Starting phenix.real_space_refine
on Tue Feb 11 11:07:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a8m_15233/02_2025/8a8m_15233.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a8m_15233/02_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_15233/02_2025/8a8m_15233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a8m_15233/02_2025/8a8m_15233.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a8m_15233/02_2025/8a8m_15233.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a8m_15233/02_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-5592/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: 4.32, per 1000 atoms: 0.82
  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: 1.34
  Conformation dependent library (CDL) restraints added in 652.0 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: 0.55
  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: 1.29

  Time building geometry restraints manager: 1.52 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:             5.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.870
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.820
-------------------------------------------------------------------------------
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  : 0.581 
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: 0.1681
  time to fit residues: 19.9778
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  : 0.578 
-------------------------------------------------------------------------------
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 = 49)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.087908 restraints weight = 22189.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.088536 restraints weight = 20446.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.089640 restraints weight = 19238.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    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 = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
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  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.8360 (t60)
REVERT: A  179 MET cc_start: 0.0891 (tpt) cc_final: 0.0587 (tpt)
REVERT: B   70 MET cc_start: 0.1291 (ttt) cc_final: 0.0507 (ttt)
REVERT: B   79 MET cc_start: 0.5656 (tmm) cc_final: 0.5268 (tmm)
REVERT: B  125 VAL cc_start: 0.2987 (OUTLIER) cc_final: 0.2782 (m)
REVERT: B  129 MET cc_start: 0.8868 (mmm) cc_final: 0.8176 (mmm)
REVERT: B  132 MET cc_start: 0.8722 (mpp) cc_final: 0.8114 (mpp)
REVERT: B  141 LYS cc_start: 0.9372 (tptt) cc_final: 0.8970 (tptp)
REVERT: B  155 LEU cc_start: 0.8540 (mt) cc_final: 0.8303 (mt)
REVERT: B  184 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8587 (p0)
REVERT: B  247 MET cc_start: 0.9803 (mmm) cc_final: 0.9601 (mmm)
REVERT: B  257 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6061 (m-80)
REVERT: B  309 MET cc_start: 0.9321 (mtt) cc_final: 0.8996 (mmm)
REVERT: B  317 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7471 (t-90)
  outliers start: 34
  outliers final: 16
  residues processed: 94
  average time/residue: 0.1675
  time to fit residues: 21.3741
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  : 0.584 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 19 optimal weight:    2.9990
   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:    6.9990
   overall best weight:    1.0080

-------------------------------------------------------------------------------
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
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.153104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.129311 restraints weight = 34109.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.131631 restraints weight = 24709.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.132817 restraints weight = 19394.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5360  Z= 0.219
  Angle     :  0.806  10.110   7272  Z= 0.396
  Chirality :  0.048   0.208    814
  Planarity :  0.005   0.060    920
  Dihedral  :  8.127  77.257    760
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 26.16
  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: -2.70 (0.30), residues: 639
  helix: -0.85 (0.33), residues: 220
  sheet: -2.97 (0.66), residues: 46
  loop : -2.31 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 187 
 HIS   0.005   0.002   HIS B 317 
 PHE   0.014   0.001   PHE B 255 
 TYR   0.013   0.001   TYR A 132 
 ARG   0.002   0.000   ARG A 237 

*********************** 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
  98 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.1436 (ttt) cc_final: -0.1751 (tpt)
REVERT: A  179 MET cc_start: 0.1119 (tpt) cc_final: 0.0215 (tpt)
REVERT: A  186 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7787 (tmm-80)
REVERT: B   79 MET cc_start: 0.5060 (tmm) cc_final: 0.4829 (tmm)
REVERT: B  125 VAL cc_start: 0.2810 (OUTLIER) cc_final: 0.2585 (m)
REVERT: B  129 MET cc_start: 0.9024 (mmm) cc_final: 0.8270 (mmm)
REVERT: B  132 MET cc_start: 0.8817 (mpp) cc_final: 0.7808 (mpp)
REVERT: B  141 LYS cc_start: 0.9304 (tptt) cc_final: 0.8890 (tptp)
REVERT: B  184 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8771 (p0)
REVERT: B  247 MET cc_start: 0.9794 (mmm) cc_final: 0.9580 (mmm)
REVERT: B  255 PHE cc_start: 0.7080 (p90) cc_final: 0.6697 (p90)
REVERT: B  257 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6631 (m-80)
REVERT: B  309 MET cc_start: 0.9343 (mtt) cc_final: 0.9032 (mmm)
  outliers start: 28
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1612
  time to fit residues: 19.5611
Evaluate side-chains
  84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
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:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 7 optimal weight:    8.9990
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 45 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.131995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.092642 restraints weight = 21897.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.093709 restraints weight = 19731.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.094737 restraints weight = 18422.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2832

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= 0.197
  Angle     :  0.778   9.295   7272  Z= 0.382
  Chirality :  0.047   0.240    814
  Planarity :  0.005   0.056    920
  Dihedral  :  7.512  72.902    759
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 26.74 %
    Favored  : 68.58 %
  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: -2.54 (0.30), residues: 639
  helix: -0.72 (0.34), residues: 222
  sheet: -2.84 (0.69), residues: 41
  loop : -2.24 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 260 
 HIS   0.005   0.001   HIS A  80 
 PHE   0.011   0.001   PHE B 264 
 TYR   0.010   0.001   TYR A 132 
 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: 27
    poor density    : 68
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.0483 (tpt) cc_final: -0.0137 (tpt)
REVERT: A  186 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7869 (tmm-80)
REVERT: A  265 MET cc_start: 0.0518 (ttp) cc_final: 0.0258 (ptt)
REVERT: B   79 MET cc_start: 0.5176 (tmm) cc_final: 0.4873 (tmm)
REVERT: B  129 MET cc_start: 0.9067 (mmm) cc_final: 0.8320 (mmm)
REVERT: B  141 LYS cc_start: 0.9289 (tptt) cc_final: 0.8878 (tptp)
REVERT: B  184 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8966 (p0)
REVERT: B  220 MET cc_start: 0.5600 (mmm) cc_final: 0.4698 (tmm)
REVERT: B  247 MET cc_start: 0.9769 (mmm) cc_final: 0.9564 (mmm)
REVERT: B  255 PHE cc_start: 0.7310 (p90) cc_final: 0.6915 (p90)
REVERT: B  257 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.4740 (m-80)
REVERT: B  309 MET cc_start: 0.9314 (mtt) cc_final: 0.8981 (mmm)
  outliers start: 27
  outliers final: 14
  residues processed: 89
  average time/residue: 0.1587
  time to fit residues: 18.8739
Evaluate side-chains
  80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
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  166 ILE
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   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:    0.0770
   chunk 36 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   overall best weight:    1.5942

-------------------------------------------------------------------------------
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
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 GLN
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.127462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.089017 restraints weight = 21434.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.090248 restraints weight = 19281.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.090807 restraints weight = 17797.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5360  Z= 0.239
  Angle     :  0.785   8.772   7272  Z= 0.389
  Chirality :  0.047   0.296    814
  Planarity :  0.005   0.056    920
  Dihedral  :  7.470  72.365    759
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 27.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 26.91 %
    Favored  : 67.01 %
  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: -2.48 (0.31), residues: 639
  helix: -0.63 (0.34), residues: 223
  sheet: -2.86 (0.80), residues: 36
  loop : -2.25 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 260 
 HIS   0.005   0.001   HIS A 148 
 PHE   0.012   0.002   PHE B 255 
 TYR   0.014   0.001   TYR B 140 
 ARG   0.004   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
  103 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 68
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.1656 (OUTLIER) cc_final: 0.1237 (mmm160)
REVERT: A   78 MET cc_start: -0.0745 (ttt) cc_final: -0.1017 (tpt)
REVERT: A  179 MET cc_start: 0.1013 (tpt) cc_final: 0.0370 (tpt)
REVERT: A  186 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.7908 (tmm-80)
REVERT: B   79 MET cc_start: 0.5336 (tmm) cc_final: 0.4942 (tmm)
REVERT: B  129 MET cc_start: 0.9155 (mmm) cc_final: 0.8361 (mmm)
REVERT: B  141 LYS cc_start: 0.9336 (tptt) cc_final: 0.8954 (tptp)
REVERT: B  184 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8937 (p0)
REVERT: B  220 MET cc_start: 0.5971 (mmm) cc_final: 0.5034 (tmm)
REVERT: B  255 PHE cc_start: 0.7436 (p90) cc_final: 0.7053 (p90)
REVERT: B  257 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.5323 (m-80)
REVERT: B  309 MET cc_start: 0.9305 (mtt) cc_final: 0.9031 (mmm)
  outliers start: 35
  outliers final: 21
  residues processed: 96
  average time/residue: 0.1726
  time to fit residues: 21.6529
Evaluate side-chains
  90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
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  128 GLN
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   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:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   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  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B 148 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 = 0.4592 r_free = 0.4592 target = 0.130397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.091577 restraints weight = 21917.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.092966 restraints weight = 19580.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.094099 restraints weight = 17863.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.3469

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= 0.204
  Angle     :  0.802   9.278   7272  Z= 0.389
  Chirality :  0.047   0.310    814
  Planarity :  0.005   0.047    920
  Dihedral  :  7.366  72.149    759
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 24.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 28.99 %
    Favored  : 67.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.37 (0.31), residues: 639
  helix: -0.49 (0.34), residues: 223
  sheet: -2.90 (0.74), residues: 39
  loop : -2.19 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 337 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.013   0.001   PHE B 283 
 TYR   0.012   0.002   TYR A 132 
 ARG   0.003   0.000   ARG B  95 

*********************** 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
  90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.0750 (ttt) cc_final: -0.1164 (tpt)
REVERT: A  179 MET cc_start: 0.1037 (tpt) cc_final: 0.0535 (tpt)
REVERT: A  186 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.7971 (tmm-80)
REVERT: A  288 MET cc_start: 0.8645 (mmp) cc_final: 0.7641 (ptp)
REVERT: B   70 MET cc_start: 0.0850 (ttt) cc_final: 0.0619 (ttt)
REVERT: B   79 MET cc_start: 0.5235 (tmm) cc_final: 0.4924 (tmm)
REVERT: B  129 MET cc_start: 0.9126 (mmm) cc_final: 0.8323 (mmm)
REVERT: B  141 LYS cc_start: 0.9335 (tptt) cc_final: 0.8942 (tptp)
REVERT: B  155 LEU cc_start: 0.8363 (mt) cc_final: 0.8064 (mt)
REVERT: B  184 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8965 (p0)
REVERT: B  220 MET cc_start: 0.5996 (mmm) cc_final: 0.5049 (tmm)
REVERT: B  255 PHE cc_start: 0.7414 (p90) cc_final: 0.7022 (p90)
REVERT: B  257 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.5386 (m-80)
REVERT: B  309 MET cc_start: 0.9263 (mtt) cc_final: 0.9006 (mmm)
  outliers start: 22
  outliers final: 18
  residues processed: 83
  average time/residue: 0.1638
  time to fit residues: 18.1536
Evaluate side-chains
  86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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  135 LEU
Chi-restraints excluded: chain A residue  166 ILE
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   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:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0000
   chunk 14 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 128 GLN
** B 148 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 = 0.151576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.127899 restraints weight = 34777.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.130346 restraints weight = 24417.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.131885 restraints weight = 18981.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5360  Z= 0.201
  Angle     :  0.787   9.511   7272  Z= 0.382
  Chirality :  0.046   0.264    814
  Planarity :  0.004   0.046    920
  Dihedral  :  7.178  69.756    759
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 23.30
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.36 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 28.47 %
    Favored  : 67.01 %
  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: -2.24 (0.32), residues: 639
  helix: -0.43 (0.34), residues: 229
  sheet: -2.92 (0.72), residues: 39
  loop : -2.09 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   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   0.002   0.000   ARG B  85 

*********************** 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
  96 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.8093 (t60)
REVERT: A   78 MET cc_start: -0.0967 (ttt) cc_final: -0.1346 (tpt)
REVERT: A  179 MET cc_start: 0.1509 (tpt) cc_final: 0.0947 (tpt)
REVERT: A  186 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.8035 (tmm-80)
REVERT: A  288 MET cc_start: 0.8327 (mmp) cc_final: 0.7437 (ptp)
REVERT: B  129 MET cc_start: 0.9115 (mmm) cc_final: 0.8242 (mmm)
REVERT: B  134 THR cc_start: 0.3942 (OUTLIER) cc_final: 0.3741 (m)
REVERT: B  141 LYS cc_start: 0.9310 (tptt) cc_final: 0.8900 (tptp)
REVERT: B  155 LEU cc_start: 0.8485 (mt) cc_final: 0.8243 (mt)
REVERT: B  220 MET cc_start: 0.5933 (mmm) cc_final: 0.4616 (tmm)
REVERT: B  255 PHE cc_start: 0.7397 (p90) cc_final: 0.6997 (p90)
REVERT: B  257 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5619 (m-80)
REVERT: B  309 MET cc_start: 0.9238 (mtt) cc_final: 0.8997 (mmm)
  outliers start: 26
  outliers final: 17
  residues processed: 90
  average time/residue: 0.1844
  time to fit residues: 21.5849
Evaluate side-chains
  86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
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  128 GLN
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  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  134 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 148 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 = 0.4599 r_free = 0.4599 target = 0.130078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.090687 restraints weight = 21662.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.092222 restraints weight = 18914.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.093413 restraints weight = 17106.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.3944

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= 0.207
  Angle     :  0.827  11.576   7272  Z= 0.396
  Chirality :  0.046   0.330    814
  Planarity :  0.005   0.045    920
  Dihedral  :  7.155  68.680    757
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 22.35
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.51 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 28.82 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.30 (0.32), residues: 639
  helix: -0.55 (0.34), residues: 234
  sheet: -3.03 (0.71), residues: 39
  loop : -2.07 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 197 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.013   0.001   PHE B 255 
 TYR   0.009   0.001   TYR B 140 
 ARG   0.004   0.001   ARG A   5 

*********************** 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
  96 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.8137 (t60)
REVERT: A   78 MET cc_start: -0.0652 (ttt) cc_final: -0.1056 (tpt)
REVERT: A  179 MET cc_start: 0.1372 (tpt) cc_final: 0.0849 (tpt)
REVERT: A  186 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.8047 (tmm-80)
REVERT: A  216 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8386 (mm)
REVERT: B  129 MET cc_start: 0.9079 (mmm) cc_final: 0.8309 (mmm)
REVERT: B  134 THR cc_start: 0.3807 (OUTLIER) cc_final: 0.3536 (m)
REVERT: B  141 LYS cc_start: 0.9337 (tptt) cc_final: 0.8934 (tptp)
REVERT: B  155 LEU cc_start: 0.8473 (mt) cc_final: 0.8238 (mt)
REVERT: B  220 MET cc_start: 0.5761 (mmm) cc_final: 0.4883 (tmm)
REVERT: B  255 PHE cc_start: 0.7457 (p90) cc_final: 0.7068 (p90)
REVERT: B  257 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5471 (m-80)
REVERT: B  309 MET cc_start: 0.9289 (mtt) cc_final: 0.9048 (mmm)
  outliers start: 28
  outliers final: 18
  residues processed: 87
  average time/residue: 0.1645
  time to fit residues: 19.0131
Evaluate side-chains
  86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
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   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 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  114 THR
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  134 THR
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:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0030
   chunk 29 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.9996

-------------------------------------------------------------------------------
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  44 GLN
B 148 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.129841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.093606 restraints weight = 21626.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.094540 restraints weight = 20048.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.094954 restraints weight = 18844.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.4127

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= 0.217
  Angle     :  0.870  13.064   7272  Z= 0.411
  Chirality :  0.047   0.321    814
  Planarity :  0.004   0.046    920
  Dihedral  :  7.225  68.143    757
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 22.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 29.34 %
    Favored  : 65.97 %
  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: -2.31 (0.32), residues: 639
  helix: -0.55 (0.34), residues: 234
  sheet: -3.43 (0.65), residues: 35
  loop : -2.06 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 197 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.012   0.001   PHE B 255 
 TYR   0.022   0.002   TYR A 182 
 ARG   0.004   0.000   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
  95 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8432 (OUTLIER) cc_final: 0.8118 (t60)
REVERT: A   57 ARG cc_start: 0.1460 (OUTLIER) cc_final: 0.1067 (mmm160)
REVERT: A   78 MET cc_start: -0.0856 (ttt) cc_final: -0.1888 (tpp)
REVERT: A  216 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8355 (mm)
REVERT: B  129 MET cc_start: 0.9107 (mmm) cc_final: 0.8340 (mmm)
REVERT: B  141 LYS cc_start: 0.9331 (tptt) cc_final: 0.8916 (tptp)
REVERT: B  155 LEU cc_start: 0.8508 (mt) cc_final: 0.8283 (mt)
REVERT: B  220 MET cc_start: 0.5817 (mmm) cc_final: 0.4942 (tmm)
REVERT: B  255 PHE cc_start: 0.7446 (p90) cc_final: 0.7048 (p90)
REVERT: B  257 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.5544 (m-80)
REVERT: B  309 MET cc_start: 0.9274 (mtt) cc_final: 0.9036 (mmm)
  outliers start: 27
  outliers final: 19
  residues processed: 87
  average time/residue: 0.1821
  time to fit residues: 20.4426
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  : 0.602 
-------------------------------------------------------------------------------
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  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  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   44 GLN
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:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** 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 = 0.4437 r_free = 0.4437 target = 0.106548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.073623 restraints weight = 25291.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.075192 restraints weight = 21524.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.076434 restraints weight = 18915.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.4786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   5360  Z= 0.377
  Angle     :  0.944  13.205   7272  Z= 0.472
  Chirality :  0.051   0.296    814
  Planarity :  0.006   0.046    920
  Dihedral  :  7.848  68.965    757
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 39.25
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.45 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 30.56 %
    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: -2.76 (0.31), residues: 639
  helix: -1.15 (0.31), residues: 236
  sheet: -3.59 (0.65), residues: 39
  loop : -2.14 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 197 
 HIS   0.011   0.002   HIS A 312 
 PHE   0.021   0.003   PHE B  46 
 TYR   0.017   0.002   TYR A 132 
 ARG   0.005   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
  86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.0367 (ttt) cc_final: -0.0688 (ttt)
REVERT: A  216 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8544 (mm)
REVERT: B  129 MET cc_start: 0.9353 (mmm) cc_final: 0.8437 (mmm)
REVERT: B  141 LYS cc_start: 0.9401 (tptt) cc_final: 0.8918 (tptp)
REVERT: B  155 LEU cc_start: 0.8593 (mt) cc_final: 0.8391 (mt)
REVERT: B  220 MET cc_start: 0.5813 (mmm) cc_final: 0.5070 (tmm)
REVERT: B  255 PHE cc_start: 0.7396 (p90) cc_final: 0.6982 (p90)
REVERT: B  257 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.5990 (m-80)
REVERT: B  309 MET cc_start: 0.9283 (mtt) cc_final: 0.9023 (mmm)
  outliers start: 21
  outliers final: 16
  residues processed: 80
  average time/residue: 0.1658
  time to fit residues: 17.4952
Evaluate side-chains
  79 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  135 LEU
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  257 TYR
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  301 GLU
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:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 40 optimal weight:    8.9990
   chunk 35 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7742

-------------------------------------------------------------------------------
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  44 GLN
** B 142 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 = 0.4581 r_free = 0.4581 target = 0.128606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.091519 restraints weight = 21932.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.092370 restraints weight = 20751.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.092735 restraints weight = 19670.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.4743

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= 0.223
  Angle     :  0.883  11.696   7272  Z= 0.425
  Chirality :  0.049   0.344    814
  Planarity :  0.005   0.047    920
  Dihedral  :  7.422  68.391    755
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 25.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 30.73 %
    Favored  : 65.62 %
  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: -2.56 (0.31), residues: 639
  helix: -0.81 (0.33), residues: 232
  sheet: -3.86 (0.60), residues: 42
  loop : -2.07 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 241 
 HIS   0.005   0.001   HIS B 317 
 PHE   0.014   0.002   PHE B 255 
 TYR   0.011   0.001   TYR A 182 
 ARG   0.005   0.001   ARG B  95 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2288.91 seconds
wall clock time: 41 minutes 51.60 seconds (2511.60 seconds total)