Starting phenix.real_space_refine
on Thu Mar  6 07:41:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a8m_15233/03_2025/8a8m_15233.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a8m_15233/03_2025/8a8m_15233.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2025/8a8m_15233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2025/8a8m_15233.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2025/8a8m_15233.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2025/8a8m_15233.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      4      5.21       5
     S      29      5.16       5
     C    3348      2.51       5
     N     886      2.21       5
     O     973      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5244
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2816
          Classifications: {'peptide': 349}
          Link IDs: {'PTRANS': 17, 'TRANS': 331}
    Chain: "B"
      Number of atoms: 2370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2370
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 18, 'TRANS': 279}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'AP2': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'AP2': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ASP A 177 " occ=0.78
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 177 " occ=0.78
  Time building chain proxies: 4.60, per 1000 atoms: 0.88
  Number of scatterers: 5244
  At special positions: 0
  Unit cell: (61.248, 81.026, 102.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      29     16.00
     P       4     15.00
     Mg      4     11.99
     O     973      8.00
     N     886      7.00
     C    3348      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 589.0 milliseconds
  

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1228

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      42.7% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 76
    Processing helix  chain 'A' and resid 113 through 120
      removed outlier: 4.298A  pdb=" N   LYS A 118 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 145
    Processing helix  chain 'A' and resid 189 through 195
      removed outlier: 3.807A  pdb=" N   ILE A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   LEU A 195 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 218
      removed outlier: 3.866A  pdb=" N   ASP A 205 " --> pdb=" O   ASN A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 240
      removed outlier: 4.118A  pdb=" N   LEU A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 278 through 289
      removed outlier: 3.556A  pdb=" N   VAL A 282 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 304 through 311
      removed outlier: 6.710A  pdb=" N   TYR A 307 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE A 308 " --> pdb=" O   HIS A 305 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   GLN A 310 " --> pdb=" O   TYR A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 3.650A  pdb=" N   ARG A 330 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 346
      removed outlier: 4.059A  pdb=" N   SER A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 89 through 106
      removed outlier: 4.447A  pdb=" N   ARG B  95 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 147
      removed outlier: 3.659A  pdb=" N   ASP B 145 " --> pdb=" O   LYS B 141 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS B 146 " --> pdb=" O   GLN B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 173
      removed outlier: 3.745A  pdb=" N   LYS B 164 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 183
      No H-bonds generated for 'chain 'B' and resid 181 through 183'
    Processing helix  chain 'B' and resid 221 through 226
    Processing helix  chain 'B' and resid 235 through 253
    Processing helix  chain 'B' and resid 262 through 273
    Processing helix  chain 'B' and resid 284 through 295
    Processing helix  chain 'B' and resid 304 through 311
    Processing helix  chain 'B' and resid 311 through 320
      removed outlier: 3.550A  pdb=" N   THR B 315 " --> pdb=" O   HIS B 311 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER B 319 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 3.544A  pdb=" N   LEU A  13 " --> pdb=" O   THR A  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 53
    Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 112
    Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41
      removed outlier: 3.684A  pdb=" N   ILE B  41 " --> pdb=" O   GLN B  44 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN B  44 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 58
      removed outlier: 7.376A  pdb=" N   LYS B  69 " --> pdb=" O   ILE B  56 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135
      removed outlier: 4.148A  pdb=" N   THR B 134 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE B 187 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 176

    192 hydrogen bonds defined for protein.
    534 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1709
        1.35 -     1.48: 1265
        1.48 -     1.61: 2331
        1.61 -     1.74: 2
        1.74 -     1.87: 53
  Bond restraints: 5360
  Sorted by residual:
  bond pdb=" CA  VAL A  89 "
       pdb=" CB  VAL A  89 "
    ideal  model  delta    sigma   weight residual
    1.553  1.539  0.014 7.40e-03 1.83e+04 3.55e+00
  bond pdb=" CA  LEU A  74 "
       pdb=" C   LEU A  74 "
    ideal  model  delta    sigma   weight residual
    1.524  1.505  0.018 1.27e-02 6.20e+03 2.06e+00
  bond pdb=" N   HIS A 312 "
       pdb=" CA  HIS A 312 "
    ideal  model  delta    sigma   weight residual
    1.456  1.474 -0.018 1.44e-02 4.82e+03 1.49e+00
  bond pdb=" CB  LYS B 329 "
       pdb=" CG  LYS B 329 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.34e+00
  bond pdb=" N   VAL A  83 "
       pdb=" CA  VAL A  83 "
    ideal  model  delta    sigma   weight residual
    1.459  1.445  0.014 1.25e-02 6.40e+03 1.32e+00
  ... (remaining 5355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 6978
        1.91 -     3.82: 233
        3.82 -     5.73: 36
        5.73 -     7.65: 19
        7.65 -     9.56: 6
  Bond angle restraints: 7272
  Sorted by residual:
  angle pdb=" N   LEU A  74 "
        pdb=" CA  LEU A  74 "
        pdb=" C   LEU A  74 "
      ideal   model   delta    sigma   weight residual
     111.07  105.64    5.43 1.07e+00 8.73e-01 2.57e+01
  angle pdb=" CA  LYS B 329 "
        pdb=" CB  LYS B 329 "
        pdb=" CG  LYS B 329 "
      ideal   model   delta    sigma   weight residual
     114.10  122.34   -8.24 2.00e+00 2.50e-01 1.70e+01
  angle pdb=" N   SER B 275 "
        pdb=" CA  SER B 275 "
        pdb=" C   SER B 275 "
      ideal   model   delta    sigma   weight residual
     109.81  118.62   -8.81 2.21e+00 2.05e-01 1.59e+01
  angle pdb=" CA  GLU B  68 "
        pdb=" CB  GLU B  68 "
        pdb=" CG  GLU B  68 "
      ideal   model   delta    sigma   weight residual
     114.10  121.53   -7.43 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" C   ILE A 235 "
        pdb=" N   LEU A 236 "
        pdb=" CA  LEU A 236 "
      ideal   model   delta    sigma   weight residual
     120.28  125.16   -4.88 1.34e+00 5.57e-01 1.33e+01
  ... (remaining 7267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 2740
       17.80 -    35.61: 394
       35.61 -    53.41: 100
       53.41 -    71.21: 29
       71.21 -    89.02: 13
  Dihedral angle restraints: 3276
    sinusoidal: 1381
      harmonic: 1895
  Sorted by residual:
  dihedral pdb=" CA  LEU A 108 "
           pdb=" C   LEU A 108 "
           pdb=" N   MET A 109 "
           pdb=" CA  MET A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.02  -24.98     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  LEU A 234 "
           pdb=" C   LEU A 234 "
           pdb=" N   ILE A 235 "
           pdb=" CA  ILE A 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.46   23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  LEU B 131 "
           pdb=" C   LEU B 131 "
           pdb=" N   MET B 132 "
           pdb=" CA  MET B 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.05   22.95     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 3273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 565
       0.043 -    0.087: 186
       0.087 -    0.130: 49
       0.130 -    0.173: 10
       0.173 -    0.217: 4
  Chirality restraints: 814
  Sorted by residual:
  chirality pdb=" CA  LEU B 267 "
            pdb=" N   LEU B 267 "
            pdb=" C   LEU B 267 "
            pdb=" CB  LEU B 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  ILE B  84 "
            pdb=" CA  ILE B  84 "
            pdb=" CG1 ILE B  84 "
            pdb=" CG2 ILE B  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.55e-01
  chirality pdb=" CA  TYR B 305 "
            pdb=" N   TYR B 305 "
            pdb=" C   TYR B 305 "
            pdb=" CB  TYR B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.93e-01
  ... (remaining 811 not shown)

  Planarity restraints: 920
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  68 "    0.012 2.00e-02 2.50e+03   2.51e-02 6.31e+00
        pdb=" CD  GLU B  68 "   -0.043 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  68 "    0.016 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  68 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 152 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.94e+00
        pdb=" N   PRO A 153 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 153 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 153 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 150 "    0.028 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO B 151 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 151 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 151 "    0.024 5.00e-02 4.00e+02
  ... (remaining 917 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 720
        2.75 -     3.29: 5782
        3.29 -     3.83: 9180
        3.83 -     4.36: 10880
        4.36 -     4.90: 16814
  Nonbonded interactions: 43376
  Sorted by model distance:
  nonbonded pdb=" O   SER B 235 "
            pdb=" OG  SER B 238 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR B 140 "
            pdb=" OE1 GLU B 249 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OE2 GLU A 215 "
            pdb=" OG1 THR A 221 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ASP A 205 "
            pdb=" OG  SER A 208 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" NH2 ARG B 178 "
            pdb=" O   TYR B 203 "
     model   vdw
     2.243 3.120
  ... (remaining 43371 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.78 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:             4.500
  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:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.390
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5469
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      :  0.004   0.037   5360  Z= 0.238
  Angle     :  0.888   9.558   7272  Z= 0.471
  Chirality :  0.048   0.217    814
  Planarity :  0.005   0.050    920
  Dihedral  : 18.817  89.016   2048
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 29.09
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.45 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 26.39 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.31), residues: 639
  helix: -0.84 (0.34), residues: 219
  sheet: -2.27 (0.64), residues: 53
  loop : -2.31 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  18 
 HIS   0.013   0.002   HIS A 312 
 PHE   0.013   0.002   PHE B 313 
 TYR   0.012   0.001   TYR B 140 
 ARG   0.005   0.001   ARG B  85 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 MET cc_start: -0.1395 (ttm) cc_final: -0.3126 (tmm)
REVERT: B   79 MET cc_start: 0.3563 (tmm) cc_final: 0.3054 (tpp)
REVERT: B  141 LYS cc_start: 0.9204 (tptt) cc_final: 0.8769 (tptp)
REVERT: B  184 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.7021 (p0)
REVERT: B  220 MET cc_start: 0.5295 (mmm) cc_final: 0.4956 (tmm)
  outliers start: 9
  outliers final: 3
  residues processed: 91
  average time/residue: 0.1854
  time to fit residues: 22.0044
Evaluate side-chains
  73 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  184 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 199 HIS
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 ASN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 HIS
B 177 HIS
B 184 ASN
B 226 ASN
B 231 GLN
B 265 GLN
B 266 GLN
B 269 GLN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.126035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.087751 restraints weight = 22189.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.088924 restraints weight = 20601.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.089632 restraints weight = 19165.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3923 r_free = 0.3923    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3919 r_free = 0.3919    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   5360  Z= 0.367
  Angle     :  0.896   9.490   7272  Z= 0.454
  Chirality :  0.053   0.217    814
  Planarity :  0.006   0.054    920
  Dihedral  :  9.522  80.680    762
  Min Nonbonded Distance : 1.652

Molprobity Statistics.
  All-atom Clashscore : 37.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 24.31 %
    Favored  : 69.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.30), residues: 639
  helix: -1.21 (0.31), residues: 224
  sheet: -2.76 (0.69), residues: 46
  loop : -2.31 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 187 
 HIS   0.009   0.003   HIS B 317 
 PHE   0.015   0.002   PHE B 283 
 TYR   0.015   0.002   TYR A 132 
 ARG   0.004   0.001   ARG B   5 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 68
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8795 (OUTLIER) cc_final: 0.8349 (t60)
REVERT: A  179 MET cc_start: 0.0901 (tpt) cc_final: 0.0596 (tpt)
REVERT: B   70 MET cc_start: 0.1289 (ttt) cc_final: 0.0506 (ttt)
REVERT: B   79 MET cc_start: 0.5663 (tmm) cc_final: 0.5276 (tmm)
REVERT: B  125 VAL cc_start: 0.2982 (OUTLIER) cc_final: 0.2777 (m)
REVERT: B  129 MET cc_start: 0.8867 (mmm) cc_final: 0.8176 (mmm)
REVERT: B  132 MET cc_start: 0.8724 (mpp) cc_final: 0.8114 (mpp)
REVERT: B  141 LYS cc_start: 0.9372 (tptt) cc_final: 0.8971 (tptp)
REVERT: B  155 LEU cc_start: 0.8543 (mt) cc_final: 0.8306 (mt)
REVERT: B  184 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8584 (p0)
REVERT: B  247 MET cc_start: 0.9803 (mmm) cc_final: 0.9601 (mmm)
REVERT: B  257 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.6057 (m-80)
REVERT: B  309 MET cc_start: 0.9319 (mtt) cc_final: 0.8996 (mmm)
REVERT: B  317 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7468 (t-90)
  outliers start: 34
  outliers final: 16
  residues processed: 94
  average time/residue: 0.1569
  time to fit residues: 19.8484
Evaluate side-chains
  85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  268 MET
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  317 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 43 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    0.4980
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.152134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.128471 restraints weight = 34151.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.130746 restraints weight = 24699.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.132182 restraints weight = 19419.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5360  Z= 0.226
  Angle     :  0.806   9.898   7272  Z= 0.397
  Chirality :  0.048   0.213    814
  Planarity :  0.005   0.060    920
  Dihedral  :  8.141  77.233    760
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 27.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.08 %
    Favored  : 68.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.30), residues: 639
  helix: -0.86 (0.33), residues: 220
  sheet: -2.98 (0.66), residues: 46
  loop : -2.31 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 187 
 HIS   0.005   0.002   HIS B 317 
 PHE   0.014   0.002   PHE B 255 
 TYR   0.014   0.002   TYR A 132 
 ARG   0.002   0.000   ARG B  85 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.1329 (ttt) cc_final: -0.1702 (tpt)
REVERT: A  186 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7981 (tmm-80)
REVERT: B   79 MET cc_start: 0.5100 (tmm) cc_final: 0.4876 (tmm)
REVERT: B  125 VAL cc_start: 0.2742 (OUTLIER) cc_final: 0.2517 (m)
REVERT: B  129 MET cc_start: 0.9028 (mmm) cc_final: 0.8264 (mmm)
REVERT: B  132 MET cc_start: 0.8830 (mpp) cc_final: 0.7822 (mpp)
REVERT: B  141 LYS cc_start: 0.9318 (tptt) cc_final: 0.8954 (tptp)
REVERT: B  184 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8761 (p0)
REVERT: B  247 MET cc_start: 0.9796 (mmm) cc_final: 0.9584 (mmm)
REVERT: B  255 PHE cc_start: 0.7092 (p90) cc_final: 0.6716 (p90)
REVERT: B  257 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6600 (m-80)
REVERT: B  309 MET cc_start: 0.9343 (mtt) cc_final: 0.9034 (mmm)
  outliers start: 27
  outliers final: 14
  residues processed: 90
  average time/residue: 0.1618
  time to fit residues: 19.5712
Evaluate side-chains
  82 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  179 ASP
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.130694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.091393 restraints weight = 21472.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.092845 restraints weight = 19258.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.093612 restraints weight = 17570.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5360  Z= 0.202
  Angle     :  0.780   9.152   7272  Z= 0.384
  Chirality :  0.047   0.216    814
  Planarity :  0.005   0.055    920
  Dihedral  :  7.592  73.519    759
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 24.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 27.26 %
    Favored  : 67.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.31), residues: 639
  helix: -0.69 (0.34), residues: 220
  sheet: -2.98 (0.74), residues: 36
  loop : -2.27 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 260 
 HIS   0.005   0.001   HIS A  80 
 PHE   0.012   0.001   PHE B 255 
 TYR   0.010   0.001   TYR B 257 
 ARG   0.002   0.000   ARG B  85 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 67
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7950 (tmm-80)
REVERT: A  265 MET cc_start: 0.0526 (ttp) cc_final: 0.0257 (ptt)
REVERT: B   79 MET cc_start: 0.5255 (tmm) cc_final: 0.4913 (tmm)
REVERT: B  129 MET cc_start: 0.9065 (mmm) cc_final: 0.8306 (mmm)
REVERT: B  141 LYS cc_start: 0.9310 (tptt) cc_final: 0.8942 (tptp)
REVERT: B  184 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8951 (p0)
REVERT: B  220 MET cc_start: 0.5685 (mmm) cc_final: 0.4784 (tmm)
REVERT: B  247 MET cc_start: 0.9770 (mmm) cc_final: 0.9568 (mmm)
REVERT: B  255 PHE cc_start: 0.7334 (p90) cc_final: 0.6935 (p90)
REVERT: B  257 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.4807 (m-80)
REVERT: B  309 MET cc_start: 0.9297 (mtt) cc_final: 0.8954 (mmm)
  outliers start: 28
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1614
  time to fit residues: 19.3298
Evaluate side-chains
  82 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   chunk 54 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0370
   chunk 16 optimal weight:    9.9990
   overall best weight:    1.0862

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 GLN
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.129492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.090354 restraints weight = 21749.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.091748 restraints weight = 19789.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.092395 restraints weight = 18056.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5360  Z= 0.211
  Angle     :  0.767   8.815   7272  Z= 0.380
  Chirality :  0.046   0.161    814
  Planarity :  0.005   0.056    920
  Dihedral  :  7.397  72.136    759
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 24.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 27.08 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.31), residues: 639
  helix: -0.55 (0.34), residues: 225
  sheet: -2.84 (0.81), residues: 36
  loop : -2.23 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 126 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.013   0.001   PHE B 255 
 TYR   0.014   0.001   TYR B 140 
 ARG   0.003   0.000   ARG A 237 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 69
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.1558 (OUTLIER) cc_final: 0.1158 (mmm160)
REVERT: A   78 MET cc_start: -0.0935 (ttt) cc_final: -0.1166 (tpt)
REVERT: A  186 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7961 (tmm-80)
REVERT: B   79 MET cc_start: 0.5199 (tmm) cc_final: 0.4850 (tmm)
REVERT: B  129 MET cc_start: 0.9125 (mmm) cc_final: 0.8343 (mmm)
REVERT: B  141 LYS cc_start: 0.9332 (tptt) cc_final: 0.8944 (tptp)
REVERT: B  184 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8953 (p0)
REVERT: B  220 MET cc_start: 0.5920 (mmm) cc_final: 0.4976 (tmm)
REVERT: B  255 PHE cc_start: 0.7398 (p90) cc_final: 0.6997 (p90)
REVERT: B  257 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.5270 (m-80)
REVERT: B  309 MET cc_start: 0.9297 (mtt) cc_final: 0.9012 (mmm)
  outliers start: 32
  outliers final: 20
  residues processed: 93
  average time/residue: 0.1783
  time to fit residues: 21.6035
Evaluate side-chains
  88 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 13 optimal weight:    0.3980
   chunk 25 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.130357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.091447 restraints weight = 21731.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.092814 restraints weight = 19346.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.093581 restraints weight = 17660.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5360  Z= 0.202
  Angle     :  0.792   9.174   7272  Z= 0.387
  Chirality :  0.046   0.308    814
  Planarity :  0.004   0.047    920
  Dihedral  :  7.313  71.642    759
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 23.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.17 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.31), residues: 639
  helix: -0.53 (0.34), residues: 227
  sheet: -2.92 (0.74), residues: 39
  loop : -2.16 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 126 
 HIS   0.005   0.001   HIS A 148 
 PHE   0.014   0.001   PHE B 283 
 TYR   0.011   0.001   TYR A 182 
 ARG   0.003   0.000   ARG B  61 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.0782 (ttt) cc_final: -0.1223 (tpt)
REVERT: A  179 MET cc_start: 0.2404 (mmm) cc_final: 0.2176 (tpt)
REVERT: A  186 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.7982 (tmm-80)
REVERT: A  288 MET cc_start: 0.8585 (mmp) cc_final: 0.7732 (ptp)
REVERT: B   70 MET cc_start: 0.0824 (ttt) cc_final: 0.0606 (ttt)
REVERT: B   79 MET cc_start: 0.5265 (tmm) cc_final: 0.4952 (tmm)
REVERT: B  129 MET cc_start: 0.9127 (mmm) cc_final: 0.8317 (mmm)
REVERT: B  141 LYS cc_start: 0.9336 (tptt) cc_final: 0.8944 (tptp)
REVERT: B  155 LEU cc_start: 0.8377 (mt) cc_final: 0.8104 (mt)
REVERT: B  184 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8962 (p0)
REVERT: B  220 MET cc_start: 0.6041 (mmm) cc_final: 0.4655 (tmm)
REVERT: B  255 PHE cc_start: 0.7440 (p90) cc_final: 0.7046 (p90)
REVERT: B  257 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.5431 (m-80)
REVERT: B  309 MET cc_start: 0.9270 (mtt) cc_final: 0.9028 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 86
  average time/residue: 0.1634
  time to fit residues: 18.8661
Evaluate side-chains
  85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 26 optimal weight:    0.1980
   chunk 60 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.126516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.088423 restraints weight = 21547.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.089655 restraints weight = 19644.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.090124 restraints weight = 18128.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5360  Z= 0.245
  Angle     :  0.815  10.331   7272  Z= 0.396
  Chirality :  0.046   0.284    814
  Planarity :  0.005   0.046    920
  Dihedral  :  7.416  71.002    759
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 27.60
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.98 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 28.65 %
    Favored  : 65.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.31), residues: 639
  helix: -0.52 (0.34), residues: 228
  sheet: -2.92 (0.71), residues: 39
  loop : -2.15 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 126 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.014   0.002   PHE B 255 
 TYR   0.016   0.002   TYR B 140 
 ARG   0.004   0.001   ARG B 302 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 69
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8687 (OUTLIER) cc_final: 0.8253 (t60)
REVERT: A   57 ARG cc_start: 0.1553 (OUTLIER) cc_final: 0.1153 (mmm160)
REVERT: A  216 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8419 (mm)
REVERT: B   79 MET cc_start: 0.5607 (tmm) cc_final: 0.5359 (tmm)
REVERT: B  129 MET cc_start: 0.9161 (mmm) cc_final: 0.8274 (mmm)
REVERT: B  141 LYS cc_start: 0.9363 (tptt) cc_final: 0.8950 (tptp)
REVERT: B  155 LEU cc_start: 0.8514 (mt) cc_final: 0.8272 (mt)
REVERT: B  184 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8909 (p0)
REVERT: B  220 MET cc_start: 0.5765 (mmm) cc_final: 0.4902 (tmm)
REVERT: B  255 PHE cc_start: 0.7458 (p90) cc_final: 0.7062 (p90)
REVERT: B  257 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.5592 (m-80)
REVERT: B  309 MET cc_start: 0.9297 (mtt) cc_final: 0.9048 (mmm)
  outliers start: 32
  outliers final: 20
  residues processed: 92
  average time/residue: 0.1746
  time to fit residues: 21.0049
Evaluate side-chains
  90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  268 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 184 ASN
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.128170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.088652 restraints weight = 21382.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.089915 restraints weight = 19035.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.090846 restraints weight = 17394.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5360  Z= 0.226
  Angle     :  0.845   9.959   7272  Z= 0.404
  Chirality :  0.047   0.300    814
  Planarity :  0.005   0.046    920
  Dihedral  :  7.402  70.149    759
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 25.69
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.98 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 29.86 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.31), residues: 639
  helix: -0.69 (0.33), residues: 234
  sheet: -2.96 (0.73), residues: 39
  loop : -2.13 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 197 
 HIS   0.005   0.001   HIS A 148 
 PHE   0.013   0.002   PHE B 255 
 TYR   0.010   0.001   TYR A 132 
 ARG   0.005   0.001   ARG A 186 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.8181 (t60)
REVERT: A   57 ARG cc_start: 0.1530 (OUTLIER) cc_final: 0.1156 (mmm160)
REVERT: A   78 MET cc_start: -0.0468 (ttt) cc_final: -0.0994 (tpt)
REVERT: A  179 MET cc_start: 0.1810 (tpt) cc_final: 0.1338 (mmm)
REVERT: A  186 ARG cc_start: 0.8748 (tmm-80) cc_final: 0.8046 (tmm-80)
REVERT: A  216 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8415 (mm)
REVERT: B  129 MET cc_start: 0.9147 (mmm) cc_final: 0.8302 (mmm)
REVERT: B  141 LYS cc_start: 0.9364 (tptt) cc_final: 0.8933 (tptp)
REVERT: B  155 LEU cc_start: 0.8487 (mt) cc_final: 0.8258 (mt)
REVERT: B  220 MET cc_start: 0.5786 (mmm) cc_final: 0.4935 (tmm)
REVERT: B  255 PHE cc_start: 0.7477 (p90) cc_final: 0.7078 (p90)
REVERT: B  257 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.5566 (m-80)
REVERT: B  309 MET cc_start: 0.9287 (mtt) cc_final: 0.9049 (mmm)
  outliers start: 26
  outliers final: 17
  residues processed: 88
  average time/residue: 0.1811
  time to fit residues: 20.9510
Evaluate side-chains
  85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  224 ARG
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 49 optimal weight:    0.4980
   chunk 55 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.125679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.087831 restraints weight = 21835.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.089169 restraints weight = 19576.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.089816 restraints weight = 17929.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.4463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5360  Z= 0.253
  Angle     :  0.869  10.365   7272  Z= 0.417
  Chirality :  0.047   0.284    814
  Planarity :  0.005   0.047    920
  Dihedral  :  7.461  68.897    757
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 29.03
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.61 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 30.38 %
    Favored  : 64.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.31), residues: 639
  helix: -0.76 (0.33), residues: 234
  sheet: -3.46 (0.59), residues: 47
  loop : -2.09 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 197 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.013   0.002   PHE B 255 
 TYR   0.015   0.002   TYR A 182 
 ARG   0.004   0.001   ARG A   5 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8675 (OUTLIER) cc_final: 0.8291 (t60)
REVERT: A   57 ARG cc_start: 0.1732 (OUTLIER) cc_final: 0.1320 (mmm160)
REVERT: A  186 ARG cc_start: 0.8774 (tmm-80) cc_final: 0.8076 (tmm-80)
REVERT: A  216 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8418 (mm)
REVERT: B  129 MET cc_start: 0.9213 (mmm) cc_final: 0.8419 (mmm)
REVERT: B  141 LYS cc_start: 0.9396 (tptt) cc_final: 0.8944 (tptp)
REVERT: B  220 MET cc_start: 0.6017 (mmm) cc_final: 0.5219 (tmm)
REVERT: B  255 PHE cc_start: 0.7456 (p90) cc_final: 0.7056 (p90)
REVERT: B  257 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.5686 (m-80)
REVERT: B  309 MET cc_start: 0.9264 (mtt) cc_final: 0.9031 (mmm)
  outliers start: 28
  outliers final: 21
  residues processed: 89
  average time/residue: 0.1717
  time to fit residues: 19.9714
Evaluate side-chains
  93 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  224 ARG
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 29 optimal weight:    0.0370
   chunk 49 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 36 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.128959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.091783 restraints weight = 21392.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.092490 restraints weight = 20024.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.092490 restraints weight = 18393.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5360  Z= 0.219
  Angle     :  0.900  13.285   7272  Z= 0.424
  Chirality :  0.049   0.323    814
  Planarity :  0.005   0.048    920
  Dihedral  :  7.430  68.206    757
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 25.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 30.73 %
    Favored  : 64.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.32), residues: 639
  helix: -0.69 (0.33), residues: 237
  sheet: -3.89 (0.57), residues: 47
  loop : -2.10 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 197 
 HIS   0.010   0.001   HIS A 228 
 PHE   0.013   0.001   PHE B 255 
 TYR   0.009   0.001   TYR A   9 
 ARG   0.003   0.001   ARG A 186 

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

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

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1278 Ramachandran restraints generated.
    639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.8153 (t60)
REVERT: A   57 ARG cc_start: 0.1525 (OUTLIER) cc_final: 0.1114 (mmm160)
REVERT: A  179 MET cc_start: 0.2569 (tpt) cc_final: 0.1371 (tpt)
REVERT: A  186 ARG cc_start: 0.8725 (tmm-80) cc_final: 0.8005 (tmm-80)
REVERT: A  216 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8401 (mm)
REVERT: A  288 MET cc_start: 0.8585 (mmp) cc_final: 0.8318 (mmp)
REVERT: B  129 MET cc_start: 0.9161 (mmm) cc_final: 0.8439 (mmm)
REVERT: B  141 LYS cc_start: 0.9348 (tptt) cc_final: 0.8870 (tptp)
REVERT: B  220 MET cc_start: 0.5860 (mmm) cc_final: 0.5067 (tmm)
REVERT: B  255 PHE cc_start: 0.7434 (p90) cc_final: 0.7035 (p90)
REVERT: B  257 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.5544 (m-80)
REVERT: B  309 MET cc_start: 0.9260 (mtt) cc_final: 0.9012 (mmm)
  outliers start: 25
  outliers final: 19
  residues processed: 83
  average time/residue: 0.1743
  time to fit residues: 18.8179
Evaluate side-chains
  87 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TRP
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  224 ARG
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 58 optimal weight:    0.0870
   chunk 32 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 35 optimal weight:    0.2980
   chunk 19 optimal weight:    6.9990
   overall best weight:    0.8560

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.149930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.125791 restraints weight = 34718.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.128120 restraints weight = 25028.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.129561 restraints weight = 19629.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5360  Z= 0.221
  Angle     :  0.880  11.412   7272  Z= 0.416
  Chirality :  0.049   0.324    814
  Planarity :  0.005   0.052    920
  Dihedral  :  7.342  66.635    757
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 24.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 30.90 %
    Favored  : 65.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.32), residues: 639
  helix: -0.62 (0.34), residues: 237
  sheet: -4.16 (0.51), residues: 48
  loop : -2.05 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 197 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.012   0.001   PHE B 255 
 TYR   0.016   0.001   TYR A 182 
 ARG   0.003   0.000   ARG A 186 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2375.01 seconds
wall clock time: 42 minutes 16.43 seconds (2536.43 seconds total)