Starting phenix.real_space_refine
on Fri Aug 22 19:20:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9f_15930/08_2025/8b9f_15930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9f_15930/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9f_15930/08_2025/8b9f_15930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9f_15930/08_2025/8b9f_15930.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b9f_15930/08_2025/8b9f_15930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9f_15930/08_2025/8b9f_15930.map"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.53, per 1000 atoms: 0.28
  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: 0.44
  Conformation dependent library (CDL) restraints added in 220.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.21
  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: 0.78

  Time building geometry restraints manager: 0.59 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:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.560
-------------------------------------------------------------------------------
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   5686  Z= 0.332
  Angle     :  0.762  10.927   7743  Z= 0.465
  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  :  2.29 %
    Favored  : 97.42 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.001   ARG A 254 
 TYR   0.011   0.001   TYR A 258 
 PHE   0.015   0.002   PHE A 110 
 TRP   0.017   0.002   TRP E 276 
 HIS   0.005   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 5678)
  covalent geometry    : angle       0.76115 ( 7727)
  SS BOND              : bond        0.00472 (    8)
  SS BOND              : angle       1.15219 (   16)
  hydrogen bonds       : bond        0.19415 (  150)
  hydrogen bonds       : angle       8.93034 (  369)

*********************** 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  : 0.198 
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: -0.0762 (t)
REVERT: E   71 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7599 (mttm)
REVERT: E  105 ASN cc_start: 0.7654 (m-40) cc_final: 0.7218 (m-40)
REVERT: E  113 TYR cc_start: 0.7818 (m-80) cc_final: 0.7351 (m-80)
REVERT: E  157 PHE cc_start: 0.5165 (p90) cc_final: 0.4903 (p90)
REVERT: E  165 ASN cc_start: 0.8326 (t0) cc_final: 0.8055 (t0)
REVERT: B   74 ASP cc_start: 0.8221 (p0) cc_final: 0.7705 (p0)
REVERT: B   95 ASN cc_start: 0.8641 (m-40) cc_final: 0.8314 (m-40)
REVERT: B  100 TYR cc_start: 0.7824 (t80) cc_final: 0.6470 (t80)
REVERT: B  129 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6639 (mm-30)
REVERT: B  132 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8789 (mmm)
REVERT: B  215 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.4933 (mmt180)
REVERT: B  219 PHE cc_start: 0.8713 (p90) cc_final: 0.8487 (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: 0.7737 (mttt)
REVERT: C  179 VAL cc_start: 0.8318 (t) cc_final: 0.8024 (t)
REVERT: C  195 GLN cc_start: 0.7618 (tp40) cc_final: 0.7319 (tp40)
REVERT: A  265 ASN cc_start: 0.8065 (m-40) cc_final: 0.7831 (m-40)
  outliers start: 9
  outliers final: 2
  residues processed: 250
  average time/residue: 0.0792
  time to fit residues: 25.1247
Evaluate side-chains
  166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 162
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
E 271 ASN
B 181 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.216276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.152409 restraints weight = 6551.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.157529 restraints weight = 3787.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.161098 restraints weight = 2519.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.163372 restraints weight = 1876.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.165110 restraints weight = 1530.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5686  Z= 0.178
  Angle     :  0.609   5.738   7743  Z= 0.322
  Chirality :  0.047   0.245    853
  Planarity :  0.005   0.061    995
  Dihedral  :  6.491  49.784    789
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 17.45 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.28), residues: 699
  helix: -0.61 (0.79), residues: 45
  sheet:  0.39 (0.39), residues: 165
  loop : -0.80 (0.24), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 254 
 TYR   0.037   0.002   TYR C 194 
 PHE   0.023   0.002   PHE B 226 
 TRP   0.023   0.002   TRP E 276 
 HIS   0.004   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 5678)
  covalent geometry    : angle       0.60935 ( 7727)
  SS BOND              : bond        0.00168 (    8)
  SS BOND              : angle       0.49442 (   16)
  hydrogen bonds       : bond        0.03732 (  150)
  hydrogen bonds       : angle       6.48017 (  369)

*********************** 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
  200 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 170
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8138 (ptmt) cc_final: 0.7889 (mttm)
REVERT: E  105 ASN cc_start: 0.8103 (m-40) cc_final: 0.7693 (m-40)
REVERT: E  110 LYS cc_start: 0.7817 (ptmm) cc_final: 0.7609 (ptpt)
REVERT: E  113 TYR cc_start: 0.8228 (m-80) cc_final: 0.7477 (m-10)
REVERT: E  135 ARG cc_start: 0.6120 (ttt-90) cc_final: 0.5238 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7181 (tp30) cc_final: 0.6843 (tp30)
REVERT: E  205 LEU cc_start: 0.6794 (mp) cc_final: 0.6529 (mm)
REVERT: B   64 TYR cc_start: 0.8548 (m-80) cc_final: 0.8293 (m-80)
REVERT: B   70 THR cc_start: 0.9097 (m) cc_final: 0.8773 (p)
REVERT: B   72 GLU cc_start: 0.8281 (mp0) cc_final: 0.8022 (mp0)
REVERT: B   74 ASP cc_start: 0.8000 (p0) cc_final: 0.7735 (p0)
REVERT: B  129 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6776 (mm-30)
REVERT: B  132 MET cc_start: 0.9201 (mtt) cc_final: 0.8658 (mtt)
REVERT: B  167 GLN cc_start: 0.7480 (tp-100) cc_final: 0.7054 (tp-100)
REVERT: B  213 MET cc_start: 0.7695 (mmm) cc_final: 0.7391 (mtt)
REVERT: B  215 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.4779 (mmt180)
REVERT: B  218 ASN cc_start: 0.8480 (m-40) cc_final: 0.7777 (m110)
REVERT: B  256 ARG cc_start: 0.7462 (ppt90) cc_final: 0.6217 (mtp180)
REVERT: C   44 MET cc_start: 0.7608 (mmt) cc_final: 0.7066 (tpp)
REVERT: C   61 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8077 (mtmt)
REVERT: C   95 PHE cc_start: 0.6595 (m-80) cc_final: 0.5708 (m-10)
REVERT: C  102 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7133 (mm-30)
REVERT: C  134 TYR cc_start: 0.8225 (t80) cc_final: 0.7807 (t80)
REVERT: C  224 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6584 (tt)
REVERT: A   98 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7612 (mtt90)
REVERT: A  103 MET cc_start: 0.8496 (tpp) cc_final: 0.8133 (tpp)
REVERT: A  254 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8502 (mmm160)
REVERT: A  265 ASN cc_start: 0.8509 (m-40) cc_final: 0.8249 (m-40)
  outliers start: 30
  outliers final: 18
  residues processed: 191
  average time/residue: 0.0848
  time to fit residues: 20.4265
Evaluate side-chains
  163 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  108 ILE
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 B residue  181 ASN
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  209 SER
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 6 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0050
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0970
   chunk 40 optimal weight:    0.0970
   chunk 64 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.2990

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

Flipped N/Q/H residues before XYZ refinement:
E 212 GLN
B  95 ASN
** B 181 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 = 0.4424 r_free = 0.4424 target = 0.221844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.158246 restraints weight = 6533.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.163846 restraints weight = 3653.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.167747 restraints weight = 2377.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.170400 restraints weight = 1735.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.172016 restraints weight = 1392.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5686  Z= 0.116
  Angle     :  0.539   6.395   7743  Z= 0.287
  Chirality :  0.045   0.167    853
  Planarity :  0.004   0.029    995
  Dihedral  :  5.642  52.138    781
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.26 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.29), residues: 699
  helix: -0.45 (0.80), residues: 46
  sheet:  0.60 (0.40), residues: 158
  loop : -0.80 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 221 
 TYR   0.019   0.001   TYR E 118 
 PHE   0.028   0.002   PHE B 219 
 TRP   0.021   0.002   TRP E 276 
 HIS   0.005   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 5678)
  covalent geometry    : angle       0.53925 ( 7727)
  SS BOND              : bond        0.00158 (    8)
  SS BOND              : angle       0.51289 (   16)
  hydrogen bonds       : bond        0.03340 (  150)
  hydrogen bonds       : angle       6.10996 (  369)

*********************** 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: 24
    poor density    : 164
  time to evaluate  : 0.206 
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: E   71 LYS cc_start: 0.8196 (ptmt) cc_final: 0.7912 (mttm)
REVERT: E   82 LEU cc_start: 0.3843 (OUTLIER) cc_final: 0.3194 (tt)
REVERT: E  105 ASN cc_start: 0.8229 (m-40) cc_final: 0.7789 (m-40)
REVERT: E  110 LYS cc_start: 0.7824 (ptmm) cc_final: 0.7597 (ptpt)
REVERT: E  113 TYR cc_start: 0.8217 (m-80) cc_final: 0.7418 (m-10)
REVERT: E  135 ARG cc_start: 0.6203 (ttt-90) cc_final: 0.5289 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7219 (tp30) cc_final: 0.6850 (tp30)
REVERT: E  205 LEU cc_start: 0.6885 (mp) cc_final: 0.6604 (mm)
REVERT: B   64 TYR cc_start: 0.8518 (m-80) cc_final: 0.8314 (m-80)
REVERT: B   70 THR cc_start: 0.9146 (m) cc_final: 0.8812 (p)
REVERT: B   72 GLU cc_start: 0.8331 (mp0) cc_final: 0.8065 (mp0)
REVERT: B   74 ASP cc_start: 0.7911 (p0) cc_final: 0.7575 (p0)
REVERT: B   81 LYS cc_start: 0.8707 (mttm) cc_final: 0.8362 (mttt)
REVERT: B   84 ASP cc_start: 0.7758 (t0) cc_final: 0.7502 (t0)
REVERT: B   87 LYS cc_start: 0.8406 (pttt) cc_final: 0.7965 (ptpt)
REVERT: B  129 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6674 (mm-30)
REVERT: B  132 MET cc_start: 0.8976 (mtt) cc_final: 0.8594 (mtt)
REVERT: B  167 GLN cc_start: 0.7469 (tp-100) cc_final: 0.6981 (tp-100)
REVERT: B  215 ARG cc_start: 0.6552 (ttp-170) cc_final: 0.4619 (mmt180)
REVERT: B  256 ARG cc_start: 0.7397 (ppt90) cc_final: 0.6116 (mtp180)
REVERT: C   44 MET cc_start: 0.7594 (mmt) cc_final: 0.7286 (tpp)
REVERT: C   61 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8103 (mtmt)
REVERT: C   86 GLN cc_start: 0.8554 (mt0) cc_final: 0.8296 (pt0)
REVERT: C   95 PHE cc_start: 0.6561 (m-80) cc_final: 0.5805 (m-10)
REVERT: C  134 TYR cc_start: 0.8223 (t80) cc_final: 0.7823 (t80)
REVERT: A   98 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7662 (mtt90)
REVERT: A  265 ASN cc_start: 0.8452 (m-40) cc_final: 0.8196 (m110)
  outliers start: 24
  outliers final: 14
  residues processed: 179
  average time/residue: 0.0889
  time to fit residues: 19.9848
Evaluate side-chains
  163 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  236 ILE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  122 LEU
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 C residue  104 LEU
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  209 SER
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 9 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0040
   chunk 22 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
E 212 GLN
B  95 ASN
C  86 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.213318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.150205 restraints weight = 6554.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.154983 restraints weight = 3855.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.158072 restraints weight = 2618.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.160527 restraints weight = 1988.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.161864 restraints weight = 1627.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5686  Z= 0.144
  Angle     :  0.560   5.886   7743  Z= 0.295
  Chirality :  0.046   0.175    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.974  45.397    780
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 19.55 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.29), residues: 699
  helix: -0.50 (0.79), residues: 46
  sheet:  0.37 (0.39), residues: 164
  loop : -0.75 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 254 
 TYR   0.028   0.002   TYR C 194 
 PHE   0.031   0.002   PHE B 219 
 TRP   0.014   0.002   TRP E 276 
 HIS   0.005   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5678)
  covalent geometry    : angle       0.55991 ( 7727)
  SS BOND              : bond        0.00276 (    8)
  SS BOND              : angle       0.77101 (   16)
  hydrogen bonds       : bond        0.03331 (  150)
  hydrogen bonds       : angle       5.93233 (  369)

*********************** 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
  184 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7901 (mttm)
REVERT: E   82 LEU cc_start: 0.3772 (OUTLIER) cc_final: 0.3136 (tt)
REVERT: E  105 ASN cc_start: 0.8293 (m-40) cc_final: 0.7902 (m-40)
REVERT: E  113 TYR cc_start: 0.8077 (m-80) cc_final: 0.7296 (m-10)
REVERT: E  205 LEU cc_start: 0.6674 (mp) cc_final: 0.6362 (mm)
REVERT: B   64 TYR cc_start: 0.8470 (m-80) cc_final: 0.8252 (m-80)
REVERT: B   72 GLU cc_start: 0.8483 (mp0) cc_final: 0.8281 (mp0)
REVERT: B   74 ASP cc_start: 0.7952 (p0) cc_final: 0.7611 (p0)
REVERT: B   81 LYS cc_start: 0.8710 (mttm) cc_final: 0.8381 (mttt)
REVERT: B   84 ASP cc_start: 0.7744 (t0) cc_final: 0.7520 (t0)
REVERT: B   87 LYS cc_start: 0.8338 (pttt) cc_final: 0.7978 (ptpt)
REVERT: B  129 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7029 (mm-30)
REVERT: B  132 MET cc_start: 0.8928 (mtt) cc_final: 0.8440 (mtt)
REVERT: B  213 MET cc_start: 0.7198 (mtt) cc_final: 0.6980 (mpp)
REVERT: B  215 ARG cc_start: 0.6580 (ttp-170) cc_final: 0.4733 (mmt180)
REVERT: B  256 ARG cc_start: 0.7712 (ppt90) cc_final: 0.6242 (mtp180)
REVERT: C   44 MET cc_start: 0.7783 (mmt) cc_final: 0.7435 (tpp)
REVERT: C   61 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8098 (mtmt)
REVERT: C   95 PHE cc_start: 0.6807 (m-80) cc_final: 0.5887 (m-10)
REVERT: C  134 TYR cc_start: 0.8218 (t80) cc_final: 0.7906 (t80)
REVERT: C  211 MET cc_start: 0.7223 (ttp) cc_final: 0.7011 (ttm)
REVERT: A   98 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7706 (mtt90)
REVERT: A  105 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.7718 (ttt90)
REVERT: A  256 CYS cc_start: 0.6994 (m) cc_final: 0.6646 (m)
  outliers start: 29
  outliers final: 21
  residues processed: 173
  average time/residue: 0.0879
  time to fit residues: 19.3541
Evaluate side-chains
  161 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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  211 VAL
Chi-restraints excluded: chain E residue  236 ILE
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  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  155 ILE
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  224 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  95 ASN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.204686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.146613 restraints weight = 6888.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.143059 restraints weight = 4527.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146474 restraints weight = 3352.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147779 restraints weight = 2378.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.148606 restraints weight = 1925.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   5686  Z= 0.282
  Angle     :  0.692   7.394   7743  Z= 0.367
  Chirality :  0.048   0.172    853
  Planarity :  0.005   0.032    995
  Dihedral  :  5.142  39.090    780
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 19.87 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.29), residues: 699
  helix: -1.25 (0.76), residues: 46
  sheet:  0.06 (0.40), residues: 162
  loop : -0.87 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  62 
 TYR   0.058   0.003   TYR C 194 
 PHE   0.033   0.003   PHE B 219 
 TRP   0.023   0.002   TRP B  80 
 HIS   0.007   0.002   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 ( 5678)
  covalent geometry    : angle       0.69141 ( 7727)
  SS BOND              : bond        0.00199 (    8)
  SS BOND              : angle       0.74306 (   16)
  hydrogen bonds       : bond        0.03820 (  150)
  hydrogen bonds       : angle       6.30151 (  369)

*********************** 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
  180 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7900 (mttm)
REVERT: E   82 LEU cc_start: 0.3797 (OUTLIER) cc_final: 0.3030 (tt)
REVERT: E  105 ASN cc_start: 0.8402 (m-40) cc_final: 0.7934 (m-40)
REVERT: E  205 LEU cc_start: 0.6956 (mp) cc_final: 0.6628 (mm)
REVERT: E  246 ARG cc_start: 0.7817 (ptp-170) cc_final: 0.7313 (ptp-170)
REVERT: B   64 TYR cc_start: 0.8659 (m-80) cc_final: 0.8414 (m-80)
REVERT: B   72 GLU cc_start: 0.8505 (mp0) cc_final: 0.8291 (mp0)
REVERT: B   84 ASP cc_start: 0.7788 (t0) cc_final: 0.7390 (t0)
REVERT: B   87 LYS cc_start: 0.8504 (pttt) cc_final: 0.7966 (ptpt)
REVERT: B  100 TYR cc_start: 0.6956 (t80) cc_final: 0.6235 (t80)
REVERT: B  132 MET cc_start: 0.9109 (mtt) cc_final: 0.8619 (mtt)
REVERT: B  213 MET cc_start: 0.7926 (mtt) cc_final: 0.7638 (mpp)
REVERT: B  215 ARG cc_start: 0.7135 (ttp-170) cc_final: 0.5023 (mmt180)
REVERT: B  256 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6354 (mtt-85)
REVERT: C   61 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7931 (mtmt)
REVERT: C   88 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7333 (mp10)
REVERT: C  134 TYR cc_start: 0.8437 (t80) cc_final: 0.8201 (t80)
REVERT: C  185 THR cc_start: 0.7278 (p) cc_final: 0.6948 (m)
REVERT: C  211 MET cc_start: 0.7427 (ttp) cc_final: 0.7127 (ttm)
REVERT: A   98 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7567 (mtt90)
  outliers start: 32
  outliers final: 22
  residues processed: 171
  average time/residue: 0.0880
  time to fit residues: 19.1116
Evaluate side-chains
  158 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  211 VAL
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  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
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   58 VAL
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  198 ILE
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 18 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 27 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 217 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.214129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.147276 restraints weight = 7240.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.152061 restraints weight = 4396.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.155413 restraints weight = 3053.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.157722 restraints weight = 2341.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.159160 restraints weight = 1943.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.5127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5686  Z= 0.153
  Angle     :  0.581   6.278   7743  Z= 0.309
  Chirality :  0.046   0.180    853
  Planarity :  0.004   0.031    995
  Dihedral  :  4.649  31.378    780
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 22.29 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.29), residues: 699
  helix: -1.05 (0.75), residues: 47
  sheet:  0.13 (0.40), residues: 167
  loop : -0.83 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 240 
 TYR   0.025   0.002   TYR C 194 
 PHE   0.033   0.002   PHE B 219 
 TRP   0.011   0.001   TRP B  80 
 HIS   0.007   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5678)
  covalent geometry    : angle       0.58160 ( 7727)
  SS BOND              : bond        0.00203 (    8)
  SS BOND              : angle       0.53074 (   16)
  hydrogen bonds       : bond        0.03187 (  150)
  hydrogen bonds       : angle       5.87668 (  369)

*********************** 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
  178 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7894 (mttm)
REVERT: E   82 LEU cc_start: 0.3944 (OUTLIER) cc_final: 0.3341 (tt)
REVERT: E  105 ASN cc_start: 0.8451 (m-40) cc_final: 0.7996 (m-40)
REVERT: E  205 LEU cc_start: 0.6936 (mp) cc_final: 0.6650 (mm)
REVERT: B   64 TYR cc_start: 0.8570 (m-80) cc_final: 0.8290 (m-80)
REVERT: B   72 GLU cc_start: 0.8454 (mp0) cc_final: 0.8048 (mp0)
REVERT: B   84 ASP cc_start: 0.7721 (t0) cc_final: 0.7345 (t0)
REVERT: B   87 LYS cc_start: 0.8377 (pttt) cc_final: 0.7838 (ptpt)
REVERT: B  132 MET cc_start: 0.8993 (mtt) cc_final: 0.8545 (mtt)
REVERT: B  213 MET cc_start: 0.7546 (mtt) cc_final: 0.7242 (mtt)
REVERT: B  215 ARG cc_start: 0.7115 (ttp-170) cc_final: 0.4926 (mmt180)
REVERT: B  256 ARG cc_start: 0.7743 (ppt90) cc_final: 0.6217 (mtt-85)
REVERT: C   61 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7854 (mtmm)
REVERT: C   88 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7285 (mp10)
REVERT: C  134 TYR cc_start: 0.8127 (t80) cc_final: 0.7773 (t80)
REVERT: A   98 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7429 (mtt90)
REVERT: A  100 MET cc_start: 0.5094 (mtp) cc_final: 0.4719 (ttp)
REVERT: A  254 ARG cc_start: 0.8551 (ttt-90) cc_final: 0.8023 (mtp-110)
  outliers start: 27
  outliers final: 23
  residues processed: 167
  average time/residue: 0.0842
  time to fit residues: 17.8853
Evaluate side-chains
  166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  203 PHE
Chi-restraints excluded: chain E residue  211 VAL
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  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 B residue  241 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  155 ILE
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 44 optimal weight:    5.9990
   chunk 49 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 16 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0670
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
B 218 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.218556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.152602 restraints weight = 7379.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.157527 restraints weight = 4470.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.160911 restraints weight = 3095.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.162999 restraints weight = 2360.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.164764 restraints weight = 1965.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.5331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5686  Z= 0.125
  Angle     :  0.578   9.134   7743  Z= 0.305
  Chirality :  0.046   0.226    853
  Planarity :  0.004   0.033    995
  Dihedral  :  4.439  24.671    780
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.75 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.29), residues: 699
  helix: -0.45 (0.77), residues: 47
  sheet:  0.20 (0.41), residues: 161
  loop : -0.86 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 246 
 TYR   0.025   0.002   TYR B 100 
 PHE   0.032   0.002   PHE B 219 
 TRP   0.012   0.001   TRP B  78 
 HIS   0.005   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5678)
  covalent geometry    : angle       0.57843 ( 7727)
  SS BOND              : bond        0.00174 (    8)
  SS BOND              : angle       0.47603 (   16)
  hydrogen bonds       : bond        0.03136 (  150)
  hydrogen bonds       : angle       5.70438 (  369)

*********************** 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
  175 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   35 ASP cc_start: 0.3909 (OUTLIER) cc_final: 0.3368 (t70)
REVERT: E   71 LYS cc_start: 0.8227 (ptmt) cc_final: 0.7908 (mttm)
REVERT: E   82 LEU cc_start: 0.3958 (OUTLIER) cc_final: 0.3402 (tt)
REVERT: E  105 ASN cc_start: 0.8437 (m-40) cc_final: 0.8021 (m-40)
REVERT: E  113 TYR cc_start: 0.8151 (m-80) cc_final: 0.7264 (m-10)
REVERT: E  157 PHE cc_start: 0.4825 (p90) cc_final: 0.4470 (p90)
REVERT: E  205 LEU cc_start: 0.7012 (mp) cc_final: 0.6755 (mm)
REVERT: B   64 TYR cc_start: 0.8560 (m-80) cc_final: 0.8294 (m-80)
REVERT: B   72 GLU cc_start: 0.8432 (mp0) cc_final: 0.7924 (mp0)
REVERT: B   81 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8250 (mttp)
REVERT: B   84 ASP cc_start: 0.7671 (t0) cc_final: 0.7438 (t0)
REVERT: B   87 LYS cc_start: 0.8342 (pttt) cc_final: 0.7842 (ptpt)
REVERT: B  129 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6900 (mm-30)
REVERT: B  132 MET cc_start: 0.8997 (mtt) cc_final: 0.8667 (mtt)
REVERT: B  213 MET cc_start: 0.7444 (mtt) cc_final: 0.7161 (mtt)
REVERT: B  215 ARG cc_start: 0.7012 (ttp-170) cc_final: 0.4913 (mmt180)
REVERT: B  256 ARG cc_start: 0.7710 (ppt90) cc_final: 0.6201 (mtt-85)
REVERT: C   44 MET cc_start: 0.8254 (mmt) cc_final: 0.7926 (tpp)
REVERT: C  134 TYR cc_start: 0.8178 (t80) cc_final: 0.7840 (t80)
REVERT: A   98 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7439 (mtt90)
REVERT: A  254 ARG cc_start: 0.8336 (ttt-90) cc_final: 0.8099 (mtp-110)
  outliers start: 24
  outliers final: 14
  residues processed: 169
  average time/residue: 0.0855
  time to fit residues: 18.3257
Evaluate side-chains
  154 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  203 PHE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  112 CYS
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 C residue  127 THR
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  199 VAL
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 52 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 56 optimal weight:    0.1980
   chunk 17 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0970
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
B 218 ASN
C  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.220236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.154047 restraints weight = 7304.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.158841 restraints weight = 4439.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.162338 restraints weight = 3084.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.164525 restraints weight = 2359.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.166241 restraints weight = 1960.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.5455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5686  Z= 0.124
  Angle     :  0.590   9.211   7743  Z= 0.311
  Chirality :  0.045   0.165    853
  Planarity :  0.004   0.034    995
  Dihedral  :  4.385  20.418    780
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.30), residues: 699
  helix: -0.24 (0.78), residues: 47
  sheet:  0.29 (0.42), residues: 159
  loop : -0.87 (0.25), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 246 
 TYR   0.025   0.002   TYR B 100 
 PHE   0.034   0.001   PHE B 219 
 TRP   0.020   0.001   TRP B  78 
 HIS   0.005   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5678)
  covalent geometry    : angle       0.59039 ( 7727)
  SS BOND              : bond        0.00163 (    8)
  SS BOND              : angle       0.53574 (   16)
  hydrogen bonds       : bond        0.03123 (  150)
  hydrogen bonds       : angle       5.63194 (  369)

*********************** 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
  166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   35 ASP cc_start: 0.3957 (OUTLIER) cc_final: 0.3370 (t70)
REVERT: E   71 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7913 (mttm)
REVERT: E   82 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3390 (tt)
REVERT: E  105 ASN cc_start: 0.8369 (m-40) cc_final: 0.7989 (m-40)
REVERT: E  113 TYR cc_start: 0.8077 (m-80) cc_final: 0.7286 (m-10)
REVERT: E  157 PHE cc_start: 0.4737 (p90) cc_final: 0.4173 (p90)
REVERT: E  205 LEU cc_start: 0.7047 (mp) cc_final: 0.6780 (mm)
REVERT: B   64 TYR cc_start: 0.8481 (m-80) cc_final: 0.8219 (m-80)
REVERT: B   74 ASP cc_start: 0.8138 (p0) cc_final: 0.7713 (p0)
REVERT: B   81 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8253 (mmtp)
REVERT: B   84 ASP cc_start: 0.7669 (t0) cc_final: 0.7453 (t0)
REVERT: B   87 LYS cc_start: 0.8341 (pttt) cc_final: 0.7821 (ptpt)
REVERT: B  129 GLU cc_start: 0.7768 (mm-30) cc_final: 0.6988 (mm-30)
REVERT: B  132 MET cc_start: 0.8999 (mtt) cc_final: 0.8559 (mtt)
REVERT: B  215 ARG cc_start: 0.6897 (ttp-170) cc_final: 0.4645 (mmt180)
REVERT: B  256 ARG cc_start: 0.7671 (ppt90) cc_final: 0.6186 (mtt-85)
REVERT: C   44 MET cc_start: 0.8231 (mmt) cc_final: 0.7989 (tpp)
REVERT: C   61 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7767 (mtmt)
REVERT: C   86 GLN cc_start: 0.8454 (mt0) cc_final: 0.8243 (pt0)
REVERT: C  134 TYR cc_start: 0.8188 (t80) cc_final: 0.7859 (t80)
REVERT: A   98 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7431 (mtt90)
  outliers start: 20
  outliers final: 13
  residues processed: 159
  average time/residue: 0.0753
  time to fit residues: 15.2639
Evaluate side-chains
  154 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
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  203 PHE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  112 CYS
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 C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  224 LEU
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 34 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 39 optimal weight:    0.0970
   chunk 15 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
C  78 GLN
** 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 = 0.4369 r_free = 0.4369 target = 0.214698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.147645 restraints weight = 6847.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.152788 restraints weight = 3997.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.156522 restraints weight = 2696.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.158966 restraints weight = 2013.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.160413 restraints weight = 1644.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.5665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5686  Z= 0.172
  Angle     :  0.652   9.427   7743  Z= 0.344
  Chirality :  0.046   0.157    853
  Planarity :  0.004   0.032    995
  Dihedral  :  4.542  23.012    780
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 25.04 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.30), residues: 699
  helix: -0.31 (0.79), residues: 47
  sheet:  0.02 (0.41), residues: 165
  loop : -0.89 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 246 
 TYR   0.027   0.002   TYR C 194 
 PHE   0.031   0.002   PHE B 219 
 TRP   0.026   0.002   TRP B  78 
 HIS   0.008   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 5678)
  covalent geometry    : angle       0.65217 ( 7727)
  SS BOND              : bond        0.00166 (    8)
  SS BOND              : angle       0.51010 (   16)
  hydrogen bonds       : bond        0.03193 (  150)
  hydrogen bonds       : angle       5.91439 (  369)

*********************** 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
  162 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: E   35 ASP cc_start: 0.4056 (OUTLIER) cc_final: 0.3390 (t70)
REVERT: E   71 LYS cc_start: 0.8215 (ptmt) cc_final: 0.7908 (mttm)
REVERT: E   82 LEU cc_start: 0.3901 (OUTLIER) cc_final: 0.3278 (tt)
REVERT: E  113 TYR cc_start: 0.7816 (m-80) cc_final: 0.7289 (m-10)
REVERT: E  205 LEU cc_start: 0.7041 (mp) cc_final: 0.6767 (mm)
REVERT: B   81 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8243 (mmtp)
REVERT: B   84 ASP cc_start: 0.7690 (t0) cc_final: 0.7479 (t0)
REVERT: B   87 LYS cc_start: 0.8350 (pttt) cc_final: 0.7845 (ptpt)
REVERT: B   96 MET cc_start: 0.8255 (ttp) cc_final: 0.7714 (ttm)
REVERT: B  129 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7033 (mm-30)
REVERT: B  132 MET cc_start: 0.9051 (mtt) cc_final: 0.8357 (mtt)
REVERT: B  215 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.4928 (mmt180)
REVERT: B  256 ARG cc_start: 0.7687 (ppt90) cc_final: 0.6173 (mtt-85)
REVERT: C   44 MET cc_start: 0.8196 (mmt) cc_final: 0.7926 (tpp)
REVERT: C   61 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7843 (mtmt)
REVERT: C   86 GLN cc_start: 0.8495 (mt0) cc_final: 0.8135 (pt0)
REVERT: C  134 TYR cc_start: 0.8264 (t80) cc_final: 0.7976 (t80)
REVERT: A   98 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7514 (mtt90)
  outliers start: 23
  outliers final: 19
  residues processed: 155
  average time/residue: 0.0819
  time to fit residues: 16.2036
Evaluate side-chains
  152 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  203 PHE
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  135 SER
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  218 ASN
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  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 37 optimal weight:    0.4980
   chunk 42 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 27 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 20 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
E 247 GLN
** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
** C 181 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 = 0.4421 r_free = 0.4421 target = 0.220151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.151768 restraints weight = 7354.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.157330 restraints weight = 4269.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.160929 restraints weight = 2878.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.163609 restraints weight = 2166.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.165134 restraints weight = 1767.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.5774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5686  Z= 0.142
  Angle     :  0.671   9.715   7743  Z= 0.351
  Chirality :  0.046   0.171    853
  Planarity :  0.006   0.125    995
  Dihedral  :  4.631  24.286    780
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 25.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.30), residues: 699
  helix: -0.07 (0.80), residues: 47
  sheet: -0.11 (0.40), residues: 170
  loop : -0.87 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 254 
 TYR   0.027   0.002   TYR B  64 
 PHE   0.021   0.001   PHE B 219 
 TRP   0.033   0.001   TRP B  78 
 HIS   0.013   0.002   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5678)
  covalent geometry    : angle       0.67158 ( 7727)
  SS BOND              : bond        0.00125 (    8)
  SS BOND              : angle       0.45068 (   16)
  hydrogen bonds       : bond        0.03126 (  150)
  hydrogen bonds       : angle       5.92048 (  369)

********************** 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
  154 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8217 (ptmt) cc_final: 0.7920 (mttm)
REVERT: E   82 LEU cc_start: 0.4012 (OUTLIER) cc_final: 0.3468 (tt)
REVERT: E  113 TYR cc_start: 0.8234 (m-80) cc_final: 0.7472 (m-10)
REVERT: E  205 LEU cc_start: 0.7172 (mp) cc_final: 0.6914 (mm)
REVERT: B   64 TYR cc_start: 0.8174 (m-80) cc_final: 0.7333 (m-80)
REVERT: B   84 ASP cc_start: 0.7657 (t0) cc_final: 0.7392 (t0)
REVERT: B   87 LYS cc_start: 0.8223 (pttt) cc_final: 0.7704 (ptpt)
REVERT: B  129 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7030 (mm-30)
REVERT: B  132 MET cc_start: 0.9012 (mtt) cc_final: 0.8484 (mtt)
REVERT: B  213 MET cc_start: 0.6791 (mtt) cc_final: 0.6464 (mpp)
REVERT: B  215 ARG cc_start: 0.6724 (ttp-170) cc_final: 0.4828 (mmt180)
REVERT: B  256 ARG cc_start: 0.7628 (ppt90) cc_final: 0.6096 (mtt-85)
REVERT: C   44 MET cc_start: 0.8272 (mmt) cc_final: 0.7948 (tpp)
REVERT: C   61 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7722 (mtmt)
REVERT: C   86 GLN cc_start: 0.8409 (mt0) cc_final: 0.8147 (pt0)
REVERT: C  134 TYR cc_start: 0.8268 (t80) cc_final: 0.7972 (t80)
REVERT: A   98 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7344 (mtt90)
  outliers start: 19
  outliers final: 17
  residues processed: 146
  average time/residue: 0.0829
  time to fit residues: 15.4936
Evaluate side-chains
  150 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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  203 PHE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  112 CYS
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  218 ASN
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
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 65 optimal weight:    0.2980
   chunk 39 optimal weight:    0.0770
   chunk 1 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0670
   chunk 38 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
E 165 ASN
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
** C 181 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 = 0.4436 r_free = 0.4436 target = 0.221533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.153191 restraints weight = 7331.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158455 restraints weight = 4359.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.162065 restraints weight = 2975.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.164373 restraints weight = 2256.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.166172 restraints weight = 1867.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.5946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5686  Z= 0.136
  Angle     :  0.651   9.705   7743  Z= 0.342
  Chirality :  0.046   0.155    853
  Planarity :  0.004   0.035    995
  Dihedral  :  4.546  23.449    780
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 25.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.30), residues: 699
  helix: -0.01 (0.81), residues: 47
  sheet: -0.15 (0.40), residues: 170
  loop : -0.88 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 104 
 TYR   0.024   0.002   TYR B 100 
 PHE   0.045   0.002   PHE B 219 
 TRP   0.030   0.002   TRP B  78 
 HIS   0.006   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5678)
  covalent geometry    : angle       0.65136 ( 7727)
  SS BOND              : bond        0.00417 (    8)
  SS BOND              : angle       0.68301 (   16)
  hydrogen bonds       : bond        0.03297 (  150)
  hydrogen bonds       : angle       5.99278 (  369)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1557.77 seconds
wall clock time: 27 minutes 21.65 seconds (1641.65 seconds total)