYR cc_start: 0.8106 (t80) cc_final: 0.7888 (t80)
  outliers start: 24
  outliers final: 15
  residues processed: 119
  average time/residue: 1.0137
  time to fit residues: 127.8312
Evaluate side-chains
  111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  111 VAL
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   95 HIS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  290 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.152793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.102446 restraints weight = 7621.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.21
r_work: 0.3123 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6440  Z= 0.180
  Angle     :  0.537   9.232   8698  Z= 0.280
  Chirality :  0.036   0.128    996
  Planarity :  0.003   0.038   1094
  Dihedral  :  3.891  17.892    858
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 26.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.22 (0.30), residues: 792
  helix:  2.99 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.76 (0.47), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A 193 
 PHE   0.017   0.001   PHE B 264 
 TYR   0.016   0.001   TYR B  50 
 ARG   0.008   0.000   ARG B   9 

********************** 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
  113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7115 (mtt-85) cc_final: 0.6386 (mmp-170)
REVERT: A    7 ILE cc_start: 0.8166 (tt) cc_final: 0.7841 (mt)
REVERT: A   95 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.8019 (m-70)
REVERT: A  201 ASP cc_start: 0.8144 (t0) cc_final: 0.7922 (t0)
REVERT: A  209 ASP cc_start: 0.7365 (m-30) cc_final: 0.6830 (m-30)
REVERT: A  291 TYR cc_start: 0.7998 (t80) cc_final: 0.7767 (t80)
REVERT: B    5 ARG cc_start: 0.7067 (mtt-85) cc_final: 0.6521 (mmp-170)
REVERT: B    7 ILE cc_start: 0.8183 (tt) cc_final: 0.7870 (mt)
REVERT: B   95 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.8047 (m-70)
REVERT: B  129 TRP cc_start: 0.6816 (t-100) cc_final: 0.6592 (t60)
REVERT: B  201 ASP cc_start: 0.8177 (t0) cc_final: 0.7861 (t70)
REVERT: B  209 ASP cc_start: 0.7327 (m-30) cc_final: 0.6800 (m-30)
REVERT: B  291 TYR cc_start: 0.8004 (t80) cc_final: 0.7723 (t80)
  outliers start: 18
  outliers final: 15
  residues processed: 110
  average time/residue: 0.9893
  time to fit residues: 115.4721
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
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  111 VAL
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  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   95 HIS
Chi-restraints excluded: chain B residue  111 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.149655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.100091 restraints weight = 7713.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.19
r_work: 0.3119 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6440  Z= 0.218
  Angle     :  0.556   9.337   8698  Z= 0.292
  Chirality :  0.036   0.129    996
  Planarity :  0.003   0.038   1094
  Dihedral  :  3.955  18.017    858
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 26.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.10 (0.30), residues: 792
  helix:  2.94 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.89 (0.46), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 129 
 HIS   0.004   0.001   HIS B 193 
 PHE   0.013   0.001   PHE B 206 
 TYR   0.017   0.001   TYR A  50 
 ARG   0.008   0.000   ARG B   9 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4957.25 seconds
wall clock time: 85 minutes 15.59 seconds (5115.59 seconds total)