Starting phenix.real_space_refine
on Tue Mar  3 14:18:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vq7_32087/03_2026/7vq7_32087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vq7_32087/03_2026/7vq7_32087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vq7_32087/03_2026/7vq7_32087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vq7_32087/03_2026/7vq7_32087.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vq7_32087/03_2026/7vq7_32087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vq7_32087/03_2026/7vq7_32087.map"
  }
  resolution = 3.6
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     S      34      5.16       5
     C    3942      2.51       5
     N    1030      2.21       5
     O    1120      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  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: 6127
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3063
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 10, 'TRANS': 378}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3063
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 10, 'TRANS': 378}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' AL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.53, per 1000 atoms: 0.25
  Number of scatterers: 6127
  At special positions: 0
  Unit cell: (86.19, 84.162, 111.54, 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      34     16.00
     Al      1     13.00
     O    1120      8.00
     N    1030      7.00
     C    3942      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: 0.60
  Conformation dependent library (CDL) restraints added in 226.9 milliseconds
  

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
      removed outlier: 3.743A  pdb=" N   ARG A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASP A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 39
      removed outlier: 3.728A  pdb=" N   GLY A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 66
      removed outlier: 3.518A  pdb=" N   PHE A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 102
      removed outlier: 3.966A  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
      removed outlier: 3.876A  pdb=" N   LYS A 133 " --> pdb=" O   TRP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 150
    Processing helix  chain 'A' and resid 154 through 183
      removed outlier: 3.766A  pdb=" N   ILE A 158 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   MET A 159 " --> pdb=" O   ASP A 155 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A 183 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 214
    Processing helix  chain 'A' and resid 223 through 240
      removed outlier: 5.001A  pdb=" N   ARG A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   TYR A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 267 through 293
      removed outlier: 3.611A  pdb=" N   TYR A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 304
      removed outlier: 3.638A  pdb=" N   LYS A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 331
    Processing helix  chain 'A' and resid 335 through 356
      removed outlier: 4.058A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 399
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 3.811A  pdb=" N   ASP B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 39
      removed outlier: 3.728A  pdb=" N   GLY B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 66
      removed outlier: 3.518A  pdb=" N   PHE B  66 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 102
      removed outlier: 3.967A  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
      removed outlier: 3.876A  pdb=" N   LYS B 133 " --> pdb=" O   TRP B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 150
    Processing helix  chain 'B' and resid 154 through 183
      removed outlier: 3.766A  pdb=" N   ILE B 158 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   MET B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL B 183 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 214
    Processing helix  chain 'B' and resid 223 through 240
      removed outlier: 5.000A  pdb=" N   ARG B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   TYR B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 254
    Processing helix  chain 'B' and resid 267 through 293
      removed outlier: 3.610A  pdb=" N   TYR B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
      removed outlier: 3.638A  pdb=" N   LYS B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 331
    Processing helix  chain 'B' and resid 335 through 356
      removed outlier: 4.058A  pdb=" N   ILE B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 399

    514 hydrogen bonds defined for protein.
    1542 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: 0.81

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1960
        1.34 -     1.46: 1387
        1.46 -     1.58: 2833
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 6240
  Sorted by residual:
  bond pdb=" N   HIS A 266 "
       pdb=" CA  HIS A 266 "
    ideal  model  delta    sigma   weight residual
    1.458  1.437  0.022 1.25e-02 6.40e+03 2.97e+00
  bond pdb=" N   HIS B 266 "
       pdb=" CA  HIS B 266 "
    ideal  model  delta    sigma   weight residual
    1.458  1.438  0.021 1.25e-02 6.40e+03 2.71e+00
  bond pdb=" C   TRP A 255 "
       pdb=" N   GLU A 256 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.023 1.60e-02 3.91e+03 2.11e+00
  bond pdb=" C   TRP B 255 "
       pdb=" N   GLU B 256 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.60e-02 3.91e+03 2.03e+00
  bond pdb=" CB  THR A  73 "
       pdb=" CG2 THR A  73 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.90e+00
  ... (remaining 6235 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 7745
        1.30 -     2.60: 589
        2.60 -     3.90: 65
        3.90 -     5.20: 13
        5.20 -     6.50: 10
  Bond angle restraints: 8422
  Sorted by residual:
  angle pdb=" N   HIS A 266 "
        pdb=" CA  HIS A 266 "
        pdb=" C   HIS A 266 "
      ideal   model   delta    sigma   weight residual
     109.10  102.60    6.50 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" N   HIS B 266 "
        pdb=" CA  HIS B 266 "
        pdb=" C   HIS B 266 "
      ideal   model   delta    sigma   weight residual
     109.10  102.63    6.47 1.91e+00 2.74e-01 1.15e+01
  angle pdb=" CA  LYS B   3 "
        pdb=" CB  LYS B   3 "
        pdb=" CG  LYS B   3 "
      ideal   model   delta    sigma   weight residual
     114.10  120.24   -6.14 2.00e+00 2.50e-01 9.41e+00
  angle pdb=" CA  LYS A   3 "
        pdb=" CB  LYS A   3 "
        pdb=" CG  LYS A   3 "
      ideal   model   delta    sigma   weight residual
     114.10  120.23   -6.13 2.00e+00 2.50e-01 9.38e+00
  angle pdb=" C   PHE B 134 "
        pdb=" CA  PHE B 134 "
        pdb=" CB  PHE B 134 "
      ideal   model   delta    sigma   weight residual
     111.13  107.09    4.04 1.61e+00 3.86e-01 6.29e+00
  ... (remaining 8417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 3200
       16.55 -    33.10: 396
       33.10 -    49.65: 112
       49.65 -    66.21: 38
       66.21 -    82.76: 10
  Dihedral angle restraints: 3756
    sinusoidal: 1494
      harmonic: 2262
  Sorted by residual:
  dihedral pdb=" CA  LEU B 233 "
           pdb=" C   LEU B 233 "
           pdb=" N   GLU B 234 "
           pdb=" CA  GLU B 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.86  -21.14     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  LEU A 233 "
           pdb=" C   LEU A 233 "
           pdb=" N   GLU A 234 "
           pdb=" CA  GLU A 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  ILE B 181 "
           pdb=" C   ILE B 181 "
           pdb=" N   PHE B 182 "
           pdb=" CA  PHE B 182 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.63  -18.37     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 3753 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 412
       0.027 -    0.055: 411
       0.055 -    0.082: 98
       0.082 -    0.109: 40
       0.109 -    0.136: 13
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" CA  PRO B 365 "
            pdb=" N   PRO B 365 "
            pdb=" C   PRO B 365 "
            pdb=" CB  PRO B 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  PRO A 365 "
            pdb=" N   PRO A 365 "
            pdb=" C   PRO A 365 "
            pdb=" CB  PRO A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ILE B 298 "
            pdb=" N   ILE B 298 "
            pdb=" C   ILE B 298 "
            pdb=" CB  ILE B 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 971 not shown)

  Planarity restraints: 1052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 184 "   -0.023 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 185 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 185 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 185 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 184 "   -0.023 5.00e-02 4.00e+02   3.54e-02 2.01e+00
        pdb=" N   PRO A 185 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 364 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A 365 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 365 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 365 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1049 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 68
        2.64 -     3.20: 5998
        3.20 -     3.77: 9393
        3.77 -     4.33: 12175
        4.33 -     4.90: 20108
  Nonbonded interactions: 47742
  Sorted by model distance:
  nonbonded pdb=" SD  MET B  60 "
            pdb="AL    AL A 601 "
     model   vdw
     2.070 2.380
  nonbonded pdb=" O   CYS A 176 "
            pdb=" OG  SER A 180 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   SER A 294 "
            pdb=" NE2 GLN A 297 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   SER B 294 "
            pdb=" NE2 GLN B 297 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   LYS B 228 "
            pdb=" ND2 ASN B 232 "
     model   vdw
     2.255 3.120
  ... (remaining 47737 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 405)
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.270
  Find NCS groups from input model:        0.080
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
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      :  0.007   0.046   6240  Z= 0.333
  Angle     :  0.755   6.503   8422  Z= 0.452
  Chirality :  0.042   0.136    974
  Planarity :  0.004   0.036   1052
  Dihedral  : 16.807  82.757   2288
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  :  7.82 %
    Favored  : 87.32 %
  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: -1.30 (0.27), residues: 766
  helix: -0.48 (0.18), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.07 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   9 
 TYR   0.011   0.002   TYR B 291 
 PHE   0.017   0.002   PHE B 206 
 TRP   0.012   0.001   TRP A 255 
 HIS   0.004   0.002   HIS A 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00744 ( 6240)
  covalent geometry    : angle       0.75471 ( 8422)
  hydrogen bonds       : bond        0.12335 (  514)
  hydrogen bonds       : angle       6.08029 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.6940 (mtt-85) cc_final: 0.6086 (ttm110)
REVERT: A  230 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7110 (tptp)
REVERT: A  265 ARG cc_start: 0.7029 (mmt180) cc_final: 0.6633 (tpp-160)
REVERT: A  304 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6693 (ttpt)
REVERT: A  321 MET cc_start: 0.8308 (mtt) cc_final: 0.8093 (mtt)
REVERT: A  331 MET cc_start: 0.5936 (mtm) cc_final: 0.5244 (mpp)
REVERT: B  265 ARG cc_start: 0.6818 (mmt180) cc_final: 0.6558 (tpp-160)
REVERT: B  321 MET cc_start: 0.8252 (mtt) cc_final: 0.8001 (mtt)
REVERT: B  331 MET cc_start: 0.6491 (mtm) cc_final: 0.5717 (mpp)
  outliers start: 33
  outliers final: 6
  residues processed: 167
  average time/residue: 0.0856
  time to fit residues: 18.4016
Evaluate side-chains
  121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  304 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 193 HIS
A 261 GLN
A 289 ASN
B 193 HIS
B 232 ASN
B 261 GLN
B 289 ASN
B 293 ASN
B 330 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.165404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.120896 restraints weight = 8315.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.124311 restraints weight = 5363.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.126438 restraints weight = 4185.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.127618 restraints weight = 3638.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.128223 restraints weight = 3362.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6240  Z= 0.156
  Angle     :  0.509   5.330   8422  Z= 0.278
  Chirality :  0.038   0.145    974
  Planarity :  0.004   0.034   1052
  Dihedral  :  5.850  54.656    842
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.26 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.30), residues: 766
  helix:  1.43 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.50 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 311 
 TYR   0.016   0.001   TYR B  40 
 PHE   0.024   0.001   PHE B  38 
 TRP   0.008   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6240)
  covalent geometry    : angle       0.50873 ( 8422)
  hydrogen bonds       : bond        0.05309 (  514)
  hydrogen bonds       : angle       4.11158 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A    3 LYS cc_start: 0.6268 (pptt) cc_final: 0.5543 (pptt)
REVERT: A    5 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6274 (ttm110)
REVERT: A  230 LYS cc_start: 0.7324 (mmtt) cc_final: 0.7090 (tptp)
REVERT: A  331 MET cc_start: 0.5640 (mtm) cc_final: 0.5295 (mpp)
REVERT: B  265 ARG cc_start: 0.6948 (mmt180) cc_final: 0.6705 (tpp-160)
REVERT: B  331 MET cc_start: 0.6270 (mtm) cc_final: 0.5485 (mpp)
  outliers start: 24
  outliers final: 15
  residues processed: 147
  average time/residue: 0.0756
  time to fit residues: 14.8247
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.171342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.123790 restraints weight = 8524.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127222 restraints weight = 5667.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.129289 restraints weight = 4543.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.130332 restraints weight = 4029.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.130851 restraints weight = 3788.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6240  Z= 0.171
  Angle     :  0.504   5.556   8422  Z= 0.273
  Chirality :  0.038   0.151    974
  Planarity :  0.004   0.038   1052
  Dihedral  :  4.714  44.780    836
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 19.47 %
    Favored  : 76.40 %
  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:  2.48 (0.31), residues: 766
  helix:  2.17 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.28 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 235 
 TYR   0.020   0.002   TYR B  40 
 PHE   0.024   0.002   PHE B  38 
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6240)
  covalent geometry    : angle       0.50366 ( 8422)
  hydrogen bonds       : bond        0.05116 (  514)
  hydrogen bonds       : angle       3.95104 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.6121 (pptt) cc_final: 0.5892 (pptt)
REVERT: A    5 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.6390 (ttm110)
REVERT: A   56 MET cc_start: 0.7530 (ptp) cc_final: 0.7269 (ptp)
REVERT: A  230 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6724 (tptp)
REVERT: A  321 MET cc_start: 0.8134 (mtt) cc_final: 0.7637 (mtt)
REVERT: A  377 MET cc_start: 0.7387 (mmt) cc_final: 0.6954 (mtt)
REVERT: B  244 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8061 (t)
REVERT: B  265 ARG cc_start: 0.7070 (mmt180) cc_final: 0.6702 (tpp-160)
REVERT: B  270 GLN cc_start: 0.7899 (mt0) cc_final: 0.7624 (mp10)
REVERT: B  321 MET cc_start: 0.7955 (mtt) cc_final: 0.7436 (mtt)
REVERT: B  331 MET cc_start: 0.6071 (mtm) cc_final: 0.5448 (mpp)
REVERT: B  405 MET cc_start: 0.3369 (ttm) cc_final: 0.2223 (mpp)
  outliers start: 28
  outliers final: 18
  residues processed: 140
  average time/residue: 0.0818
  time to fit residues: 15.0766
Evaluate side-chains
  129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  320 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  261 GLN
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 393 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.174332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.126189 restraints weight = 8526.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.130041 restraints weight = 5512.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.132314 restraints weight = 4339.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.133363 restraints weight = 3805.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.134238 restraints weight = 3561.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6240  Z= 0.125
  Angle     :  0.469   6.208   8422  Z= 0.252
  Chirality :  0.037   0.160    974
  Planarity :  0.003   0.039   1052
  Dihedral  :  4.322  38.298    835
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.27 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.06 (0.31), residues: 766
  helix:  2.50 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -0.87 (0.64), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 311 
 TYR   0.020   0.002   TYR B  40 
 PHE   0.023   0.001   PHE B  38 
 TRP   0.007   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6240)
  covalent geometry    : angle       0.46925 ( 8422)
  hydrogen bonds       : bond        0.04340 (  514)
  hydrogen bonds       : angle       3.68337 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.6151 (pptt) cc_final: 0.5900 (pptt)
REVERT: A    5 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.6190 (ttm110)
REVERT: A   56 MET cc_start: 0.7557 (ptp) cc_final: 0.7299 (ptp)
REVERT: A  208 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7912 (mt0)
REVERT: A  265 ARG cc_start: 0.7061 (tpp-160) cc_final: 0.6742 (tpp-160)
REVERT: A  321 MET cc_start: 0.7952 (mtt) cc_final: 0.7365 (mtt)
REVERT: A  331 MET cc_start: 0.5578 (mpp) cc_final: 0.4719 (mpp)
REVERT: B  244 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.7955 (t)
REVERT: B  265 ARG cc_start: 0.7080 (mmt180) cc_final: 0.6650 (tpp-160)
REVERT: B  321 MET cc_start: 0.7832 (mtt) cc_final: 0.7313 (mtt)
REVERT: B  331 MET cc_start: 0.5897 (mtm) cc_final: 0.5141 (mpp)
REVERT: B  405 MET cc_start: 0.3760 (ttm) cc_final: 0.3200 (ttm)
  outliers start: 24
  outliers final: 14
  residues processed: 136
  average time/residue: 0.0882
  time to fit residues: 15.5568
Evaluate side-chains
  129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  261 GLN
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  363 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 261 GLN
B  79 ASN
B 261 GLN
B 330 GLN
B 393 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.175009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.126678 restraints weight = 8718.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.130612 restraints weight = 5575.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.132944 restraints weight = 4359.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.134021 restraints weight = 3834.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.134021 restraints weight = 3596.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6240  Z= 0.122
  Angle     :  0.453   5.784   8422  Z= 0.242
  Chirality :  0.036   0.156    974
  Planarity :  0.003   0.038   1052
  Dihedral  :  3.992  30.215    835
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.57 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.45 (0.31), residues: 766
  helix:  2.83 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.77 (0.62), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  20 
 TYR   0.021   0.002   TYR B  40 
 PHE   0.018   0.001   PHE B  38 
 TRP   0.007   0.001   TRP B 255 
 HIS   0.002   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6240)
  covalent geometry    : angle       0.45279 ( 8422)
  hydrogen bonds       : bond        0.04180 (  514)
  hydrogen bonds       : angle       3.60239 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.6249 (ttm110)
REVERT: A   56 MET cc_start: 0.7592 (ptp) cc_final: 0.7331 (ptp)
REVERT: A  208 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7855 (mt0)
REVERT: A  321 MET cc_start: 0.7822 (mtt) cc_final: 0.7240 (mtt)
REVERT: A  331 MET cc_start: 0.5547 (mpp) cc_final: 0.4909 (mpp)
REVERT: B  244 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.7978 (t)
REVERT: B  265 ARG cc_start: 0.7125 (mmt180) cc_final: 0.6687 (tpp-160)
REVERT: B  321 MET cc_start: 0.7817 (mtt) cc_final: 0.7289 (mtt)
REVERT: B  331 MET cc_start: 0.5898 (mtm) cc_final: 0.5140 (mpp)
REVERT: B  405 MET cc_start: 0.3977 (ttm) cc_final: 0.3366 (ttm)
  outliers start: 20
  outliers final: 13
  residues processed: 129
  average time/residue: 0.0887
  time to fit residues: 14.9519
Evaluate side-chains
  121 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  261 GLN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0670
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 330 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.172680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.126672 restraints weight = 8235.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.130131 restraints weight = 5342.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.132409 restraints weight = 4222.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.133496 restraints weight = 3680.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134361 restraints weight = 3421.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6240  Z= 0.113
  Angle     :  0.454   8.064   8422  Z= 0.240
  Chirality :  0.037   0.152    974
  Planarity :  0.003   0.036   1052
  Dihedral  :  3.786  21.471    833
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.12 %
    Favored  : 74.93 %
  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:  3.62 (0.31), residues: 766
  helix:  2.84 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.35 (0.66), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  20 
 TYR   0.014   0.001   TYR A  40 
 PHE   0.016   0.001   PHE B  38 
 TRP   0.006   0.001   TRP B 255 
 HIS   0.002   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6240)
  covalent geometry    : angle       0.45425 ( 8422)
  hydrogen bonds       : bond        0.03940 (  514)
  hydrogen bonds       : angle       3.57277 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7474 (mtt-85) cc_final: 0.6361 (ttm110)
REVERT: A   56 MET cc_start: 0.7560 (ptp) cc_final: 0.7317 (ptp)
REVERT: A  208 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7850 (mt0)
REVERT: A  321 MET cc_start: 0.7755 (mtt) cc_final: 0.7181 (mtt)
REVERT: A  331 MET cc_start: 0.5636 (mpp) cc_final: 0.4975 (mpp)
REVERT: B  244 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.7999 (t)
REVERT: B  265 ARG cc_start: 0.7034 (mmt180) cc_final: 0.6555 (tpp-160)
REVERT: B  321 MET cc_start: 0.7883 (mtt) cc_final: 0.7377 (mtt)
REVERT: B  331 MET cc_start: 0.5922 (mtm) cc_final: 0.4996 (mpp)
REVERT: B  405 MET cc_start: 0.3948 (ttm) cc_final: 0.3655 (mpp)
  outliers start: 20
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0849
  time to fit residues: 14.7026
Evaluate side-chains
  124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASN
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0570
   chunk 54 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.9302

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.171538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.125382 restraints weight = 8245.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.128812 restraints weight = 5403.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.131043 restraints weight = 4267.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.132378 restraints weight = 3721.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.132863 restraints weight = 3443.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6240  Z= 0.118
  Angle     :  0.472   8.567   8422  Z= 0.248
  Chirality :  0.037   0.161    974
  Planarity :  0.003   0.034   1052
  Dihedral  :  3.694  18.237    832
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.75 %
    Favored  : 73.45 %
  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:  3.66 (0.31), residues: 766
  helix:  2.88 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.43 (0.64), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 284 
 TYR   0.022   0.002   TYR B  40 
 PHE   0.015   0.001   PHE B  38 
 TRP   0.006   0.001   TRP A 255 
 HIS   0.003   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6240)
  covalent geometry    : angle       0.47208 ( 8422)
  hydrogen bonds       : bond        0.03989 (  514)
  hydrogen bonds       : angle       3.57291 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.6332 (ttm110)
REVERT: A   56 MET cc_start: 0.7581 (ptp) cc_final: 0.7326 (ptp)
REVERT: A  208 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7890 (mt0)
REVERT: A  321 MET cc_start: 0.7798 (mtt) cc_final: 0.7203 (mtt)
REVERT: A  331 MET cc_start: 0.5706 (mpp) cc_final: 0.5039 (mpp)
REVERT: B    3 LYS cc_start: 0.6414 (pptt) cc_final: 0.6020 (pptt)
REVERT: B  244 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8000 (t)
REVERT: B  265 ARG cc_start: 0.7030 (mmt180) cc_final: 0.6580 (tpp-160)
REVERT: B  321 MET cc_start: 0.7816 (mtt) cc_final: 0.7278 (mtt)
REVERT: B  323 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7195 (tm-30)
REVERT: B  331 MET cc_start: 0.5931 (mtm) cc_final: 0.5023 (mpp)
REVERT: B  405 MET cc_start: 0.4011 (ttm) cc_final: 0.3644 (mpp)
  outliers start: 19
  outliers final: 12
  residues processed: 127
  average time/residue: 0.0827
  time to fit residues: 13.8590
Evaluate side-chains
  124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASN
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.172613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.126698 restraints weight = 8231.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.130206 restraints weight = 5336.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.132414 restraints weight = 4191.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.133565 restraints weight = 3659.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.134018 restraints weight = 3405.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6240  Z= 0.124
  Angle     :  0.489   8.364   8422  Z= 0.263
  Chirality :  0.037   0.150    974
  Planarity :  0.003   0.031   1052
  Dihedral  :  3.733  18.015    832
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 24.34 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.63 (0.31), residues: 766
  helix:  2.86 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.38 (0.65), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  20 
 TYR   0.032   0.002   TYR B 291 
 PHE   0.013   0.001   PHE B  38 
 TRP   0.006   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6240)
  covalent geometry    : angle       0.48867 ( 8422)
  hydrogen bonds       : bond        0.04030 (  514)
  hydrogen bonds       : angle       3.66256 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.6470 (ttm110)
REVERT: A   56 MET cc_start: 0.7487 (ptp) cc_final: 0.7256 (ptp)
REVERT: A  321 MET cc_start: 0.7695 (mtt) cc_final: 0.7086 (mtt)
REVERT: A  331 MET cc_start: 0.5738 (mpp) cc_final: 0.5016 (mpp)
REVERT: B    3 LYS cc_start: 0.6329 (pptt) cc_final: 0.5985 (pptt)
REVERT: B  244 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.7943 (t)
REVERT: B  265 ARG cc_start: 0.7014 (mmt180) cc_final: 0.6721 (ttm170)
REVERT: B  293 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8218 (t0)
REVERT: B  331 MET cc_start: 0.5869 (mtm) cc_final: 0.5001 (mpp)
REVERT: B  405 MET cc_start: 0.4064 (ttm) cc_final: 0.3664 (mpp)
  outliers start: 21
  outliers final: 13
  residues processed: 123
  average time/residue: 0.0899
  time to fit residues: 14.3419
Evaluate side-chains
  124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASN
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 GLU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.169879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.124364 restraints weight = 8282.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.127789 restraints weight = 5387.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.129954 restraints weight = 4227.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.131107 restraints weight = 3680.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.131695 restraints weight = 3425.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6240  Z= 0.140
  Angle     :  0.514   9.487   8422  Z= 0.274
  Chirality :  0.038   0.158    974
  Planarity :  0.003   0.032   1052
  Dihedral  :  3.806  18.386    832
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 24.93 %
    Favored  : 72.27 %
  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:  3.63 (0.31), residues: 766
  helix:  2.87 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.43 (0.65), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  20 
 TYR   0.030   0.002   TYR B 291 
 PHE   0.014   0.001   PHE B 206 
 TRP   0.006   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6240)
  covalent geometry    : angle       0.51377 ( 8422)
  hydrogen bonds       : bond        0.04255 (  514)
  hydrogen bonds       : angle       3.68156 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.6267 (ttm110)
REVERT: A   56 MET cc_start: 0.7502 (ptp) cc_final: 0.7280 (ptp)
REVERT: A  321 MET cc_start: 0.7784 (mtt) cc_final: 0.7177 (mtt)
REVERT: A  331 MET cc_start: 0.5867 (mpp) cc_final: 0.5155 (mpp)
REVERT: B    3 LYS cc_start: 0.6561 (pptt) cc_final: 0.6054 (pptt)
REVERT: B  244 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8134 (t)
REVERT: B  265 ARG cc_start: 0.7040 (mmt180) cc_final: 0.6746 (ttm170)
REVERT: B  293 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7957 (t0)
REVERT: B  321 MET cc_start: 0.7861 (mtt) cc_final: 0.7261 (mtt)
REVERT: B  331 MET cc_start: 0.5958 (mtm) cc_final: 0.5274 (mpp)
REVERT: B  405 MET cc_start: 0.4170 (ttm) cc_final: 0.3693 (mpp)
  outliers start: 19
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0850
  time to fit residues: 13.2459
Evaluate side-chains
  122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASN
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 GLU
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0050
   overall best weight:    1.2000

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.170603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.124958 restraints weight = 8227.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.128341 restraints weight = 5402.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.130433 restraints weight = 4252.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.131499 restraints weight = 3719.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.132342 restraints weight = 3462.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6240  Z= 0.136
  Angle     :  0.515   9.041   8422  Z= 0.273
  Chirality :  0.038   0.186    974
  Planarity :  0.003   0.031   1052
  Dihedral  :  3.780  18.283    832
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 24.63 %
    Favored  : 72.71 %
  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:  3.70 (0.31), residues: 766
  helix:  2.91 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.36 (0.65), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  20 
 TYR   0.014   0.001   TYR B 291 
 PHE   0.013   0.001   PHE B  38 
 TRP   0.006   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6240)
  covalent geometry    : angle       0.51509 ( 8422)
  hydrogen bonds       : bond        0.04210 (  514)
  hydrogen bonds       : angle       3.65495 ( 1542)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.6333 (ttm110)
REVERT: A   56 MET cc_start: 0.7514 (ptp) cc_final: 0.7291 (ptp)
REVERT: A  319 ASN cc_start: 0.7983 (m-40) cc_final: 0.7255 (t0)
REVERT: A  321 MET cc_start: 0.7720 (mtt) cc_final: 0.7119 (mtt)
REVERT: A  331 MET cc_start: 0.5972 (mpp) cc_final: 0.5275 (mpp)
REVERT: B  244 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8056 (t)
REVERT: B  265 ARG cc_start: 0.7067 (mmt180) cc_final: 0.6750 (ttm170)
REVERT: B  293 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7884 (t0)
REVERT: B  321 MET cc_start: 0.7736 (mtt) cc_final: 0.7125 (mtt)
REVERT: B  331 MET cc_start: 0.5997 (mtm) cc_final: 0.5035 (mpp)
  outliers start: 18
  outliers final: 13
  residues processed: 118
  average time/residue: 0.0738
  time to fit residues: 11.5543
Evaluate side-chains
  122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASN
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  244 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
B 261 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.169715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.123876 restraints weight = 8210.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.127246 restraints weight = 5388.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.129305 restraints weight = 4248.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.130409 restraints weight = 3720.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.130409 restraints weight = 3465.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
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      :  0.004   0.048   6240  Z= 0.152
  Angle     :  0.539   9.369   8422  Z= 0.284
  Chirality :  0.038   0.174    974
  Planarity :  0.003   0.031   1052
  Dihedral  :  3.895  18.661    832
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 24.93 %
    Favored  : 72.42 %
  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:  3.69 (0.31), residues: 766
  helix:  2.91 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.40 (0.65), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 312 
 TYR   0.032   0.002   TYR A 291 
 PHE   0.013   0.001   PHE B 206 
 TRP   0.006   0.001   TRP A 255 
 HIS   0.002   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6240)
  covalent geometry    : angle       0.53891 ( 8422)
  hydrogen bonds       : bond        0.04428 (  514)
  hydrogen bonds       : angle       3.72308 ( 1542)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1186.67 seconds
wall clock time: 21 minutes 8.32 seconds (1268.32 seconds total)