Starting phenix.real_space_refine
on Wed Mar 12 03:55:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9f_15930/03_2025/8b9f_15930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9f_15930/03_2025/8b9f_15930.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b9f_15930/03_2025/8b9f_15930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9f_15930/03_2025/8b9f_15930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9f_15930/03_2025/8b9f_15930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9f_15930/03_2025/8b9f_15930.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1946 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Se      1      7.20       5
     S      47      5.16       5
     C    3516      2.51       5
     N     931      2.21       5
     O    1038      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5533
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "E"
      Number of atoms: 1946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1946
          Classifications: {'peptide': 251}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 227}
    Chain: "B"
      Number of atoms: 1579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1579
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 194}
    Chain: "C"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1501
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 10, 'TRANS': 184}
    Chain: "A"
      Number of atoms: 486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 486
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 5, 'TRANS': 53}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'SPH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.17, per 1000 atoms: 0.93
  Number of scatterers: 5533
  At special positions: 0
  Unit cell: (74.55, 105, 137.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Se      1     33.99
     S      47     16.00
     O    1038      8.00
     N     931      7.00
     C    3516      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  36 " - pdb=" SG  CYS E  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  98 " - pdb=" SG  CYS E 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 129 " - pdb=" SG  CYS E 158 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 163 " - pdb=" SG  CYS E 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 190 " - pdb=" SG  CYS E 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 225 " - pdb=" SG  CYS E 267 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 253 " - pdb=" SG  CYS E 283 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.66
  Conformation dependent library (CDL) restraints added in 786.7 milliseconds
  

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1314

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 16 sheets defined
      9.7% alpha, 30.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'E' and resid 112 through 116
    Processing helix  chain 'B' and resid 83 through 87
    Processing helix  chain 'B' and resid 89 through 99
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 178 through 185
      removed outlier: 4.161A  pdb=" N   THR B 183 " --> pdb=" O   GLY B 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 48
    Processing helix  chain 'C' and resid 65 through 69
    Processing helix  chain 'C' and resid 98 through 105
    Processing helix  chain 'C' and resid 144 through 150
      removed outlier: 3.690A  pdb=" N   LEU C 150 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
    Processing sheet with id=AA1, first strand: chain 'E' and resid 45 through 47
      removed outlier: 3.640A  pdb=" N   GLN E  86 " --> pdb=" O   LEU E  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 70 through 71
    Processing sheet with id=AA3, first strand: chain 'E' and resid 107 through 109
    Processing sheet with id=AA4, first strand: chain 'E' and resid 133 through 135
    Processing sheet with id=AA5, first strand: chain 'E' and resid 172 through 175
    Processing sheet with id=AA6, first strand: chain 'E' and resid 194 through 197
    Processing sheet with id=AA7, first strand: chain 'E' and resid 234 through 236
    Processing sheet with id=AA8, first strand: chain 'E' and resid 258 through 260
    Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.495A  pdb=" N   VAL B 239 " --> pdb=" O   TRP B  71 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.105A  pdb=" N   ALA B 250 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ARG B 103 " --> pdb=" O   ALA B 250 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   TYR B 252 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU B 101 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154
      removed outlier: 6.758A  pdb=" N   CYS B 121 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   SER B 228 " --> pdb=" O   GLN B 119 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   GLN B 119 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 51 through 52
    Processing sheet with id=AB4, first strand: chain 'C' and resid 51 through 52
    Processing sheet with id=AB5, first strand: chain 'C' and resid 83 through 86
      removed outlier: 3.907A  pdb=" N   PHE C  83 " --> pdb=" O   CYS C 192 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   LYS C 129 " --> pdb=" O   GLN C 195 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   GLY C 197 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   THR C 127 " --> pdb=" O   GLY C 197 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 177 through 178
      removed outlier: 6.136A  pdb=" N   TYR C 107 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LEU C 225 " --> pdb=" O   TYR C 107 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 110 through 112
      removed outlier: 6.192A  pdb=" N   PHE A 110 " --> pdb=" O   PRO A 250 " (cutoff:3.500A)

    154 hydrogen bonds defined for protein.
    369 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 1.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 1815
        1.36 -     1.51: 1747
        1.51 -     1.66: 2050
        1.66 -     1.80: 39
        1.80 -     1.95: 27
  Bond restraints: 5678
  Sorted by residual:
  bond pdb=" C4  SPH A 300 "
       pdb=" C5  SPH A 300 "
    ideal  model  delta    sigma   weight residual
    1.334  1.463 -0.129 2.00e-02 2.50e+03 4.15e+01
  bond pdb=" CA  LYS E 161 "
       pdb=" C   LYS E 161 "
    ideal  model  delta    sigma   weight residual
    1.523  1.474  0.049 1.28e-02 6.10e+03 1.47e+01
  bond pdb=" N   ARG E  96 "
       pdb=" CA  ARG E  96 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.041 1.16e-02 7.43e+03 1.24e+01
  bond pdb=" N   ILE C  70 "
       pdb=" CA  ILE C  70 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 9.10e-03 1.21e+04 1.01e+01
  bond pdb=" N   SER E 162 "
       pdb=" CA  SER E 162 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.17e-02 7.31e+03 9.77e+00
  ... (remaining 5673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 7539
        2.19 -     4.37: 171
        4.37 -     6.56: 10
        6.56 -     8.74: 4
        8.74 -    10.93: 3
  Bond angle restraints: 7727
  Sorted by residual:
  angle pdb=" N   MET C  65 "
        pdb=" CA  MET C  65 "
        pdb=" C   MET C  65 "
      ideal   model   delta    sigma   weight residual
     113.23  104.79    8.44 1.24e+00 6.50e-01 4.63e+01
  angle pdb=" N   ARG E  96 "
        pdb=" CA  ARG E  96 "
        pdb=" C   ARG E  96 "
      ideal   model   delta    sigma   weight residual
     110.46  119.01   -8.55 1.48e+00 4.57e-01 3.34e+01
  angle pdb=" N   SER E  97 "
        pdb=" CA  SER E  97 "
        pdb=" C   SER E  97 "
      ideal   model   delta    sigma   weight residual
     108.07  116.92   -8.85 1.59e+00 3.96e-01 3.10e+01
  angle pdb=" C   THR C  64 "
        pdb=" CA  THR C  64 "
        pdb=" CB  THR C  64 "
      ideal   model   delta    sigma   weight residual
     111.48  100.92   10.56 1.91e+00 2.74e-01 3.06e+01
  angle pdb=" N   LYS E 161 "
        pdb=" CA  LYS E 161 "
        pdb=" C   LYS E 161 "
      ideal   model   delta    sigma   weight residual
     109.96  101.57    8.39 1.68e+00 3.54e-01 2.49e+01
  ... (remaining 7722 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 3115
       16.26 -    32.53: 210
       32.53 -    48.79: 40
       48.79 -    65.05: 22
       65.05 -    81.32: 9
  Dihedral angle restraints: 3396
    sinusoidal: 1349
      harmonic: 2047
  Sorted by residual:
  dihedral pdb=" CA  PHE B  82 "
           pdb=" C   PHE B  82 "
           pdb=" N   PRO B  83 "
           pdb=" CA  PRO B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   39.35  -39.35     0      5.00e+00 4.00e-02 6.19e+01
  dihedral pdb=" C   THR C  64 "
           pdb=" N   THR C  64 "
           pdb=" CA  THR C  64 "
           pdb=" CB  THR C  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -110.86  -11.14     0      2.50e+00 1.60e-01 1.99e+01
  dihedral pdb=" CA  MET A 100 "
           pdb=" C   MET A 100 "
           pdb=" N   VAL A 101 "
           pdb=" CA  VAL A 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.00  -22.00     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 3393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 668
       0.059 -    0.118: 144
       0.118 -    0.176: 31
       0.176 -    0.235: 7
       0.235 -    0.294: 3
  Chirality restraints: 853
  Sorted by residual:
  chirality pdb=" CA  THR C  64 "
            pdb=" N   THR C  64 "
            pdb=" C   THR C  64 "
            pdb=" CB  THR C  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.82   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CB  VAL A 101 "
            pdb=" CA  VAL A 101 "
            pdb=" CG1 VAL A 101 "
            pdb=" CG2 VAL A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  ILE C  70 "
            pdb=" N   ILE C  70 "
            pdb=" C   ILE C  70 "
            pdb=" CB  ILE C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 850 not shown)

  Planarity restraints: 995
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  SPH A 300 "   -0.231 2.00e-02 2.50e+03   2.61e-01 6.82e+02
        pdb=" C4  SPH A 300 "    0.170 2.00e-02 2.50e+03
        pdb=" C5  SPH A 300 "    0.337 2.00e-02 2.50e+03
        pdb=" C6  SPH A 300 "   -0.277 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C  54 "    0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   PRO C  54 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   PRO C  54 "    0.024 2.00e-02 2.50e+03
        pdb=" N   VAL C  55 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 160 "   -0.018 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   LYS E 160 "    0.061 2.00e-02 2.50e+03
        pdb=" O   LYS E 160 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LYS E 161 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 992 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 349
        2.73 -     3.27: 5311
        3.27 -     3.81: 8990
        3.81 -     4.36: 11662
        4.36 -     4.90: 19253
  Nonbonded interactions: 45565
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 214 "
            pdb=" OD1 ASP E 215 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OE1 GLU A 108 "
            pdb=" OH  TYR A 258 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OD1 ASP C 182 "
            pdb=" OG1 THR C 185 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLY E 132 "
            pdb=" N   LYS E 161 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OG1 THR B 183 "
            pdb=" O   ASP C  50 "
     model   vdw
     2.326 3.040
  ... (remaining 45560 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.290
  Find NCS groups from input model:        0.060
  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:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6237
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      :  0.006   0.129   5678  Z= 0.382
  Angle     :  0.761  10.927   7727  Z= 0.464
  Chirality :  0.056   0.294    853
  Planarity :  0.010   0.261    995
  Dihedral  : 13.303  81.316   2058
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.43 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  5.82 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.29), residues: 699
  helix: -1.62 (0.67), residues: 43
  sheet:  0.25 (0.38), residues: 174
  loop : -1.27 (0.25), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 276 
 HIS   0.005   0.001   HIS C 109 
 PHE   0.015   0.002   PHE A 110 
 TYR   0.011   0.001   TYR A 258 
 ARG   0.005   0.001   ARG A 254 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 246
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   42 VAL cc_start: -0.0379 (t) cc_final: -0.0752 (t)
REVERT: E   71 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7597 (mttm)
REVERT: E  105 ASN cc_start: 0.7654 (m-40) cc_final: 0.7217 (m-40)
REVERT: E  113 TYR cc_start: 0.7818 (m-80) cc_final: 0.7354 (m-80)
REVERT: E  157 PHE cc_start: 0.5165 (p90) cc_final: 0.4901 (p90)
REVERT: E  165 ASN cc_start: 0.8326 (t0) cc_final: 0.8056 (t0)
REVERT: E  251 TYR cc_start: 0.2438 (m-80) cc_final: 0.2219 (m-80)
REVERT: B   74 ASP cc_start: 0.8221 (p0) cc_final: 0.7701 (p0)
REVERT: B   95 ASN cc_start: 0.8641 (m-40) cc_final: 0.8313 (m-40)
REVERT: B  100 TYR cc_start: 0.7824 (t80) cc_final: 0.6471 (t80)
REVERT: B  129 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6640 (mm-30)
REVERT: B  132 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8788 (mmm)
REVERT: B  215 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.4934 (mmt180)
REVERT: B  219 PHE cc_start: 0.8713 (p90) cc_final: 0.8485 (p90)
REVERT: B  256 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5594 (ptp-170)
REVERT: C   61 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7755 (mttt)
REVERT: C  179 VAL cc_start: 0.8318 (t) cc_final: 0.8024 (t)
REVERT: A  265 ASN cc_start: 0.8065 (m-40) cc_final: 0.7832 (m-40)
  outliers start: 9
  outliers final: 2
  residues processed: 250
  average time/residue: 0.1892
  time to fit residues: 59.5748
Evaluate side-chains
  167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 163
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  225 CYS
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain A residue  277 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
B 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.215186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.153449 restraints weight = 6314.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.158420 restraints weight = 3656.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.161675 restraints weight = 2424.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5678  Z= 0.231
  Angle     :  0.579   5.739   7727  Z= 0.307
  Chirality :  0.046   0.223    853
  Planarity :  0.005   0.061    995
  Dihedral  :  6.598  54.609    789
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 16.80 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.28), residues: 699
  helix: -0.56 (0.79), residues: 45
  sheet:  0.38 (0.40), residues: 159
  loop : -0.82 (0.24), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  80 
 HIS   0.006   0.001   HIS B 109 
 PHE   0.018   0.002   PHE B 226 
 TYR   0.025   0.002   TYR C 194 
 ARG   0.005   0.001   ARG C 177 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7868 (mttm)
REVERT: E   82 LEU cc_start: 0.4117 (OUTLIER) cc_final: 0.3292 (tt)
REVERT: E  105 ASN cc_start: 0.8109 (m-40) cc_final: 0.7709 (m-40)
REVERT: E  113 TYR cc_start: 0.8268 (m-80) cc_final: 0.7526 (m-10)
REVERT: E  135 ARG cc_start: 0.6275 (ttt-90) cc_final: 0.5320 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7197 (tp30) cc_final: 0.6802 (tp30)
REVERT: B   64 TYR cc_start: 0.8596 (m-80) cc_final: 0.8395 (m-80)
REVERT: B   70 THR cc_start: 0.9077 (m) cc_final: 0.8677 (p)
REVERT: B   72 GLU cc_start: 0.8204 (mp0) cc_final: 0.7864 (mp0)
REVERT: B   74 ASP cc_start: 0.7973 (p0) cc_final: 0.7696 (p0)
REVERT: B   84 ASP cc_start: 0.7708 (t0) cc_final: 0.7272 (t0)
REVERT: B   87 LYS cc_start: 0.8164 (pttt) cc_final: 0.7627 (ptpt)
REVERT: B  129 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6720 (mm-30)
REVERT: B  132 MET cc_start: 0.9231 (mtt) cc_final: 0.8827 (mmm)
REVERT: B  167 GLN cc_start: 0.7373 (tp-100) cc_final: 0.6909 (tp40)
REVERT: B  213 MET cc_start: 0.7727 (mmm) cc_final: 0.7389 (mtt)
REVERT: B  215 ARG cc_start: 0.6907 (ttp-170) cc_final: 0.4753 (mmt180)
REVERT: B  218 ASN cc_start: 0.8481 (m-40) cc_final: 0.7808 (m110)
REVERT: B  256 ARG cc_start: 0.7317 (ppt90) cc_final: 0.6129 (mtp-110)
REVERT: C   44 MET cc_start: 0.7356 (mmt) cc_final: 0.6829 (tpp)
REVERT: C   61 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7910 (mtmt)
REVERT: C  102 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7036 (mm-30)
REVERT: C  134 TYR cc_start: 0.8251 (t80) cc_final: 0.7768 (t80)
REVERT: A   98 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7546 (mtt90)
REVERT: A  103 MET cc_start: 0.8549 (tpp) cc_final: 0.8183 (tpp)
REVERT: A  254 ARG cc_start: 0.8814 (mmm160) cc_final: 0.8417 (mmm160)
REVERT: A  265 ASN cc_start: 0.8493 (m-40) cc_final: 0.8230 (m-40)
  outliers start: 26
  outliers final: 19
  residues processed: 188
  average time/residue: 0.1900
  time to fit residues: 45.4765
Evaluate side-chains
  168 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  197 PHE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  225 CYS
Chi-restraints excluded: chain E residue  236 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  231 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 14 optimal weight:    0.3980
   chunk 63 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:   30.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
E 212 GLN
E 271 ASN
B  95 ASN
** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.216000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.153607 restraints weight = 6381.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.158689 restraints weight = 3695.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.162062 restraints weight = 2454.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5678  Z= 0.225
  Angle     :  0.552   5.279   7727  Z= 0.292
  Chirality :  0.045   0.167    853
  Planarity :  0.004   0.032    995
  Dihedral  :  5.731  53.896    781
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 18.42 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.29), residues: 699
  helix: -0.45 (0.80), residues: 45
  sheet:  0.54 (0.41), residues: 159
  loop : -0.75 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  80 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.028   0.002   PHE B 219 
 TYR   0.027   0.002   TYR C 194 
 ARG   0.004   0.000   ARG E 221 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8196 (ptmt) cc_final: 0.7901 (mttm)
REVERT: E   82 LEU cc_start: 0.3995 (OUTLIER) cc_final: 0.3226 (tt)
REVERT: E  105 ASN cc_start: 0.8262 (m-40) cc_final: 0.7823 (m-40)
REVERT: E  113 TYR cc_start: 0.8128 (m-80) cc_final: 0.7384 (m-10)
REVERT: E  135 ARG cc_start: 0.6173 (ttt-90) cc_final: 0.5253 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7181 (tp30) cc_final: 0.6801 (tp30)
REVERT: E  205 LEU cc_start: 0.6971 (mp) cc_final: 0.6668 (mm)
REVERT: B   64 TYR cc_start: 0.8573 (m-80) cc_final: 0.8309 (m-80)
REVERT: B   70 THR cc_start: 0.9158 (m) cc_final: 0.8626 (p)
REVERT: B   72 GLU cc_start: 0.8349 (mp0) cc_final: 0.7780 (mp0)
REVERT: B   74 ASP cc_start: 0.7937 (p0) cc_final: 0.7623 (p0)
REVERT: B   81 LYS cc_start: 0.8742 (mttm) cc_final: 0.8526 (mttt)
REVERT: B   84 ASP cc_start: 0.7648 (t0) cc_final: 0.7366 (t0)
REVERT: B   87 LYS cc_start: 0.8304 (pttt) cc_final: 0.7655 (ptpt)
REVERT: B  129 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: B  215 ARG cc_start: 0.6598 (ttp-170) cc_final: 0.4628 (mmt180)
REVERT: B  256 ARG cc_start: 0.7399 (ppt90) cc_final: 0.6128 (mtp-110)
REVERT: C   44 MET cc_start: 0.7545 (mmt) cc_final: 0.7322 (tpp)
REVERT: C   61 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8014 (mtmt)
REVERT: C  134 TYR cc_start: 0.8264 (t80) cc_final: 0.7782 (t80)
REVERT: C  156 TRP cc_start: 0.7304 (t60) cc_final: 0.5845 (t60)
REVERT: C  224 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6497 (tt)
REVERT: A   98 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7668 (mtt90)
REVERT: A  254 ARG cc_start: 0.8874 (mmm160) cc_final: 0.8478 (mmm160)
REVERT: A  265 ASN cc_start: 0.8449 (m-40) cc_final: 0.8241 (m-40)
  outliers start: 27
  outliers final: 20
  residues processed: 175
  average time/residue: 0.1842
  time to fit residues: 41.1171
Evaluate side-chains
  164 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  236 ILE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  231 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 4 optimal weight:    8.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B  95 ASN
C  86 GLN
C 109 HIS
C 195 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.210652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.145789 restraints weight = 6784.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.150459 restraints weight = 4073.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.153546 restraints weight = 2795.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.4357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5678  Z= 0.315
  Angle     :  0.601   6.121   7727  Z= 0.316
  Chirality :  0.046   0.155    853
  Planarity :  0.005   0.043    995
  Dihedral  :  5.126  47.666    780
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 18.90 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.29), residues: 699
  helix: -0.92 (0.75), residues: 46
  sheet:  0.24 (0.39), residues: 174
  loop : -0.87 (0.25), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 276 
 HIS   0.003   0.001   HIS C  97 
 PHE   0.032   0.002   PHE B 219 
 TYR   0.044   0.002   TYR C 194 
 ARG   0.005   0.001   ARG B  62 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8213 (ptmt) cc_final: 0.7910 (mttm)
REVERT: E  105 ASN cc_start: 0.8376 (m-40) cc_final: 0.7933 (m-40)
REVERT: E  113 TYR cc_start: 0.8158 (m-80) cc_final: 0.7524 (m-10)
REVERT: E  205 LEU cc_start: 0.6765 (mp) cc_final: 0.6461 (mm)
REVERT: E  246 ARG cc_start: 0.7481 (ptp-170) cc_final: 0.6721 (ptm160)
REVERT: E  247 GLN cc_start: 0.8439 (mt0) cc_final: 0.8158 (tt0)
REVERT: B   64 TYR cc_start: 0.8554 (m-80) cc_final: 0.8331 (m-80)
REVERT: B   70 THR cc_start: 0.9291 (m) cc_final: 0.8937 (p)
REVERT: B   72 GLU cc_start: 0.8519 (mp0) cc_final: 0.8225 (mp0)
REVERT: B   74 ASP cc_start: 0.8072 (p0) cc_final: 0.7741 (p0)
REVERT: B   84 ASP cc_start: 0.7646 (t0) cc_final: 0.7393 (t0)
REVERT: B   87 LYS cc_start: 0.8417 (pttt) cc_final: 0.7789 (ptpt)
REVERT: B   95 ASN cc_start: 0.8596 (m-40) cc_final: 0.8371 (m-40)
REVERT: B  129 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7135 (mm-30)
REVERT: B  215 ARG cc_start: 0.6613 (ttp-170) cc_final: 0.4581 (mmt180)
REVERT: B  256 ARG cc_start: 0.7894 (ppt90) cc_final: 0.6284 (mtp-110)
REVERT: C   44 MET cc_start: 0.7808 (mmt) cc_final: 0.7548 (tpp)
REVERT: C   61 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8095 (mtmt)
REVERT: C  134 TYR cc_start: 0.8200 (t80) cc_final: 0.7860 (t80)
REVERT: A   98 ARG cc_start: 0.8368 (mtt180) cc_final: 0.7731 (mtt90)
REVERT: A  254 ARG cc_start: 0.8917 (mmm160) cc_final: 0.8357 (mmm160)
  outliers start: 34
  outliers final: 23
  residues processed: 172
  average time/residue: 0.1832
  time to fit residues: 40.4675
Evaluate side-chains
  167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  236 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  199 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 68 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0870
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    0.2980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
E 242 HIS
C  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.219018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.150667 restraints weight = 7087.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.156241 restraints weight = 4110.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.159750 restraints weight = 2753.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.4621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5678  Z= 0.192
  Angle     :  0.538   6.861   7727  Z= 0.284
  Chirality :  0.045   0.170    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.706  41.064    780
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.36 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.29), residues: 699
  helix: -0.74 (0.77), residues: 47
  sheet:  0.52 (0.41), residues: 157
  loop : -0.73 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 276 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.036   0.002   PHE B 219 
 TYR   0.023   0.002   TYR B 100 
 ARG   0.005   0.000   ARG A 105 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7920 (mttm)
REVERT: E   82 LEU cc_start: 0.3949 (OUTLIER) cc_final: 0.3433 (tt)
REVERT: E  105 ASN cc_start: 0.8532 (m-40) cc_final: 0.8064 (m-40)
REVERT: E  113 TYR cc_start: 0.8278 (m-80) cc_final: 0.7717 (m-10)
REVERT: E  197 PHE cc_start: 0.7789 (m-80) cc_final: 0.7547 (m-80)
REVERT: E  205 LEU cc_start: 0.7035 (mp) cc_final: 0.6754 (mm)
REVERT: E  247 GLN cc_start: 0.8873 (mt0) cc_final: 0.8070 (tt0)
REVERT: B   64 TYR cc_start: 0.8582 (m-80) cc_final: 0.8284 (m-80)
REVERT: B   70 THR cc_start: 0.9250 (m) cc_final: 0.9030 (p)
REVERT: B   72 GLU cc_start: 0.8529 (mp0) cc_final: 0.8084 (mp0)
REVERT: B   74 ASP cc_start: 0.8121 (p0) cc_final: 0.7804 (p0)
REVERT: B   81 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8378 (mttp)
REVERT: B   84 ASP cc_start: 0.7601 (t0) cc_final: 0.7330 (t0)
REVERT: B   87 LYS cc_start: 0.8261 (pttt) cc_final: 0.7658 (ptpt)
REVERT: B   95 ASN cc_start: 0.8598 (m-40) cc_final: 0.8375 (m-40)
REVERT: B  129 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7101 (mm-30)
REVERT: B  215 ARG cc_start: 0.6464 (ttp-170) cc_final: 0.4488 (mmt180)
REVERT: B  226 PHE cc_start: 0.8498 (m-10) cc_final: 0.8091 (m-10)
REVERT: C   44 MET cc_start: 0.7894 (mmt) cc_final: 0.7546 (tpp)
REVERT: C   61 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7913 (mtmt)
REVERT: C  134 TYR cc_start: 0.8221 (t80) cc_final: 0.7799 (t80)
REVERT: A   98 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7569 (mtt90)
REVERT: A  254 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8227 (mmm160)
REVERT: A  265 ASN cc_start: 0.8567 (m-40) cc_final: 0.8353 (m-40)
REVERT: A  286 LYS cc_start: 0.8605 (pttm) cc_final: 0.8199 (ptpp)
  outliers start: 28
  outliers final: 21
  residues processed: 172
  average time/residue: 0.1733
  time to fit residues: 38.3011
Evaluate side-chains
  167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  218 ASN
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 68 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 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 = 0.4396 r_free = 0.4396 target = 0.216717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.147837 restraints weight = 7099.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.153107 restraints weight = 4179.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.156704 restraints weight = 2846.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5678  Z= 0.244
  Angle     :  0.580   8.464   7727  Z= 0.306
  Chirality :  0.045   0.189    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.559  33.709    780
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 21.00 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.29), residues: 699
  helix: -0.89 (0.74), residues: 47
  sheet:  0.48 (0.41), residues: 153
  loop : -0.77 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  80 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.033   0.002   PHE B 219 
 TYR   0.032   0.002   TYR C 194 
 ARG   0.005   0.001   ARG B  62 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7907 (mttm)
REVERT: E  105 ASN cc_start: 0.8557 (m-40) cc_final: 0.8090 (m-40)
REVERT: E  113 TYR cc_start: 0.8222 (m-80) cc_final: 0.7942 (m-10)
REVERT: E  197 PHE cc_start: 0.7793 (m-80) cc_final: 0.7492 (m-80)
REVERT: E  205 LEU cc_start: 0.7118 (mp) cc_final: 0.6827 (mm)
REVERT: B   64 TYR cc_start: 0.8614 (m-80) cc_final: 0.8286 (m-80)
REVERT: B   70 THR cc_start: 0.9219 (m) cc_final: 0.8992 (p)
REVERT: B   72 GLU cc_start: 0.8498 (mp0) cc_final: 0.7947 (mp0)
REVERT: B   74 ASP cc_start: 0.8145 (p0) cc_final: 0.7823 (p0)
REVERT: B   81 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8160 (mttp)
REVERT: B   84 ASP cc_start: 0.7491 (t0) cc_final: 0.7207 (t0)
REVERT: B   87 LYS cc_start: 0.8273 (pttt) cc_final: 0.7662 (ptpt)
REVERT: B   95 ASN cc_start: 0.8663 (m-40) cc_final: 0.8423 (m-40)
REVERT: B  129 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7242 (mm-30)
REVERT: B  215 ARG cc_start: 0.6522 (ttp-170) cc_final: 0.4432 (mmt180)
REVERT: B  226 PHE cc_start: 0.8529 (m-10) cc_final: 0.8155 (m-10)
REVERT: B  256 ARG cc_start: 0.7850 (ppt90) cc_final: 0.6211 (mtt-85)
REVERT: C   44 MET cc_start: 0.7964 (mmt) cc_final: 0.7640 (tpp)
REVERT: C   61 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7920 (mtmt)
REVERT: C  134 TYR cc_start: 0.8262 (t80) cc_final: 0.7887 (t80)
REVERT: A   98 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7576 (mtt90)
REVERT: A  254 ARG cc_start: 0.8885 (mmm160) cc_final: 0.8313 (mmm160)
REVERT: A  265 ASN cc_start: 0.8600 (m-40) cc_final: 0.8321 (m-40)
REVERT: A  286 LYS cc_start: 0.8641 (pttm) cc_final: 0.8323 (pttm)
  outliers start: 34
  outliers final: 24
  residues processed: 178
  average time/residue: 0.1840
  time to fit residues: 42.0445
Evaluate side-chains
  173 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0980
   chunk 17 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
C 181 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.216569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.150162 restraints weight = 7202.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.155242 restraints weight = 4340.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158638 restraints weight = 2971.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.5195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5678  Z= 0.218
  Angle     :  0.567   8.528   7727  Z= 0.298
  Chirality :  0.046   0.182    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.381  26.268    780
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.46 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.29), residues: 699
  helix: -0.45 (0.78), residues: 47
  sheet:  0.52 (0.42), residues: 151
  loop : -0.74 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  78 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.027   0.001   PHE B 219 
 TYR   0.024   0.002   TYR C 194 
 ARG   0.005   0.001   ARG A 105 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7904 (mttm)
REVERT: E   82 LEU cc_start: 0.3887 (OUTLIER) cc_final: 0.3316 (tt)
REVERT: E  105 ASN cc_start: 0.8449 (m-40) cc_final: 0.8035 (m-40)
REVERT: E  113 TYR cc_start: 0.8225 (m-80) cc_final: 0.7319 (m-10)
REVERT: E  205 LEU cc_start: 0.7045 (mp) cc_final: 0.6744 (mm)
REVERT: E  246 ARG cc_start: 0.7581 (ptp-170) cc_final: 0.7350 (ptp-170)
REVERT: B   64 TYR cc_start: 0.8521 (m-80) cc_final: 0.8251 (m-80)
REVERT: B   72 GLU cc_start: 0.8528 (mp0) cc_final: 0.7923 (mp0)
REVERT: B   74 ASP cc_start: 0.8108 (p0) cc_final: 0.7777 (p0)
REVERT: B   81 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7811 (mmtp)
REVERT: B   84 ASP cc_start: 0.7553 (t0) cc_final: 0.7338 (t0)
REVERT: B   87 LYS cc_start: 0.8271 (pttt) cc_final: 0.7645 (ptpt)
REVERT: B   95 ASN cc_start: 0.8717 (m-40) cc_final: 0.8458 (m-40)
REVERT: B  129 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7172 (mm-30)
REVERT: B  215 ARG cc_start: 0.6473 (ttp-170) cc_final: 0.4395 (mmt180)
REVERT: B  226 PHE cc_start: 0.8500 (m-10) cc_final: 0.8229 (m-10)
REVERT: B  256 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6267 (mtt-85)
REVERT: C   44 MET cc_start: 0.8056 (mmt) cc_final: 0.7697 (tpp)
REVERT: C   61 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7995 (mtmt)
REVERT: C  134 TYR cc_start: 0.8211 (t80) cc_final: 0.7774 (t80)
REVERT: A   98 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7553 (mtt90)
REVERT: A  254 ARG cc_start: 0.8878 (mmm160) cc_final: 0.8340 (mmm160)
REVERT: A  265 ASN cc_start: 0.8554 (m-40) cc_final: 0.8332 (m-40)
REVERT: A  286 LYS cc_start: 0.8599 (pttm) cc_final: 0.8348 (pttm)
  outliers start: 31
  outliers final: 23
  residues processed: 166
  average time/residue: 0.1775
  time to fit residues: 37.9239
Evaluate side-chains
  163 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  218 ASN
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0670
   chunk 63 optimal weight:    0.5980
   chunk 54 optimal weight:    0.1980
   chunk 19 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.218855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.151530 restraints weight = 7080.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.156483 restraints weight = 4298.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.159886 restraints weight = 2982.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.5315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5678  Z= 0.185
  Angle     :  0.576   9.423   7727  Z= 0.302
  Chirality :  0.045   0.168    853
  Planarity :  0.004   0.031    995
  Dihedral  :  4.324  22.127    780
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.26 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.29), residues: 699
  helix: -0.13 (0.81), residues: 47
  sheet:  0.62 (0.42), residues: 149
  loop : -0.73 (0.25), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  78 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.023   0.001   PHE B 219 
 TYR   0.023   0.001   TYR B 100 
 ARG   0.004   0.000   ARG A 105 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   35 ASP cc_start: 0.3869 (OUTLIER) cc_final: 0.3334 (t70)
REVERT: E   71 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7908 (mttm)
REVERT: E   82 LEU cc_start: 0.3890 (OUTLIER) cc_final: 0.3349 (tt)
REVERT: E  105 ASN cc_start: 0.8396 (m-40) cc_final: 0.8029 (m-40)
REVERT: E  113 TYR cc_start: 0.8193 (m-80) cc_final: 0.7362 (m-10)
REVERT: E  157 PHE cc_start: 0.5157 (p90) cc_final: 0.4844 (p90)
REVERT: E  205 LEU cc_start: 0.7080 (mp) cc_final: 0.6782 (mm)
REVERT: B   64 TYR cc_start: 0.8494 (m-80) cc_final: 0.8190 (m-80)
REVERT: B   74 ASP cc_start: 0.8081 (p0) cc_final: 0.7711 (p0)
REVERT: B   84 ASP cc_start: 0.7515 (t0) cc_final: 0.7303 (t0)
REVERT: B   87 LYS cc_start: 0.8189 (pttt) cc_final: 0.7661 (ptpt)
REVERT: B   96 MET cc_start: 0.7851 (ttp) cc_final: 0.7570 (ttp)
REVERT: B  215 ARG cc_start: 0.6489 (ttp-170) cc_final: 0.4602 (mmt180)
REVERT: C   44 MET cc_start: 0.7974 (mmt) cc_final: 0.7567 (tpp)
REVERT: C   61 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7937 (mtmt)
REVERT: C  134 TYR cc_start: 0.8126 (t80) cc_final: 0.7734 (t80)
REVERT: A   98 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7508 (mtt90)
  outliers start: 28
  outliers final: 18
  residues processed: 160
  average time/residue: 0.1724
  time to fit residues: 35.3678
Evaluate side-chains
  158 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue  181 GLN
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
E 271 ASN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 GLN
** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 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 = 0.4391 r_free = 0.4391 target = 0.215987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.147496 restraints weight = 7236.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.152346 restraints weight = 4488.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.155737 restraints weight = 3146.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.5527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5678  Z= 0.326
  Angle     :  0.664   8.760   7727  Z= 0.348
  Chirality :  0.047   0.177    853
  Planarity :  0.005   0.062    995
  Dihedral  :  4.688  21.632    780
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 23.59 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.29), residues: 699
  helix: -0.48 (0.79), residues: 47
  sheet:  0.39 (0.42), residues: 154
  loop : -0.81 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B  78 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.027   0.002   PHE B 219 
 TYR   0.038   0.002   TYR C 194 
 ARG   0.007   0.001   ARG E 246 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7923 (mttm)
REVERT: E   82 LEU cc_start: 0.3913 (OUTLIER) cc_final: 0.3382 (tt)
REVERT: E  105 ASN cc_start: 0.8534 (m-40) cc_final: 0.8133 (t0)
REVERT: E  113 TYR cc_start: 0.8183 (m-80) cc_final: 0.7614 (m-10)
REVERT: E  205 LEU cc_start: 0.7125 (mp) cc_final: 0.6836 (mm)
REVERT: E  247 GLN cc_start: 0.8702 (mt0) cc_final: 0.8259 (mt0)
REVERT: B   64 TYR cc_start: 0.8584 (m-80) cc_final: 0.8349 (m-80)
REVERT: B   72 GLU cc_start: 0.8496 (mp0) cc_final: 0.8254 (mp0)
REVERT: B   84 ASP cc_start: 0.7660 (t0) cc_final: 0.7382 (t0)
REVERT: B   87 LYS cc_start: 0.8339 (pttt) cc_final: 0.7712 (ptpt)
REVERT: B  129 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7242 (mm-30)
REVERT: B  215 ARG cc_start: 0.6560 (ttp-170) cc_final: 0.4548 (mmt180)
REVERT: B  256 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6274 (mtt-85)
REVERT: C   44 MET cc_start: 0.8044 (mmt) cc_final: 0.7730 (tpp)
REVERT: C  125 MET cc_start: 0.6772 (tpt) cc_final: 0.6300 (tpp)
REVERT: C  134 TYR cc_start: 0.8278 (t80) cc_final: 0.7897 (t80)
REVERT: A   98 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7526 (mtt90)
REVERT: A  103 MET cc_start: 0.8371 (tpp) cc_final: 0.8027 (tpp)
  outliers start: 30
  outliers final: 25
  residues processed: 155
  average time/residue: 0.1853
  time to fit residues: 36.3080
Evaluate side-chains
  163 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  203 PHE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  181 GLN
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0470
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    0.3980
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
C 181 GLN
** C 189 ASN ** 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 = 0.4407 r_free = 0.4407 target = 0.218479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.151364 restraints weight = 7237.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.156345 restraints weight = 4405.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.159793 restraints weight = 3066.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.5615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5678  Z= 0.203
  Angle     :  0.627   9.550   7727  Z= 0.325
  Chirality :  0.045   0.160    853
  Planarity :  0.004   0.035    995
  Dihedral  :  4.531  22.925    780
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 24.56 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.30), residues: 699
  helix:  0.05 (0.84), residues: 47
  sheet:  0.45 (0.42), residues: 152
  loop : -0.77 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B  78 
 HIS   0.007   0.001   HIS B 109 
 PHE   0.026   0.001   PHE B 219 
 TYR   0.023   0.002   TYR B 100 
 ARG   0.007   0.001   ARG E 246 

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

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

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1398 Ramachandran restraints generated.
    699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   35 ASP cc_start: 0.4046 (OUTLIER) cc_final: 0.3421 (t70)
REVERT: E   71 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7904 (mttm)
REVERT: E   82 LEU cc_start: 0.3953 (OUTLIER) cc_final: 0.3394 (tt)
REVERT: E  113 TYR cc_start: 0.8330 (m-80) cc_final: 0.7590 (m-10)
REVERT: E  157 PHE cc_start: 0.5192 (p90) cc_final: 0.4947 (p90)
REVERT: E  205 LEU cc_start: 0.7151 (mp) cc_final: 0.6893 (mm)
REVERT: B   64 TYR cc_start: 0.8464 (m-80) cc_final: 0.8242 (m-80)
REVERT: B   72 GLU cc_start: 0.8482 (mp0) cc_final: 0.8261 (mp0)
REVERT: B   74 ASP cc_start: 0.8110 (p0) cc_final: 0.7774 (p0)
REVERT: B   84 ASP cc_start: 0.7627 (t0) cc_final: 0.7411 (t0)
REVERT: B   87 LYS cc_start: 0.8277 (pttt) cc_final: 0.7654 (ptpt)
REVERT: B   96 MET cc_start: 0.7886 (ttp) cc_final: 0.7634 (ttp)
REVERT: B  215 ARG cc_start: 0.6375 (ttp-170) cc_final: 0.4363 (mmt180)
REVERT: B  256 ARG cc_start: 0.7745 (ppt90) cc_final: 0.6227 (mtt-85)
REVERT: C   44 MET cc_start: 0.7988 (mmt) cc_final: 0.7664 (tpp)
REVERT: C   61 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7803 (mtmt)
REVERT: C  134 TYR cc_start: 0.8141 (t80) cc_final: 0.7762 (t80)
REVERT: A   98 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7508 (mtt90)
REVERT: A  254 ARG cc_start: 0.8759 (mmm160) cc_final: 0.8551 (ttt-90)
  outliers start: 23
  outliers final: 20
  residues processed: 159
  average time/residue: 0.2019
  time to fit residues: 40.2960
Evaluate side-chains
  156 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  203 PHE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  218 ASN
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 1 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 11 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 109 HIS
B 218 ASN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 189 ASN ** 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 = 0.4429 r_free = 0.4429 target = 0.219998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.152503 restraints weight = 7360.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.157675 restraints weight = 4495.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.161090 restraints weight = 3095.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.5647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.172   5678  Z= 0.377
  Angle     :  1.155  59.168   7727  Z= 0.696
  Chirality :  0.046   0.172    853
  Planarity :  0.005   0.038    995
  Dihedral  :  4.621  23.752    780
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 25.53 %
    Favored  : 70.44 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.30), residues: 699
  helix:  0.05 (0.84), residues: 47
  sheet:  0.47 (0.42), residues: 152
  loop : -0.78 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  78 
 HIS   0.008   0.001   HIS B 109 
 PHE   0.027   0.002   PHE B 219 
 TYR   0.021   0.002   TYR B 100 
 ARG   0.023   0.001   ARG E 240 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2898.66 seconds
wall clock time: 50 minutes 37.33 seconds (3037.33 seconds total)