Starting phenix.real_space_refine
on Sun May 11 01:11:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9f_15930/05_2025/8b9f_15930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9f_15930/05_2025/8b9f_15930.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b9f_15930/05_2025/8b9f_15930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9f_15930/05_2025/8b9f_15930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9f_15930/05_2025/8b9f_15930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9f_15930/05_2025/8b9f_15930.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5533
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "E"
      Number of atoms: 1946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1946
          Classifications: {'peptide': 251}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 227}
    Chain: "B"
      Number of atoms: 1579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1579
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 194}
    Chain: "C"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1501
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 10, 'TRANS': 184}
    Chain: "A"
      Number of atoms: 486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 486
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 5, 'TRANS': 53}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'SPH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.16, per 1000 atoms: 0.75
  Number of scatterers: 5533
  At special positions: 0
  Unit cell: (74.55, 105, 137.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Se      1     33.99
     S      47     16.00
     O    1038      8.00
     N     931      7.00
     C    3516      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 822.8 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 16 sheets defined
      9.7% alpha, 30.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'E' and resid 112 through 116
    Processing helix  chain 'B' and resid 83 through 87
    Processing helix  chain 'B' and resid 89 through 99
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 178 through 185
      removed outlier: 4.161A  pdb=" N   THR B 183 " --> pdb=" O   GLY B 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 48
    Processing helix  chain 'C' and resid 65 through 69
    Processing helix  chain 'C' and resid 98 through 105
    Processing helix  chain 'C' and resid 144 through 150
      removed outlier: 3.690A  pdb=" N   LEU C 150 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 108
    Processing sheet with id=AA1, first strand: chain 'E' and resid 45 through 47
      removed outlier: 3.640A  pdb=" N   GLN E  86 " --> pdb=" O   LEU E  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 70 through 71
    Processing sheet with id=AA3, first strand: chain 'E' and resid 107 through 109
    Processing sheet with id=AA4, first strand: chain 'E' and resid 133 through 135
    Processing sheet with id=AA5, first strand: chain 'E' and resid 172 through 175
    Processing sheet with id=AA6, first strand: chain 'E' and resid 194 through 197
    Processing sheet with id=AA7, first strand: chain 'E' and resid 234 through 236
    Processing sheet with id=AA8, first strand: chain 'E' and resid 258 through 260
    Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.495A  pdb=" N   VAL B 239 " --> pdb=" O   TRP B  71 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.105A  pdb=" N   ALA B 250 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ARG B 103 " --> pdb=" O   ALA B 250 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   TYR B 252 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU B 101 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154
      removed outlier: 6.758A  pdb=" N   CYS B 121 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   SER B 228 " --> pdb=" O   GLN B 119 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   GLN B 119 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 51 through 52
    Processing sheet with id=AB4, first strand: chain 'C' and resid 51 through 52
    Processing sheet with id=AB5, first strand: chain 'C' and resid 83 through 86
      removed outlier: 3.907A  pdb=" N   PHE C  83 " --> pdb=" O   CYS C 192 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   LYS C 129 " --> pdb=" O   GLN C 195 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   GLY C 197 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   THR C 127 " --> pdb=" O   GLY C 197 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 177 through 178
      removed outlier: 6.136A  pdb=" N   TYR C 107 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LEU C 225 " --> pdb=" O   TYR C 107 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 110 through 112
      removed outlier: 6.192A  pdb=" N   PHE A 110 " --> pdb=" O   PRO A 250 " (cutoff:3.500A)

    154 hydrogen bonds defined for protein.
    369 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.36: 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:             4.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.130
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.450
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.29), residues: 699
  helix: -1.62 (0.67), residues: 43
  sheet:  0.25 (0.38), residues: 174
  loop : -1.27 (0.25), residues: 482

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

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

*********************** 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  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   42 VAL cc_start: -0.0379 (t) cc_final: -0.0752 (t)
REVERT: E   71 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7597 (mttm)
REVERT: E  105 ASN cc_start: 0.7654 (m-40) cc_final: 0.7217 (m-40)
REVERT: E  113 TYR cc_start: 0.7818 (m-80) cc_final: 0.7354 (m-80)
REVERT: E  157 PHE cc_start: 0.5165 (p90) cc_final: 0.4901 (p90)
REVERT: E  165 ASN cc_start: 0.8326 (t0) cc_final: 0.8056 (t0)
REVERT: E  251 TYR cc_start: 0.2438 (m-80) cc_final: 0.2219 (m-80)
REVERT: B   74 ASP cc_start: 0.8221 (p0) cc_final: 0.7701 (p0)
REVERT: B   95 ASN cc_start: 0.8641 (m-40) cc_final: 0.8313 (m-40)
REVERT: B  100 TYR cc_start: 0.7824 (t80) cc_final: 0.6471 (t80)
REVERT: B  129 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6640 (mm-30)
REVERT: B  132 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8788 (mmm)
REVERT: B  215 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.4934 (mmt180)
REVERT: B  219 PHE cc_start: 0.8713 (p90) cc_final: 0.8485 (p90)
REVERT: B  256 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5594 (ptp-170)
REVERT: C   61 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7755 (mttt)
REVERT: C  179 VAL cc_start: 0.8318 (t) cc_final: 0.8024 (t)
REVERT: A  265 ASN cc_start: 0.8065 (m-40) cc_final: 0.7832 (m-40)
  outliers start: 9
  outliers final: 2
  residues processed: 250
  average time/residue: 0.1762
  time to fit residues: 55.4891
Evaluate side-chains
  167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 163
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  225 CYS
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain A residue  277 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B 113 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 = 0.4423 r_free = 0.4423 target = 0.221824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.158498 restraints weight = 6454.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.163877 restraints weight = 3660.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.167735 restraints weight = 2411.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6707
moved from start:          0.3109

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= 0.146
  Angle     :  0.581   5.576   7743  Z= 0.306
  Chirality :  0.046   0.225    853
  Planarity :  0.005   0.060    995
  Dihedral  :  6.551  51.584    789
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.48 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.28), residues: 699
  helix: -0.56 (0.79), residues: 45
  sheet:  0.32 (0.39), residues: 165
  loop : -0.81 (0.24), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  80 
 HIS   0.006   0.001   HIS B 109 
 PHE   0.020   0.002   PHE B 226 
 TYR   0.026   0.002   TYR C 194 
 ARG   0.006   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03714 (  150)
  hydrogen bonds       : angle       6.48238 (  369)
  SS BOND              : bond        0.00140 (    8)
  SS BOND              : angle       0.46203 (   16)
  covalent geometry    : bond        0.00330 ( 5678)
  covalent geometry    : angle       0.58121 ( 7727)

*********************** 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
  204 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 176
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8170 (ptmt) cc_final: 0.7898 (mttm)
REVERT: E  105 ASN cc_start: 0.8150 (m-40) cc_final: 0.7734 (m-40)
REVERT: E  110 LYS cc_start: 0.7892 (ptmm) cc_final: 0.7684 (ptpt)
REVERT: E  113 TYR cc_start: 0.8278 (m-80) cc_final: 0.7562 (m-10)
REVERT: E  135 ARG cc_start: 0.6265 (ttt-90) cc_final: 0.5197 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7269 (tp30) cc_final: 0.6898 (tp30)
REVERT: E  205 LEU cc_start: 0.6968 (mp) cc_final: 0.6696 (mm)
REVERT: B   64 TYR cc_start: 0.8591 (m-80) cc_final: 0.8364 (m-80)
REVERT: B   70 THR cc_start: 0.9086 (m) cc_final: 0.8746 (p)
REVERT: B   72 GLU cc_start: 0.8233 (mp0) cc_final: 0.7915 (mp0)
REVERT: B   74 ASP cc_start: 0.7952 (p0) cc_final: 0.7664 (p0)
REVERT: B   84 ASP cc_start: 0.7652 (t0) cc_final: 0.7324 (t0)
REVERT: B   87 LYS cc_start: 0.8238 (pttt) cc_final: 0.7717 (ptpt)
REVERT: B  129 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6728 (mm-30)
REVERT: B  132 MET cc_start: 0.9211 (mtt) cc_final: 0.8501 (mtt)
REVERT: B  167 GLN cc_start: 0.7376 (tp-100) cc_final: 0.6919 (tp40)
REVERT: B  213 MET cc_start: 0.7713 (mmm) cc_final: 0.7405 (mtt)
REVERT: B  215 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.4763 (mmt180)
REVERT: B  218 ASN cc_start: 0.8516 (m-40) cc_final: 0.7859 (m110)
REVERT: B  256 ARG cc_start: 0.7358 (ppt90) cc_final: 0.6216 (mtp-110)
REVERT: C   44 MET cc_start: 0.7379 (mmt) cc_final: 0.6831 (tpp)
REVERT: C   61 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7916 (mtmt)
REVERT: C   95 PHE cc_start: 0.6387 (m-80) cc_final: 0.5625 (m-10)
REVERT: C  102 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7054 (mm-30)
REVERT: C  134 TYR cc_start: 0.8246 (t80) cc_final: 0.7767 (t80)
REVERT: A   98 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7584 (mtt90)
REVERT: A  103 MET cc_start: 0.8480 (tpp) cc_final: 0.8093 (tpp)
REVERT: A  254 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8422 (mmm160)
REVERT: A  265 ASN cc_start: 0.8468 (m-40) cc_final: 0.8191 (m-40)
  outliers start: 28
  outliers final: 21
  residues processed: 194
  average time/residue: 0.1944
  time to fit residues: 47.1238
Evaluate side-chains
  171 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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  236 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  181 ASN
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  164 CYS
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 22 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0870
   chunk 54 optimal weight:    0.2980
   chunk 11 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.8162

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

Flipped N/Q/H residues before XYZ refinement:
E 271 ASN
B  95 ASN
** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 195 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 = 0.4413 r_free = 0.4413 target = 0.219736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.155008 restraints weight = 6489.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160681 restraints weight = 3582.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.164612 restraints weight = 2316.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.3853

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= 0.162
  Angle     :  0.576   6.515   7743  Z= 0.305
  Chirality :  0.046   0.172    853
  Planarity :  0.004   0.035    995
  Dihedral  :  5.428  51.754    780
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 17.45 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.29), residues: 699
  helix: -0.47 (0.80), residues: 45
  sheet:  0.54 (0.41), residues: 157
  loop : -0.73 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 276 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.029   0.002   PHE B 219 
 TYR   0.030   0.002   TYR C 194 
 ARG   0.004   0.000   ARG C 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  150)
  hydrogen bonds       : angle       6.10411 (  369)
  SS BOND              : bond        0.00803 (    8)
  SS BOND              : angle       0.75484 (   16)
  covalent geometry    : bond        0.00369 ( 5678)
  covalent geometry    : angle       0.57552 ( 7727)

*********************** 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
  193 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8215 (ptmt) cc_final: 0.7912 (mttm)
REVERT: E   82 LEU cc_start: 0.3854 (OUTLIER) cc_final: 0.3200 (tt)
REVERT: E  105 ASN cc_start: 0.8385 (m-40) cc_final: 0.7967 (m-40)
REVERT: E  110 LYS cc_start: 0.7800 (ptmm) cc_final: 0.7584 (ptpt)
REVERT: E  113 TYR cc_start: 0.8256 (m-80) cc_final: 0.7490 (m-10)
REVERT: E  135 ARG cc_start: 0.6277 (ttt-90) cc_final: 0.5305 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7261 (tp30) cc_final: 0.6933 (tp30)
REVERT: E  205 LEU cc_start: 0.6928 (mp) cc_final: 0.6625 (mm)
REVERT: B   64 TYR cc_start: 0.8596 (m-80) cc_final: 0.8326 (m-80)
REVERT: B   70 THR cc_start: 0.9119 (m) cc_final: 0.8580 (p)
REVERT: B   72 GLU cc_start: 0.8435 (mp0) cc_final: 0.7868 (mp0)
REVERT: B   74 ASP cc_start: 0.7984 (p0) cc_final: 0.7682 (p0)
REVERT: B   81 LYS cc_start: 0.8809 (mttm) cc_final: 0.8389 (mttt)
REVERT: B   84 ASP cc_start: 0.7734 (t0) cc_final: 0.7429 (t0)
REVERT: B   87 LYS cc_start: 0.8328 (pttt) cc_final: 0.7687 (ptpt)
REVERT: B  129 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6893 (mm-30)
REVERT: B  132 MET cc_start: 0.9053 (mtt) cc_final: 0.8503 (mtt)
REVERT: B  215 ARG cc_start: 0.6594 (ttp-170) cc_final: 0.4625 (mmt180)
REVERT: B  218 ASN cc_start: 0.8494 (m-40) cc_final: 0.8253 (m-40)
REVERT: B  226 PHE cc_start: 0.8599 (m-80) cc_final: 0.8299 (m-10)
REVERT: B  256 ARG cc_start: 0.7361 (ppt90) cc_final: 0.6046 (mtp-110)
REVERT: C   44 MET cc_start: 0.7532 (mmt) cc_final: 0.7308 (tpp)
REVERT: C   61 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8032 (mtmt)
REVERT: C  102 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6916 (mm-30)
REVERT: C  134 TYR cc_start: 0.8317 (t80) cc_final: 0.7877 (t80)
REVERT: C  156 TRP cc_start: 0.7430 (t60) cc_final: 0.6167 (t60)
REVERT: C  224 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6490 (tt)
REVERT: A   98 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7638 (mtt90)
REVERT: A  254 ARG cc_start: 0.8944 (mmm160) cc_final: 0.8517 (mmm160)
REVERT: A  265 ASN cc_start: 0.8498 (m-40) cc_final: 0.8249 (m-40)
  outliers start: 33
  outliers final: 23
  residues processed: 179
  average time/residue: 0.1873
  time to fit residues: 42.3191
Evaluate side-chains
  173 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  236 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  170 VAL
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   49 VAL
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  224 LEU
Chi-restraints excluded: chain C residue  231 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 3 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 21 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0770
   chunk 8 optimal weight:    0.3980
   chunk 56 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 4 optimal weight:   10.0000
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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 218 ASN
C 195 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.217365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.152767 restraints weight = 6660.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.158340 restraints weight = 3758.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.162110 restraints weight = 2458.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6761
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5686  Z= 0.116
  Angle     :  0.536   6.306   7743  Z= 0.281
  Chirality :  0.045   0.159    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.890  44.611    780
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.39 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.29), residues: 699
  helix: -0.50 (0.80), residues: 46
  sheet:  0.54 (0.40), residues: 163
  loop : -0.65 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 276 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.031   0.002   PHE B 219 
 TYR   0.023   0.002   TYR B 100 
 ARG   0.004   0.001   ARG E 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03098 (  150)
  hydrogen bonds       : angle       5.81140 (  369)
  SS BOND              : bond        0.00145 (    8)
  SS BOND              : angle       0.57155 (   16)
  covalent geometry    : bond        0.00266 ( 5678)
  covalent geometry    : angle       0.53631 ( 7727)

*********************** 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
  185 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7923 (mttm)
REVERT: E   82 LEU cc_start: 0.3832 (OUTLIER) cc_final: 0.3242 (tt)
REVERT: E  105 ASN cc_start: 0.8398 (m-40) cc_final: 0.7964 (m-40)
REVERT: E  110 LYS cc_start: 0.7752 (ptmm) cc_final: 0.7540 (ptpt)
REVERT: E  113 TYR cc_start: 0.8195 (m-80) cc_final: 0.7486 (m-10)
REVERT: E  205 LEU cc_start: 0.6872 (mp) cc_final: 0.6571 (mm)
REVERT: E  246 ARG cc_start: 0.7721 (ptp-170) cc_final: 0.7358 (ptp-170)
REVERT: B   64 TYR cc_start: 0.8623 (m-80) cc_final: 0.8289 (m-80)
REVERT: B   72 GLU cc_start: 0.8517 (mp0) cc_final: 0.8267 (mp0)
REVERT: B   74 ASP cc_start: 0.7981 (p0) cc_final: 0.7639 (p0)
REVERT: B   81 LYS cc_start: 0.8653 (mttm) cc_final: 0.8229 (mttt)
REVERT: B   87 LYS cc_start: 0.8320 (pttt) cc_final: 0.7698 (ptpt)
REVERT: B  129 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7002 (mm-30)
REVERT: B  132 MET cc_start: 0.8904 (mtt) cc_final: 0.8451 (mtt)
REVERT: B  213 MET cc_start: 0.7600 (mtt) cc_final: 0.6712 (mtt)
REVERT: B  215 ARG cc_start: 0.6561 (ttp-170) cc_final: 0.4620 (mmt180)
REVERT: B  226 PHE cc_start: 0.8597 (m-80) cc_final: 0.8336 (m-10)
REVERT: C   44 MET cc_start: 0.7682 (mmt) cc_final: 0.7306 (tpp)
REVERT: C   61 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8007 (mtmt)
REVERT: C   95 PHE cc_start: 0.6949 (m-80) cc_final: 0.6161 (m-10)
REVERT: C  134 TYR cc_start: 0.8216 (t80) cc_final: 0.7785 (t80)
REVERT: A   98 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7721 (mtt90)
  outliers start: 26
  outliers final: 18
  residues processed: 173
  average time/residue: 0.1707
  time to fit residues: 38.1962
Evaluate side-chains
  166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
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  266 TYR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  122 LEU
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 C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain A residue  274 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
E 242 HIS
B  95 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.216590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.151203 restraints weight = 6698.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.156581 restraints weight = 3867.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.160126 restraints weight = 2573.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.4593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5686  Z= 0.133
  Angle     :  0.540   6.726   7743  Z= 0.284
  Chirality :  0.045   0.192    853
  Planarity :  0.004   0.043    995
  Dihedral  :  4.632  38.497    780
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.87 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.29), residues: 699
  helix: -0.59 (0.79), residues: 46
  sheet:  0.57 (0.41), residues: 157
  loop : -0.72 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  78 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.032   0.002   PHE B 219 
 TYR   0.026   0.002   TYR C 194 
 ARG   0.005   0.001   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02955 (  150)
  hydrogen bonds       : angle       5.66841 (  369)
  SS BOND              : bond        0.00120 (    8)
  SS BOND              : angle       0.57516 (   16)
  covalent geometry    : bond        0.00310 ( 5678)
  covalent geometry    : angle       0.54028 ( 7727)

*********************** 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
  186 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.619 
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: 0.8185 (ptmt) cc_final: 0.7889 (mttm)
REVERT: E   82 LEU cc_start: 0.3822 (OUTLIER) cc_final: 0.3250 (tt)
REVERT: E  105 ASN cc_start: 0.8399 (m-40) cc_final: 0.7945 (m-40)
REVERT: E  113 TYR cc_start: 0.8210 (m-80) cc_final: 0.7665 (m-10)
REVERT: E  205 LEU cc_start: 0.7016 (mp) cc_final: 0.6765 (mm)
REVERT: E  246 ARG cc_start: 0.7664 (ptp-170) cc_final: 0.7189 (ptp-170)
REVERT: E  247 GLN cc_start: 0.8395 (mt0) cc_final: 0.8070 (mt0)
REVERT: B   64 TYR cc_start: 0.8611 (m-80) cc_final: 0.8311 (m-80)
REVERT: B   72 GLU cc_start: 0.8524 (mp0) cc_final: 0.7991 (mp0)
REVERT: B   74 ASP cc_start: 0.8015 (p0) cc_final: 0.7708 (p0)
REVERT: B   81 LYS cc_start: 0.8640 (mttm) cc_final: 0.8271 (mttt)
REVERT: B   84 ASP cc_start: 0.7742 (t0) cc_final: 0.7272 (t0)
REVERT: B   87 LYS cc_start: 0.8261 (pttt) cc_final: 0.7652 (ptpt)
REVERT: B   96 MET cc_start: 0.7864 (ttm) cc_final: 0.7252 (ttp)
REVERT: B  129 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7124 (mm-30)
REVERT: B  132 MET cc_start: 0.8934 (mtt) cc_final: 0.8499 (mtt)
REVERT: B  213 MET cc_start: 0.7668 (mtt) cc_final: 0.7462 (mpp)
REVERT: B  215 ARG cc_start: 0.6534 (ttp-170) cc_final: 0.4500 (mmt180)
REVERT: B  226 PHE cc_start: 0.8690 (m-80) cc_final: 0.8390 (m-10)
REVERT: C   44 MET cc_start: 0.7742 (mmt) cc_final: 0.7408 (tpp)
REVERT: C   61 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7952 (mtmt)
REVERT: C  134 TYR cc_start: 0.8285 (t80) cc_final: 0.7871 (t80)
REVERT: A   98 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7599 (mtt90)
REVERT: A  286 LYS cc_start: 0.8554 (pttm) cc_final: 0.8277 (ptpp)
  outliers start: 28
  outliers final: 22
  residues processed: 172
  average time/residue: 0.1797
  time to fit residues: 39.8073
Evaluate side-chains
  171 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
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  197 PHE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  218 ASN
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0060
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
B  95 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.219144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.149468 restraints weight = 7131.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.154891 restraints weight = 4195.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.158655 restraints weight = 2855.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.4868

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= 0.136
  Angle     :  0.541   6.908   7743  Z= 0.283
  Chirality :  0.045   0.169    853
  Planarity :  0.004   0.040    995
  Dihedral  :  4.475  30.494    780
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 20.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.29), residues: 699
  helix: -0.75 (0.72), residues: 52
  sheet:  0.50 (0.42), residues: 156
  loop : -0.71 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  78 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.029   0.002   PHE B 219 
 TYR   0.028   0.002   TYR C 194 
 ARG   0.005   0.001   ARG E 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02909 (  150)
  hydrogen bonds       : angle       5.65844 (  369)
  SS BOND              : bond        0.00246 (    8)
  SS BOND              : angle       0.58605 (   16)
  covalent geometry    : bond        0.00316 ( 5678)
  covalent geometry    : angle       0.54063 ( 7727)

*********************** 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
  187 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7912 (mttm)
REVERT: E   82 LEU cc_start: 0.3995 (OUTLIER) cc_final: 0.3482 (tt)
REVERT: E  105 ASN cc_start: 0.8540 (m-40) cc_final: 0.8068 (m-40)
REVERT: E  113 TYR cc_start: 0.8394 (m-80) cc_final: 0.7948 (m-10)
REVERT: E  157 PHE cc_start: 0.4979 (p90) cc_final: 0.4303 (p90)
REVERT: E  205 LEU cc_start: 0.7115 (mp) cc_final: 0.6878 (mm)
REVERT: E  247 GLN cc_start: 0.8387 (mt0) cc_final: 0.8044 (mt0)
REVERT: B   64 TYR cc_start: 0.8585 (m-80) cc_final: 0.8205 (m-80)
REVERT: B   72 GLU cc_start: 0.8579 (mp0) cc_final: 0.8351 (mp0)
REVERT: B   74 ASP cc_start: 0.8097 (p0) cc_final: 0.7786 (p0)
REVERT: B   81 LYS cc_start: 0.8586 (mttm) cc_final: 0.8192 (mttt)
REVERT: B   84 ASP cc_start: 0.7711 (t0) cc_final: 0.7089 (t0)
REVERT: B   87 LYS cc_start: 0.8257 (pttt) cc_final: 0.7626 (ptpt)
REVERT: B   96 MET cc_start: 0.7785 (ttm) cc_final: 0.7557 (ttp)
REVERT: B  129 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7208 (mm-30)
REVERT: B  132 MET cc_start: 0.8924 (mtt) cc_final: 0.8501 (mtt)
REVERT: B  213 MET cc_start: 0.7890 (mtt) cc_final: 0.7604 (mtt)
REVERT: B  215 ARG cc_start: 0.6654 (ttp-170) cc_final: 0.4586 (mmt180)
REVERT: B  226 PHE cc_start: 0.8682 (m-80) cc_final: 0.8456 (m-10)
REVERT: B  256 ARG cc_start: 0.7857 (ppt90) cc_final: 0.6236 (mtt-85)
REVERT: C   44 MET cc_start: 0.7886 (mmt) cc_final: 0.7561 (tpp)
REVERT: C   61 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7970 (mtmt)
REVERT: C  134 TYR cc_start: 0.8278 (t80) cc_final: 0.7840 (t80)
REVERT: C  211 MET cc_start: 0.7023 (ttp) cc_final: 0.6771 (ttm)
REVERT: A   98 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7552 (mtt90)
REVERT: A  286 LYS cc_start: 0.8610 (pttm) cc_final: 0.8357 (ptpp)
  outliers start: 29
  outliers final: 24
  residues processed: 171
  average time/residue: 0.1785
  time to fit residues: 39.0607
Evaluate side-chains
  175 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
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  197 PHE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  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  175 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 60 optimal weight:    0.3980
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 271 ASN
B 187 HIS
C  86 GLN
A 265 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.209460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.140296 restraints weight = 7270.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.144657 restraints weight = 4556.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147849 restraints weight = 3265.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.5390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058   5686  Z= 0.345
  Angle     :  0.764   8.783   7743  Z= 0.407
  Chirality :  0.050   0.169    853
  Planarity :  0.006   0.072    995
  Dihedral  :  5.309  26.996    780
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 22.13 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.30), residues: 699
  helix: -1.61 (0.68), residues: 47
  sheet:  0.12 (0.40), residues: 173
  loop : -0.93 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B  80 
 HIS   0.005   0.002   HIS B 164 
 PHE   0.033   0.003   PHE B 219 
 TYR   0.063   0.003   TYR C 194 
 ARG   0.013   0.001   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  150)
  hydrogen bonds       : angle       6.57414 (  369)
  SS BOND              : bond        0.00255 (    8)
  SS BOND              : angle       0.91941 (   16)
  covalent geometry    : bond        0.00788 ( 5678)
  covalent geometry    : angle       0.76402 ( 7727)

*********************** 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
  186 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7925 (mttm)
REVERT: E   82 LEU cc_start: 0.3862 (OUTLIER) cc_final: 0.3256 (tt)
REVERT: E  105 ASN cc_start: 0.8566 (m-40) cc_final: 0.8102 (m-40)
REVERT: E  205 LEU cc_start: 0.7225 (mp) cc_final: 0.6969 (mm)
REVERT: E  246 ARG cc_start: 0.7544 (ptp-170) cc_final: 0.7055 (ptp-170)
REVERT: E  247 GLN cc_start: 0.8198 (mt0) cc_final: 0.7903 (mt0)
REVERT: B   64 TYR cc_start: 0.8612 (m-80) cc_final: 0.8372 (m-80)
REVERT: B   72 GLU cc_start: 0.8543 (mp0) cc_final: 0.8050 (mp0)
REVERT: B   84 ASP cc_start: 0.7822 (t0) cc_final: 0.7062 (t0)
REVERT: B   87 LYS cc_start: 0.8459 (pttt) cc_final: 0.7685 (ptpt)
REVERT: B   96 MET cc_start: 0.8107 (ttm) cc_final: 0.7858 (ttp)
REVERT: B  100 TYR cc_start: 0.7091 (t80) cc_final: 0.6448 (t80)
REVERT: B  132 MET cc_start: 0.9075 (mtt) cc_final: 0.8694 (mmm)
REVERT: B  213 MET cc_start: 0.8205 (mtt) cc_final: 0.7906 (mtt)
REVERT: B  215 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.5152 (mmt180)
REVERT: B  226 PHE cc_start: 0.8855 (m-80) cc_final: 0.8645 (m-10)
REVERT: B  256 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6635 (mtt-85)
REVERT: C   61 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7875 (mtmm)
REVERT: C  106 TYR cc_start: 0.8526 (m-80) cc_final: 0.7285 (m-10)
REVERT: C  125 MET cc_start: 0.6866 (tpt) cc_final: 0.6556 (tpp)
REVERT: C  134 TYR cc_start: 0.8375 (t80) cc_final: 0.8090 (t80)
REVERT: A   98 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7650 (mtt90)
REVERT: A  286 LYS cc_start: 0.8619 (pttm) cc_final: 0.8362 (pttm)
  outliers start: 32
  outliers final: 24
  residues processed: 170
  average time/residue: 0.1888
  time to fit residues: 41.0305
Evaluate side-chains
  170 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  197 PHE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain E residue  271 ASN
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  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 B residue  241 ILE
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 11 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 46 optimal weight:    0.5980
   chunk 63 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
** C  86 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 = 0.4386 r_free = 0.4386 target = 0.215578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.148438 restraints weight = 7152.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.153275 restraints weight = 4386.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.156434 restraints weight = 3043.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.5464

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= 0.135
  Angle     :  0.602   9.186   7743  Z= 0.315
  Chirality :  0.046   0.200    853
  Planarity :  0.004   0.035    995
  Dihedral  :  4.707  21.049    780
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 23.26 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.29), residues: 699
  helix: -1.01 (0.70), residues: 53
  sheet:  0.40 (0.40), residues: 162
  loop : -0.99 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  78 
 HIS   0.007   0.001   HIS C  97 
 PHE   0.032   0.002   PHE B 219 
 TYR   0.026   0.002   TYR B 100 
 ARG   0.005   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03074 (  150)
  hydrogen bonds       : angle       5.88316 (  369)
  SS BOND              : bond        0.00239 (    8)
  SS BOND              : angle       0.67881 (   16)
  covalent geometry    : bond        0.00309 ( 5678)
  covalent geometry    : angle       0.60207 ( 7727)

*********************** 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
  180 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7933 (mttm)
REVERT: E   82 LEU cc_start: 0.3895 (OUTLIER) cc_final: 0.3315 (tt)
REVERT: E  105 ASN cc_start: 0.8528 (m-40) cc_final: 0.8073 (m-40)
REVERT: E  205 LEU cc_start: 0.7141 (mp) cc_final: 0.6876 (mm)
REVERT: E  247 GLN cc_start: 0.8324 (mt0) cc_final: 0.8002 (mt0)
REVERT: B   64 TYR cc_start: 0.8518 (m-80) cc_final: 0.8263 (m-80)
REVERT: B   72 GLU cc_start: 0.8478 (mp0) cc_final: 0.8116 (mp0)
REVERT: B   81 LYS cc_start: 0.8624 (mttp) cc_final: 0.8368 (mtmm)
REVERT: B   84 ASP cc_start: 0.7741 (t0) cc_final: 0.6989 (t0)
REVERT: B   87 LYS cc_start: 0.8363 (pttt) cc_final: 0.7501 (ptpt)
REVERT: B   96 MET cc_start: 0.7732 (ttm) cc_final: 0.7449 (ttp)
REVERT: B  132 MET cc_start: 0.8951 (mtt) cc_final: 0.8541 (mtt)
REVERT: B  215 ARG cc_start: 0.6695 (ttp-170) cc_final: 0.4629 (mmt180)
REVERT: B  256 ARG cc_start: 0.7809 (ppt90) cc_final: 0.6318 (mtt-85)
REVERT: C   61 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7896 (mtmm)
REVERT: C  134 TYR cc_start: 0.8103 (t80) cc_final: 0.7737 (t80)
REVERT: A   98 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7580 (mtt90)
REVERT: A  103 MET cc_start: 0.8453 (tpp) cc_final: 0.8214 (tpp)
  outliers start: 26
  outliers final: 19
  residues processed: 167
  average time/residue: 0.1939
  time to fit residues: 41.3514
Evaluate side-chains
  162 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain E residue  197 PHE
Chi-restraints excluded: chain E residue  203 PHE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  218 ASN
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue  104 LEU
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 0 optimal weight:   20.0000
   chunk 20 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 57 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0770
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
B 187 HIS
B 217 HIS
C  86 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.217563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.150898 restraints weight = 7319.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.155393 restraints weight = 4598.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.159010 restraints weight = 3246.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.5560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5686  Z= 0.126
  Angle     :  0.619   9.619   7743  Z= 0.322
  Chirality :  0.045   0.165    853
  Planarity :  0.004   0.032    995
  Dihedral  :  4.531  19.265    780
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 24.39 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.29), residues: 699
  helix: -0.77 (0.71), residues: 53
  sheet:  0.49 (0.43), residues: 149
  loop : -0.90 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  78 
 HIS   0.007   0.001   HIS C  97 
 PHE   0.015   0.002   PHE E 157 
 TYR   0.020   0.002   TYR B 100 
 ARG   0.005   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03042 (  150)
  hydrogen bonds       : angle       5.75830 (  369)
  SS BOND              : bond        0.00210 (    8)
  SS BOND              : angle       0.66594 (   16)
  covalent geometry    : bond        0.00295 ( 5678)
  covalent geometry    : angle       0.61914 ( 7727)

*********************** 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
  173 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.628 
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: 0.8221 (ptmt) cc_final: 0.7908 (mttm)
REVERT: E   82 LEU cc_start: 0.3777 (OUTLIER) cc_final: 0.3171 (tt)
REVERT: E  105 ASN cc_start: 0.8577 (m-40) cc_final: 0.8126 (m-40)
REVERT: E  205 LEU cc_start: 0.7335 (mp) cc_final: 0.7100 (mm)
REVERT: E  247 GLN cc_start: 0.8240 (mt0) cc_final: 0.7805 (mt0)
REVERT: B   64 TYR cc_start: 0.8517 (m-80) cc_final: 0.8254 (m-80)
REVERT: B   72 GLU cc_start: 0.8463 (mp0) cc_final: 0.8124 (mp0)
REVERT: B   84 ASP cc_start: 0.7857 (t0) cc_final: 0.7017 (t0)
REVERT: B   87 LYS cc_start: 0.8323 (pttt) cc_final: 0.7501 (ptpt)
REVERT: B  129 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7034 (mm-30)
REVERT: B  132 MET cc_start: 0.8872 (mtt) cc_final: 0.8638 (mtt)
REVERT: B  213 MET cc_start: 0.7915 (mtt) cc_final: 0.7660 (mtt)
REVERT: B  215 ARG cc_start: 0.6423 (ttp-170) cc_final: 0.4415 (mmt180)
REVERT: B  256 ARG cc_start: 0.7714 (ppt90) cc_final: 0.6185 (mtt-85)
REVERT: C  107 TYR cc_start: 0.7251 (m-80) cc_final: 0.6806 (m-80)
REVERT: C  134 TYR cc_start: 0.8101 (t80) cc_final: 0.7691 (t80)
REVERT: A   98 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7389 (mtt90)
REVERT: A  103 MET cc_start: 0.8486 (tpp) cc_final: 0.8175 (tpp)
  outliers start: 21
  outliers final: 18
  residues processed: 161
  average time/residue: 0.1824
  time to fit residues: 37.3078
Evaluate side-chains
  161 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
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  197 PHE
Chi-restraints excluded: chain E residue  203 PHE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.1980
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 189 ASN ** 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 = 0.4404 r_free = 0.4404 target = 0.217222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149120 restraints weight = 7345.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.153857 restraints weight = 4506.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.157085 restraints weight = 3163.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.5692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5686  Z= 0.134
  Angle     :  0.617   9.705   7743  Z= 0.320
  Chirality :  0.045   0.149    853
  Planarity :  0.004   0.033    995
  Dihedral  :  4.460  19.142    780
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 25.36 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.29), residues: 699
  helix: -0.79 (0.69), residues: 53
  sheet:  0.47 (0.42), residues: 159
  loop : -0.88 (0.25), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B  78 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.016   0.002   PHE B  92 
 TYR   0.026   0.002   TYR E 245 
 ARG   0.004   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03109 (  150)
  hydrogen bonds       : angle       5.76176 (  369)
  SS BOND              : bond        0.00211 (    8)
  SS BOND              : angle       0.68792 (   16)
  covalent geometry    : bond        0.00314 ( 5678)
  covalent geometry    : angle       0.61702 ( 7727)

********************** 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
  167 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8222 (ptmt) cc_final: 0.7907 (mttm)
REVERT: E  105 ASN cc_start: 0.8563 (m-40) cc_final: 0.8158 (m-40)
REVERT: E  205 LEU cc_start: 0.7226 (mp) cc_final: 0.6974 (mm)
REVERT: E  247 GLN cc_start: 0.8026 (mt0) cc_final: 0.7664 (mt0)
REVERT: B   72 GLU cc_start: 0.8501 (mp0) cc_final: 0.8147 (mp0)
REVERT: B   81 LYS cc_start: 0.8450 (mttp) cc_final: 0.8074 (mttp)
REVERT: B   84 ASP cc_start: 0.7831 (t0) cc_final: 0.7003 (t0)
REVERT: B   87 LYS cc_start: 0.8355 (pttt) cc_final: 0.7462 (ptpt)
REVERT: B   96 MET cc_start: 0.7925 (ttm) cc_final: 0.7715 (ttm)
REVERT: B  129 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7058 (mm-30)
REVERT: B  132 MET cc_start: 0.8882 (mtt) cc_final: 0.8418 (mtt)
REVERT: B  213 MET cc_start: 0.7784 (mtt) cc_final: 0.7283 (mpp)
REVERT: B  215 ARG cc_start: 0.6429 (ttp-170) cc_final: 0.4548 (mmt180)
REVERT: B  256 ARG cc_start: 0.7765 (ppt90) cc_final: 0.6213 (mtt-85)
REVERT: C  107 TYR cc_start: 0.7380 (m-80) cc_final: 0.6895 (m-80)
REVERT: C  134 TYR cc_start: 0.8163 (t80) cc_final: 0.7809 (t80)
REVERT: A   98 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7395 (mtt90)
REVERT: A  103 MET cc_start: 0.8495 (tpp) cc_final: 0.8153 (tpp)
  outliers start: 16
  outliers final: 14
  residues processed: 160
  average time/residue: 0.1858
  time to fit residues: 38.0456
Evaluate side-chains
  160 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  197 PHE
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  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  218 ASN
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 48 optimal weight:    0.5980
   chunk 41 optimal weight:    0.1980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.216573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.148921 restraints weight = 7424.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.153613 restraints weight = 4552.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156846 restraints weight = 3203.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.5714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.127   5686  Z= 0.271
  Angle     :  1.134  59.189   7743  Z= 0.685
  Chirality :  0.045   0.186    853
  Planarity :  0.004   0.032    995
  Dihedral  :  4.540  23.449    780
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 24.56 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.29), residues: 699
  helix: -0.81 (0.69), residues: 53
  sheet:  0.47 (0.42), residues: 159
  loop : -0.88 (0.25), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  78 
 HIS   0.005   0.001   HIS B 109 
 PHE   0.016   0.001   PHE B  92 
 TYR   0.020   0.002   TYR B 100 
 ARG   0.050   0.001   ARG E 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (  150)
  hydrogen bonds       : angle       5.76140 (  369)
  SS BOND              : bond        0.00239 (    8)
  SS BOND              : angle       0.68831 (   16)
  covalent geometry    : bond        0.00504 ( 5678)
  covalent geometry    : angle       1.13439 ( 7727)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2851.04 seconds
wall clock time: 50 minutes 28.89 seconds (3028.89 seconds total)