Starting phenix.real_space_refine
on Tue Mar  3 13:38:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a8m_15233/03_2026/8a8m_15233.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a8m_15233/03_2026/8a8m_15233.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2026/8a8m_15233.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2026/8a8m_15233.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2026/8a8m_15233.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a8m_15233/03_2026/8a8m_15233.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.20, per 1000 atoms: 0.23
  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: 0.55
  Conformation dependent library (CDL) restraints added in 287.4 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: 0.16
  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: 0.70

  Time building geometry restraints manager: 0.57 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:             5.960
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.460
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.910
-------------------------------------------------------------------------------
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= 0.182
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (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
 ARG   0.005   0.001   ARG B  85 
 TYR   0.012   0.001   TYR B 140 
 PHE   0.013   0.002   PHE B 313 
 TRP   0.021   0.002   TRP A  18 
 HIS   0.013   0.002   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5360)
  covalent geometry    : angle       0.88783 ( 7272)
  hydrogen bonds       : bond        0.19056 (  192)
  hydrogen bonds       : angle       8.79042 (  534)

*********************** 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  : 0.198 
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: -0.3125 (tmm)
REVERT: B   79 MET cc_start: 0.3563 (tmm) cc_final: 0.3055 (tpp)
REVERT: B  141 LYS cc_start: 0.9204 (tptt) cc_final: 0.8769 (tptp)
REVERT: B  179 ASP cc_start: 0.8562 (m-30) cc_final: 0.8253 (m-30)
REVERT: B  184 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6935 (p0)
  outliers start: 9
  outliers final: 3
  residues processed: 91
  average time/residue: 0.0758
  time to fit residues: 9.1618
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  : 0.194 
-------------------------------------------------------------------------------
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 54 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0970
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 199 HIS
** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
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 265 GLN
B 266 GLN
B 269 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.157226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.133568 restraints weight = 34008.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.135826 restraints weight = 24547.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.137302 restraints weight = 19385.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.138346 restraints weight = 16415.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.139128 restraints weight = 14530.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4220 r_free = 0.4220    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4215 r_free = 0.4215    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.1706

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= 0.169
  Angle     :  0.808   9.483   7272  Z= 0.406
  Chirality :  0.050   0.213    814
  Planarity :  0.005   0.053    920
  Dihedral  :  9.694  83.371    762
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 24.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 25.35 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.30), residues: 639
  helix: -0.87 (0.32), residues: 222
  sheet: -2.53 (0.70), residues: 46
  loop : -2.26 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 186 
 TYR   0.010   0.001   TYR A   9 
 PHE   0.011   0.002   PHE B 313 
 TRP   0.013   0.002   TRP A 187 
 HIS   0.009   0.002   HIS B 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5360)
  covalent geometry    : angle       0.80807 ( 7272)
  hydrogen bonds       : bond        0.05277 (  192)
  hydrogen bonds       : angle       7.27945 (  534)

*********************** 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
  92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.0079 (tpt) cc_final: -0.0421 (tpt)
REVERT: A  186 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7687 (tmm-80)
REVERT: B   70 MET cc_start: 0.1104 (ttt) cc_final: 0.0487 (ttt)
REVERT: B   79 MET cc_start: 0.4970 (tmm) cc_final: 0.4202 (tpp)
REVERT: B  125 VAL cc_start: 0.2747 (OUTLIER) cc_final: 0.2541 (m)
REVERT: B  129 MET cc_start: 0.8705 (mmm) cc_final: 0.8033 (mmm)
REVERT: B  132 MET cc_start: 0.8449 (mpp) cc_final: 0.7971 (mpp)
REVERT: B  141 LYS cc_start: 0.9261 (tptt) cc_final: 0.8861 (tptp)
REVERT: B  155 LEU cc_start: 0.8565 (mt) cc_final: 0.8275 (mt)
REVERT: B  184 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8378 (p0)
REVERT: B  247 MET cc_start: 0.9770 (mmm) cc_final: 0.9542 (mmm)
REVERT: B  257 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.6343 (m-80)
REVERT: B  317 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7369 (t-90)
  outliers start: 21
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0699
  time to fit residues: 8.0709
Evaluate side-chains
  80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 VAL
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 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  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  317 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 14 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0770
   chunk 46 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   chunk 9 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.0340

-------------------------------------------------------------------------------
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  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.156176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.132150 restraints weight = 33907.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4761 r_free = 0.4761 target = 0.134410 restraints weight = 24543.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.135870 restraints weight = 19361.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.136642 restraints weight = 16409.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.137491 restraints weight = 14817.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5360  Z= 0.149
  Angle     :  0.776  11.593   7272  Z= 0.383
  Chirality :  0.046   0.168    814
  Planarity :  0.005   0.058    920
  Dihedral  :  7.727  74.495    757
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 25.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 27.43 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.31), residues: 639
  helix: -0.70 (0.33), residues: 220
  sheet: -2.69 (0.65), residues: 46
  loop : -2.26 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 186 
 TYR   0.012   0.001   TYR B 140 
 PHE   0.013   0.001   PHE B 255 
 TRP   0.020   0.002   TRP B 260 
 HIS   0.005   0.001   HIS B 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5360)
  covalent geometry    : angle       0.77633 ( 7272)
  hydrogen bonds       : bond        0.04768 (  192)
  hydrogen bonds       : angle       6.93399 (  534)

*********************** 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
  89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.1720 (ttt) cc_final: -0.1937 (tpt)
REVERT: A  179 MET cc_start: 0.0324 (tpt) cc_final: -0.0164 (tpt)
REVERT: A  186 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7634 (tmm-80)
REVERT: A  288 MET cc_start: 0.8401 (mmp) cc_final: 0.7493 (ppp)
REVERT: B   70 MET cc_start: 0.0919 (ttt) cc_final: 0.0471 (ttt)
REVERT: B  125 VAL cc_start: 0.2634 (OUTLIER) cc_final: 0.2422 (m)
REVERT: B  129 MET cc_start: 0.8888 (mmm) cc_final: 0.8150 (mmm)
REVERT: B  132 MET cc_start: 0.8631 (mpp) cc_final: 0.7655 (mpp)
REVERT: B  141 LYS cc_start: 0.9253 (tptt) cc_final: 0.8852 (tptp)
REVERT: B  184 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8750 (p0)
REVERT: B  220 MET cc_start: 0.5782 (mmm) cc_final: 0.5344 (tmm)
REVERT: B  247 MET cc_start: 0.9785 (mmm) cc_final: 0.9550 (mmm)
REVERT: B  255 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6899 (p90)
REVERT: B  309 MET cc_start: 0.9287 (ptp) cc_final: 0.9053 (mmm)
  outliers start: 21
  outliers final: 12
  residues processed: 81
  average time/residue: 0.0708
  time to fit residues: 7.6199
Evaluate side-chains
  82 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  239 VAL
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  255 PHE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  275 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0170
   chunk 56 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
B  77 GLN
B 310 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.156938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.133322 restraints weight = 33852.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.135556 restraints weight = 24235.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.136995 restraints weight = 18956.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.138007 restraints weight = 16051.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.138593 restraints weight = 14279.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5360  Z= 0.137
  Angle     :  0.761   9.716   7272  Z= 0.373
  Chirality :  0.046   0.215    814
  Planarity :  0.005   0.056    920
  Dihedral  :  7.098  69.518    757
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 21.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 25.87 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.31), residues: 639
  helix: -0.57 (0.34), residues: 222
  sheet: -2.79 (0.74), residues: 36
  loop : -2.19 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 302 
 TYR   0.011   0.001   TYR B 257 
 PHE   0.010   0.001   PHE B 255 
 TRP   0.011   0.002   TRP A 337 
 HIS   0.004   0.001   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5360)
  covalent geometry    : angle       0.76103 ( 7272)
  hydrogen bonds       : bond        0.04423 (  192)
  hydrogen bonds       : angle       6.67110 (  534)

*********************** 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
  101 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 70
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.1555 (ttt) cc_final: -0.1947 (tpt)
REVERT: A  179 MET cc_start: -0.0077 (tpt) cc_final: -0.0570 (tpt)
REVERT: A  186 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7561 (tmm-80)
REVERT: A  265 MET cc_start: -0.0718 (ttp) cc_final: -0.1043 (ptt)
REVERT: A  288 MET cc_start: 0.8348 (mmp) cc_final: 0.7550 (ppp)
REVERT: B   79 MET cc_start: 0.4787 (tmm) cc_final: 0.4149 (tpp)
REVERT: B  125 VAL cc_start: 0.2496 (OUTLIER) cc_final: 0.2280 (m)
REVERT: B  129 MET cc_start: 0.8956 (mmm) cc_final: 0.8303 (mmm)
REVERT: B  132 MET cc_start: 0.8726 (mpp) cc_final: 0.7556 (mpp)
REVERT: B  140 TYR cc_start: 0.8514 (t80) cc_final: 0.8282 (t80)
REVERT: B  141 LYS cc_start: 0.9237 (tptt) cc_final: 0.8813 (tptp)
REVERT: B  184 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8759 (p0)
REVERT: B  220 MET cc_start: 0.5760 (mmm) cc_final: 0.5214 (tmm)
REVERT: B  247 MET cc_start: 0.9785 (mmm) cc_final: 0.9564 (mmm)
REVERT: B  255 PHE cc_start: 0.7306 (p90) cc_final: 0.6764 (p90)
  outliers start: 31
  outliers final: 14
  residues processed: 94
  average time/residue: 0.0654
  time to fit residues: 8.2938
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  : 0.200 
-------------------------------------------------------------------------------
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   83 VAL
Chi-restraints excluded: chain A residue  117 VAL
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  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  267 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  275 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0970
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    2.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.126831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.087995 restraints weight = 21790.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.089440 restraints weight = 19497.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.090506 restraints weight = 17735.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.091009 restraints weight = 16476.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.091573 restraints weight = 15706.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5360  Z= 0.204
  Angle     :  0.816  11.703   7272  Z= 0.406
  Chirality :  0.047   0.262    814
  Planarity :  0.005   0.053    920
  Dihedral  :  7.284  70.430    757
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 30.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.98 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 26.56 %
    Favored  : 67.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.31), residues: 639
  helix: -0.73 (0.33), residues: 228
  sheet: -2.92 (0.65), residues: 49
  loop : -2.29 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 237 
 TYR   0.014   0.002   TYR A 132 
 PHE   0.018   0.002   PHE B 283 
 TRP   0.015   0.002   TRP A 187 
 HIS   0.007   0.002   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 5360)
  covalent geometry    : angle       0.81616 ( 7272)
  hydrogen bonds       : bond        0.04791 (  192)
  hydrogen bonds       : angle       6.79751 (  534)

*********************** 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
  98 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 65
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.8312 (t60)
REVERT: A  179 MET cc_start: 0.0957 (tpt) cc_final: 0.0474 (mmm)
REVERT: B  129 MET cc_start: 0.9088 (mmm) cc_final: 0.8355 (mmm)
REVERT: B  141 LYS cc_start: 0.9338 (tptt) cc_final: 0.8958 (tptp)
REVERT: B  155 LEU cc_start: 0.8543 (mt) cc_final: 0.8296 (mt)
REVERT: B  184 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8974 (p0)
REVERT: B  220 MET cc_start: 0.6182 (mmm) cc_final: 0.5293 (tmm)
REVERT: B  255 PHE cc_start: 0.7455 (p90) cc_final: 0.7083 (p90)
REVERT: B  257 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5409 (m-80)
REVERT: B  309 MET cc_start: 0.9461 (mmm) cc_final: 0.9202 (mmm)
  outliers start: 33
  outliers final: 21
  residues processed: 91
  average time/residue: 0.0606
  time to fit residues: 7.5444
Evaluate side-chains
  88 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 64
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  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  166 ILE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  268 MET
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 29 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.2584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.129491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.090738 restraints weight = 21655.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.092183 restraints weight = 19487.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.093240 restraints weight = 17829.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.093832 restraints weight = 16593.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.094670 restraints weight = 15555.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5360  Z= 0.154
  Angle     :  0.805   9.947   7272  Z= 0.392
  Chirality :  0.046   0.268    814
  Planarity :  0.005   0.044    920
  Dihedral  :  7.244  70.737    757
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 26.17
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.82 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 27.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.31), residues: 639
  helix: -0.59 (0.34), residues: 226
  sheet: -2.94 (0.76), residues: 36
  loop : -2.19 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  85 
 TYR   0.015   0.001   TYR B 140 
 PHE   0.011   0.001   PHE B 255 
 TRP   0.010   0.002   TRP B 260 
 HIS   0.004   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5360)
  covalent geometry    : angle       0.80477 ( 7272)
  hydrogen bonds       : bond        0.04384 (  192)
  hydrogen bonds       : angle       6.65660 (  534)

*********************** 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
  98 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.0680 (ttt) cc_final: -0.1166 (tpt)
REVERT: A  179 MET cc_start: 0.0926 (tpt) cc_final: 0.0265 (tpt)
REVERT: A  186 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.7954 (tmm-80)
REVERT: B  129 MET cc_start: 0.9110 (mmm) cc_final: 0.8440 (mmm)
REVERT: B  141 LYS cc_start: 0.9344 (tptt) cc_final: 0.8941 (tptp)
REVERT: B  155 LEU cc_start: 0.8552 (mt) cc_final: 0.8319 (mt)
REVERT: B  184 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8963 (p0)
REVERT: B  220 MET cc_start: 0.6148 (mmm) cc_final: 0.5235 (tmm)
REVERT: B  255 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7047 (p90)
REVERT: B  257 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.5384 (m-80)
REVERT: B  309 MET cc_start: 0.9474 (mmm) cc_final: 0.9216 (mmm)
  outliers start: 30
  outliers final: 20
  residues processed: 91
  average time/residue: 0.0644
  time to fit residues: 7.8840
Evaluate side-chains
  86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
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  243 LEU
Chi-restraints excluded: chain B residue  255 PHE
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 14 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0770
   chunk 25 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    4.4146

-------------------------------------------------------------------------------
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 202 GLN
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 GLN
** 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 = 0.4425 r_free = 0.4425 target = 0.116178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.076912 restraints weight = 22851.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.078326 restraints weight = 19942.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.079023 restraints weight = 17911.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.080159 restraints weight = 16595.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.080538 restraints weight = 15631.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070   5360  Z= 0.351
  Angle     :  1.007  10.337   7272  Z= 0.513
  Chirality :  0.055   0.374    814
  Planarity :  0.006   0.045    920
  Dihedral  :  8.443  72.710    757
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 49.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.70 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 27.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.20 (0.30), residues: 639
  helix: -1.60 (0.30), residues: 239
  sheet: -2.82 (0.61), residues: 59
  loop : -2.40 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  10 
 TYR   0.028   0.003   TYR A 132 
 PHE   0.020   0.004   PHE A 308 
 TRP   0.020   0.004   TRP A  18 
 HIS   0.011   0.003   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00732 ( 5360)
  covalent geometry    : angle       1.00735 ( 7272)
  hydrogen bonds       : bond        0.06342 (  192)
  hydrogen bonds       : angle       7.70818 (  534)

*********************** 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
  100 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.2412 (tpt) cc_final: 0.1918 (tpt)
REVERT: B   70 MET cc_start: 0.1465 (ttt) cc_final: 0.1166 (ttt)
REVERT: B  129 MET cc_start: 0.9397 (mmm) cc_final: 0.8693 (mmm)
REVERT: B  141 LYS cc_start: 0.9451 (tptt) cc_final: 0.8980 (tptp)
REVERT: B  184 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8754 (p0)
REVERT: B  220 MET cc_start: 0.6823 (mmm) cc_final: 0.5952 (tmm)
REVERT: B  255 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7344 (p90)
REVERT: B  257 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6517 (m-80)
REVERT: B  309 MET cc_start: 0.9499 (mmm) cc_final: 0.9235 (mmm)
  outliers start: 35
  outliers final: 25
  residues processed: 88
  average time/residue: 0.0799
  time to fit residues: 9.0730
Evaluate side-chains
  90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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   77 HIS
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  265 MET
Chi-restraints excluded: chain A residue  268 MET
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  111 PHE
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  136 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  255 PHE
Chi-restraints excluded: chain B residue  257 TYR
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  324 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 38 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 184 ASN
B 293 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.126346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.086637 restraints weight = 22362.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.087751 restraints weight = 20472.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.088235 restraints weight = 19017.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.089180 restraints weight = 18003.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.089579 restraints weight = 17244.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5360  Z= 0.170
  Angle     :  0.884  15.896   7272  Z= 0.425
  Chirality :  0.051   0.380    814
  Planarity :  0.005   0.046    920
  Dihedral  :  7.872  72.065    757
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 30.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.98 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 29.86 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.31), residues: 639
  helix: -0.95 (0.33), residues: 227
  sheet: -3.12 (0.61), residues: 51
  loop : -2.27 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A   5 
 TYR   0.018   0.002   TYR A 132 
 PHE   0.014   0.002   PHE B 290 
 TRP   0.022   0.002   TRP A  18 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 5360)
  covalent geometry    : angle       0.88365 ( 7272)
  hydrogen bonds       : bond        0.04672 (  192)
  hydrogen bonds       : angle       6.92922 (  534)

*********************** 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
  92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: -0.0545 (ttt) cc_final: -0.0749 (tpt)
REVERT: B   70 MET cc_start: 0.1068 (ttt) cc_final: 0.0712 (ttt)
REVERT: B  129 MET cc_start: 0.9244 (mmm) cc_final: 0.8575 (mmm)
REVERT: B  140 TYR cc_start: 0.8568 (t80) cc_final: 0.8362 (t80)
REVERT: B  141 LYS cc_start: 0.9411 (tptt) cc_final: 0.8928 (tptp)
REVERT: B  220 MET cc_start: 0.6299 (mmm) cc_final: 0.5246 (tmm)
REVERT: B  255 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7169 (p90)
REVERT: B  257 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.5731 (m-80)
REVERT: B  309 MET cc_start: 0.9488 (mmm) cc_final: 0.9217 (mmm)
  outliers start: 26
  outliers final: 20
  residues processed: 84
  average time/residue: 0.0629
  time to fit residues: 7.0579
Evaluate side-chains
  85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  239 VAL
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  255 PHE
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 27 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0060
   chunk 18 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 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 = 0.4562 r_free = 0.4562 target = 0.127458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.087665 restraints weight = 21769.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.089146 restraints weight = 19388.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.090252 restraints weight = 17578.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.091022 restraints weight = 16292.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.091678 restraints weight = 15453.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5360  Z= 0.152
  Angle     :  0.872  15.455   7272  Z= 0.413
  Chirality :  0.050   0.317    814
  Planarity :  0.005   0.048    920
  Dihedral  :  7.680  73.098    755
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 26.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 30.56 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.31), residues: 639
  helix: -0.65 (0.34), residues: 228
  sheet: -3.63 (0.55), residues: 52
  loop : -2.21 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 186 
 TYR   0.012   0.001   TYR B 140 
 PHE   0.031   0.002   PHE B 139 
 TRP   0.025   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5360)
  covalent geometry    : angle       0.87219 ( 7272)
  hydrogen bonds       : bond        0.04390 (  192)
  hydrogen bonds       : angle       6.67129 (  534)

*********************** 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
  86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7916 (pp)
REVERT: A  179 MET cc_start: 0.2183 (tpt) cc_final: 0.1933 (tpt)
REVERT: B   70 MET cc_start: 0.1156 (ttt) cc_final: 0.0855 (ttt)
REVERT: B  129 MET cc_start: 0.9205 (mmm) cc_final: 0.8497 (mmm)
REVERT: B  141 LYS cc_start: 0.9403 (tptt) cc_final: 0.8963 (tptp)
REVERT: B  220 MET cc_start: 0.5866 (mmm) cc_final: 0.5171 (tmm)
REVERT: B  255 PHE cc_start: 0.7458 (p90) cc_final: 0.7096 (p90)
REVERT: B  257 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.5542 (m-80)
REVERT: B  309 MET cc_start: 0.9517 (mmm) cc_final: 0.9250 (mmm)
  outliers start: 22
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0706
  time to fit residues: 7.4842
Evaluate side-chains
  80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
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  113 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  162 CYS
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   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  193 VAL
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 45 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 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 = 0.4549 r_free = 0.4549 target = 0.126292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.086647 restraints weight = 22462.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.087394 restraints weight = 20001.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.088872 restraints weight = 18475.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.089716 restraints weight = 17257.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.090307 restraints weight = 16324.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.4826

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= 0.165
  Angle     :  0.858  13.616   7272  Z= 0.411
  Chirality :  0.049   0.329    814
  Planarity :  0.005   0.048    920
  Dihedral  :  7.553  70.688    755
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 29.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.61 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 30.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.31), residues: 639
  helix: -0.75 (0.33), residues: 231
  sheet: -3.61 (0.50), residues: 62
  loop : -2.18 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  95 
 TYR   0.020   0.002   TYR A 311 
 PHE   0.016   0.002   PHE B 139 
 TRP   0.018   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5360)
  covalent geometry    : angle       0.85830 ( 7272)
  hydrogen bonds       : bond        0.04444 (  192)
  hydrogen bonds       : angle       6.72715 (  534)

********************** 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
  82 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7899 (pp)
REVERT: A  179 MET cc_start: 0.2496 (tpt) cc_final: 0.2234 (tpt)
REVERT: B   70 MET cc_start: 0.1077 (ttt) cc_final: 0.0779 (ttt)
REVERT: B  129 MET cc_start: 0.9239 (mmm) cc_final: 0.8372 (mmm)
REVERT: B  141 LYS cc_start: 0.9430 (tptt) cc_final: 0.8959 (tptp)
REVERT: B  220 MET cc_start: 0.6030 (mmm) cc_final: 0.5356 (tmm)
REVERT: B  255 PHE cc_start: 0.7489 (p90) cc_final: 0.7131 (p90)
REVERT: B  257 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.5557 (m-80)
REVERT: B  309 MET cc_start: 0.9518 (mmm) cc_final: 0.9248 (mmm)
  outliers start: 18
  outliers final: 14
  residues processed: 77
  average time/residue: 0.0714
  time to fit residues: 7.4112
Evaluate side-chains
  78 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
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  113 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  199 HIS
Chi-restraints excluded: chain A residue  200 TYR
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  324 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0040
   chunk 46 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.0594

-------------------------------------------------------------------------------
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 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 = 0.4514 r_free = 0.4514 target = 0.111056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.077234 restraints weight = 25012.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.078921 restraints weight = 21018.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.080309 restraints weight = 18317.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.080964 restraints weight = 16490.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.081982 restraints weight = 15411.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.4987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5360  Z= 0.152
  Angle     :  0.858  13.795   7272  Z= 0.407
  Chirality :  0.048   0.306    814
  Planarity :  0.005   0.048    920
  Dihedral  :  7.375  69.223    755
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 26.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 30.56 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.31), residues: 639
  helix: -0.66 (0.34), residues: 233
  sheet: -3.64 (0.54), residues: 52
  loop : -2.19 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 136 
 TYR   0.012   0.001   TYR A 311 
 PHE   0.017   0.002   PHE B 139 
 TRP   0.020   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5360)
  covalent geometry    : angle       0.85767 ( 7272)
  hydrogen bonds       : bond        0.04261 (  192)
  hydrogen bonds       : angle       6.60577 (  534)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1372.47 seconds
wall clock time: 24 minutes 23.39 seconds (1463.39 seconds total)