Starting phenix.real_space_refine
on Fri Jul 25 06:42:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9f_15930/07_2025/8b9f_15930.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9f_15930/07_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_15930/07_2025/8b9f_15930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2025/8b9f_15930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2025/8b9f_15930.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 4.60, per 1000 atoms: 0.83
  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: 1.21
  Conformation dependent library (CDL) restraints added in 667.9 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: 0.60
  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: 1.40

  Time building geometry restraints manager: 1.42 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 349
        2.73 -     3.27: 5311
        3.27 -     3.81: 8990
        3.81 -     4.36: 11662
        4.36 -     4.90: 19253
  Nonbonded interactions: 45565
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 214 "
            pdb=" OD1 ASP E 215 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OE1 GLU A 108 "
            pdb=" OH  TYR A 258 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OD1 ASP C 182 "
            pdb=" OG1 THR C 185 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLY E 132 "
            pdb=" N   LYS E 161 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OG1 THR B 183 "
            pdb=" O   ASP C  50 "
     model   vdw
     2.326 3.040
  ... (remaining 45560 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.510
  Find NCS groups from input model:        0.050
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.180
-------------------------------------------------------------------------------
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  : 0.620 
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: 0.1850
  time to fit residues: 58.3504
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  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  225 CYS
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain A residue  277 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6158

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

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

Total number of N/Q/H flips: 1

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5686  Z= 0.151
  Angle     :  0.578   5.739   7743  Z= 0.307
  Chirality :  0.046   0.223    853
  Planarity :  0.005   0.061    995
  Dihedral  :  6.598  54.609    789
  Min Nonbonded Distance : 2.510

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

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

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  150)
  hydrogen bonds       : angle       6.54269 (  369)
  SS BOND              : bond        0.00135 (    8)
  SS BOND              : angle       0.45727 (   16)
  covalent geometry    : bond        0.00344 ( 5678)
  covalent geometry    : angle       0.57871 ( 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
  197 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7868 (mttm)
REVERT: E   82 LEU cc_start: 0.4117 (OUTLIER) cc_final: 0.3292 (tt)
REVERT: E  105 ASN cc_start: 0.8109 (m-40) cc_final: 0.7709 (m-40)
REVERT: E  113 TYR cc_start: 0.8268 (m-80) cc_final: 0.7526 (m-10)
REVERT: E  135 ARG cc_start: 0.6275 (ttt-90) cc_final: 0.5320 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7197 (tp30) cc_final: 0.6802 (tp30)
REVERT: B   64 TYR cc_start: 0.8596 (m-80) cc_final: 0.8395 (m-80)
REVERT: B   70 THR cc_start: 0.9077 (m) cc_final: 0.8677 (p)
REVERT: B   72 GLU cc_start: 0.8204 (mp0) cc_final: 0.7864 (mp0)
REVERT: B   74 ASP cc_start: 0.7973 (p0) cc_final: 0.7696 (p0)
REVERT: B   84 ASP cc_start: 0.7708 (t0) cc_final: 0.7272 (t0)
REVERT: B   87 LYS cc_start: 0.8164 (pttt) cc_final: 0.7627 (ptpt)
REVERT: B  129 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6720 (mm-30)
REVERT: B  132 MET cc_start: 0.9231 (mtt) cc_final: 0.8827 (mmm)
REVERT: B  167 GLN cc_start: 0.7373 (tp-100) cc_final: 0.6909 (tp40)
REVERT: B  213 MET cc_start: 0.7727 (mmm) cc_final: 0.7389 (mtt)
REVERT: B  215 ARG cc_start: 0.6907 (ttp-170) cc_final: 0.4753 (mmt180)
REVERT: B  218 ASN cc_start: 0.8481 (m-40) cc_final: 0.7808 (m110)
REVERT: B  256 ARG cc_start: 0.7317 (ppt90) cc_final: 0.6129 (mtp-110)
REVERT: C   44 MET cc_start: 0.7356 (mmt) cc_final: 0.6829 (tpp)
REVERT: C   61 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7910 (mtmt)
REVERT: C  102 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7036 (mm-30)
REVERT: C  134 TYR cc_start: 0.8251 (t80) cc_final: 0.7768 (t80)
REVERT: A   98 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7546 (mtt90)
REVERT: A  103 MET cc_start: 0.8549 (tpp) cc_final: 0.8183 (tpp)
REVERT: A  254 ARG cc_start: 0.8814 (mmm160) cc_final: 0.8417 (mmm160)
REVERT: A  265 ASN cc_start: 0.8493 (m-40) cc_final: 0.8230 (m-40)
  outliers start: 26
  outliers final: 19
  residues processed: 188
  average time/residue: 0.1909
  time to fit residues: 45.4169
Evaluate side-chains
  168 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  197 PHE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  225 CYS
Chi-restraints excluded: chain E residue  236 ILE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  231 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
E 212 GLN
E 271 ASN
B  95 ASN
C 195 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.215385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150110 restraints weight = 6513.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.155503 restraints weight = 3738.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.159080 restraints weight = 2472.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5686  Z= 0.160
  Angle     :  0.567   6.118   7743  Z= 0.300
  Chirality :  0.046   0.165    853
  Planarity :  0.004   0.039    995
  Dihedral  :  5.693  53.468    781
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 17.61 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.55 (0.29), residues: 699
  helix: -0.38 (0.85), residues: 40
  sheet:  0.45 (0.40), residues: 165
  loop : -0.67 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  80 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.029   0.002   PHE B 219 
 TYR   0.033   0.002   TYR C 194 
 ARG   0.005   0.001   ARG E 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03507 (  150)
  hydrogen bonds       : angle       6.09552 (  369)
  SS BOND              : bond        0.00152 (    8)
  SS BOND              : angle       0.48719 (   16)
  covalent geometry    : bond        0.00372 ( 5678)
  covalent geometry    : angle       0.56679 ( 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
  189 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7905 (mttm)
REVERT: E  105 ASN cc_start: 0.8299 (m-40) cc_final: 0.7857 (m-40)
REVERT: E  113 TYR cc_start: 0.8161 (m-80) cc_final: 0.7491 (m-10)
REVERT: E  135 ARG cc_start: 0.6280 (ttt-90) cc_final: 0.5288 (tpp-160)
REVERT: E  136 GLU cc_start: 0.7247 (tp30) cc_final: 0.6881 (tp30)
REVERT: E  205 LEU cc_start: 0.6960 (mp) cc_final: 0.6643 (mm)
REVERT: B   64 TYR cc_start: 0.8554 (m-80) cc_final: 0.8325 (m-80)
REVERT: B   70 THR cc_start: 0.9172 (m) cc_final: 0.8600 (p)
REVERT: B   72 GLU cc_start: 0.8470 (mp0) cc_final: 0.8026 (mp0)
REVERT: B   74 ASP cc_start: 0.7978 (p0) cc_final: 0.7670 (p0)
REVERT: B   84 ASP cc_start: 0.7704 (t0) cc_final: 0.7419 (t0)
REVERT: B   87 LYS cc_start: 0.8346 (pttt) cc_final: 0.7717 (ptpt)
REVERT: B  129 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6889 (mm-30)
REVERT: B  132 MET cc_start: 0.8984 (mtt) cc_final: 0.8615 (mtt)
REVERT: B  215 ARG cc_start: 0.6617 (ttp-170) cc_final: 0.4696 (mmt180)
REVERT: B  218 ASN cc_start: 0.8457 (m-40) cc_final: 0.8211 (m-40)
REVERT: B  256 ARG cc_start: 0.7448 (ppt90) cc_final: 0.6117 (mtp-110)
REVERT: C   44 MET cc_start: 0.7613 (mmt) cc_final: 0.7393 (tpp)
REVERT: C   61 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8056 (mtmt)
REVERT: C  134 TYR cc_start: 0.8253 (t80) cc_final: 0.7821 (t80)
REVERT: A   98 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7650 (mtt90)
REVERT: A  254 ARG cc_start: 0.8910 (mmm160) cc_final: 0.8528 (mmm160)
REVERT: A  265 ASN cc_start: 0.8469 (m-40) cc_final: 0.8259 (m-40)
  outliers start: 28
  outliers final: 22
  residues processed: 177
  average time/residue: 0.1841
  time to fit residues: 41.3087
Evaluate side-chains
  165 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
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  236 ILE
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  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  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  158 VAL
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  199 VAL
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:    0.1980
   chunk 67 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 42 optimal weight:    0.4980
   chunk 8 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   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 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 = 0.4386 r_free = 0.4386 target = 0.216869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.151162 restraints weight = 6751.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.156695 restraints weight = 3841.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.160421 restraints weight = 2529.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5686  Z= 0.137
  Angle     :  0.549   6.379   7743  Z= 0.289
  Chirality :  0.045   0.158    853
  Planarity :  0.004   0.029    995
  Dihedral  :  4.939  46.628    780
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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: -0.57 (0.29), residues: 699
  helix: -0.57 (0.79), residues: 46
  sheet:  0.51 (0.41), residues: 157
  loop : -0.68 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 276 
 HIS   0.003   0.001   HIS C  97 
 PHE   0.030   0.002   PHE B 219 
 TYR   0.025   0.002   TYR C 194 
 ARG   0.004   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03188 (  150)
  hydrogen bonds       : angle       5.82473 (  369)
  SS BOND              : bond        0.00241 (    8)
  SS BOND              : angle       0.56820 (   16)
  covalent geometry    : bond        0.00308 ( 5678)
  covalent geometry    : angle       0.54908 ( 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
  184 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7924 (mttm)
REVERT: E   82 LEU cc_start: 0.3848 (OUTLIER) cc_final: 0.3255 (tt)
REVERT: E  105 ASN cc_start: 0.8418 (m-40) cc_final: 0.7992 (m-40)
REVERT: E  113 TYR cc_start: 0.8164 (m-80) cc_final: 0.7463 (m-10)
REVERT: E  205 LEU cc_start: 0.6919 (mp) cc_final: 0.6624 (mm)
REVERT: E  247 GLN cc_start: 0.8420 (mt0) cc_final: 0.8188 (tt0)
REVERT: B   64 TYR cc_start: 0.8596 (m-80) cc_final: 0.8319 (m-80)
REVERT: B   74 ASP cc_start: 0.8044 (p0) cc_final: 0.7723 (p0)
REVERT: B   81 LYS cc_start: 0.8699 (mttm) cc_final: 0.8278 (mttt)
REVERT: B   84 ASP cc_start: 0.7701 (t0) cc_final: 0.7469 (t0)
REVERT: B   87 LYS cc_start: 0.8344 (pttt) cc_final: 0.7712 (ptpt)
REVERT: B   96 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7815 (ttm)
REVERT: B  129 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7017 (mm-30)
REVERT: B  132 MET cc_start: 0.8947 (mtt) cc_final: 0.8468 (mtt)
REVERT: B  154 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7654 (mtmm)
REVERT: B  213 MET cc_start: 0.7600 (mtt) cc_final: 0.6720 (mtt)
REVERT: B  215 ARG cc_start: 0.6581 (ttp-170) cc_final: 0.4689 (mmt180)
REVERT: B  226 PHE cc_start: 0.8678 (m-10) cc_final: 0.8465 (m-10)
REVERT: B  256 ARG cc_start: 0.7643 (ppt90) cc_final: 0.6146 (mtp-110)
REVERT: C   44 MET cc_start: 0.7727 (mmt) cc_final: 0.7391 (tpp)
REVERT: C   61 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8026 (mtmt)
REVERT: C   63 ASP cc_start: 0.7138 (t0) cc_final: 0.6897 (t0)
REVERT: C   95 PHE cc_start: 0.7083 (m-80) cc_final: 0.6251 (m-10)
REVERT: C  134 TYR cc_start: 0.8247 (t80) cc_final: 0.7854 (t80)
REVERT: A   98 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7744 (mtt90)
REVERT: A  254 ARG cc_start: 0.8880 (mmm160) cc_final: 0.8465 (mmm160)
REVERT: A  265 ASN cc_start: 0.8467 (m-40) cc_final: 0.8256 (m-40)
  outliers start: 29
  outliers final: 18
  residues processed: 170
  average time/residue: 0.1810
  time to fit residues: 39.3090
Evaluate side-chains
  166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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   96 MET
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  154 LYS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  224 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    0.4980
   chunk 47 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4364 r_free = 0.4364 target = 0.214186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.148293 restraints weight = 6669.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.153479 restraints weight = 3899.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.157165 restraints weight = 2611.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5686  Z= 0.139
  Angle     :  0.550   7.259   7743  Z= 0.287
  Chirality :  0.045   0.183    853
  Planarity :  0.004   0.033    995
  Dihedral  :  4.593  38.723    780
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 20.84 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.29), residues: 699
  helix: -0.44 (0.79), residues: 46
  sheet:  0.39 (0.42), residues: 152
  loop : -0.71 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  80 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.034   0.002   PHE B 219 
 TYR   0.029   0.002   TYR C 194 
 ARG   0.008   0.001   ARG E 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02992 (  150)
  hydrogen bonds       : angle       5.74640 (  369)
  SS BOND              : bond        0.00132 (    8)
  SS BOND              : angle       0.56457 (   16)
  covalent geometry    : bond        0.00322 ( 5678)
  covalent geometry    : angle       0.55008 ( 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
  188 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   71 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7902 (mttm)
REVERT: E   82 LEU cc_start: 0.3789 (OUTLIER) cc_final: 0.3194 (tt)
REVERT: E  105 ASN cc_start: 0.8422 (m-40) cc_final: 0.7965 (m-40)
REVERT: E  113 TYR cc_start: 0.8173 (m-80) cc_final: 0.7545 (m-10)
REVERT: E  205 LEU cc_start: 0.6911 (mp) cc_final: 0.6590 (mm)
REVERT: E  247 GLN cc_start: 0.8843 (mt0) cc_final: 0.8109 (tt0)
REVERT: B   64 TYR cc_start: 0.8550 (m-80) cc_final: 0.8232 (m-80)
REVERT: B   72 GLU cc_start: 0.8530 (mp0) cc_final: 0.8307 (mp0)
REVERT: B   74 ASP cc_start: 0.8035 (p0) cc_final: 0.7718 (p0)
REVERT: B   84 ASP cc_start: 0.7647 (t0) cc_final: 0.7368 (t0)
REVERT: B   87 LYS cc_start: 0.8340 (pttt) cc_final: 0.7724 (ptpt)
REVERT: B   95 ASN cc_start: 0.8629 (m-40) cc_final: 0.8391 (m-40)
REVERT: B  129 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7115 (mm-30)
REVERT: B  132 MET cc_start: 0.8916 (mtt) cc_final: 0.8576 (mtt)
REVERT: B  154 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7618 (mtmm)
REVERT: B  213 MET cc_start: 0.7762 (mtt) cc_final: 0.7445 (mpp)
REVERT: B  215 ARG cc_start: 0.6584 (ttp-170) cc_final: 0.4612 (mmt180)
REVERT: B  226 PHE cc_start: 0.8649 (m-10) cc_final: 0.8399 (m-10)
REVERT: C   44 MET cc_start: 0.7952 (mmt) cc_final: 0.7635 (tpp)
REVERT: C   61 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8006 (mtmt)
REVERT: C  134 TYR cc_start: 0.8197 (t80) cc_final: 0.7785 (t80)
REVERT: A   98 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7614 (mtt90)
REVERT: A  254 ARG cc_start: 0.8868 (mmm160) cc_final: 0.8397 (mmm160)
REVERT: A  265 ASN cc_start: 0.8437 (m-40) cc_final: 0.8222 (m-40)
REVERT: A  286 LYS cc_start: 0.8576 (pttm) cc_final: 0.8205 (ptpp)
  outliers start: 30
  outliers final: 22
  residues processed: 174
  average time/residue: 0.1875
  time to fit residues: 41.4733
Evaluate side-chains
  171 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain E residue  211 VAL
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  135 SER
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   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  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 48 optimal weight:    0.0970
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0670
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.9118

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

Flipped N/Q/H residues before XYZ refinement:
E 271 ASN
C  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.216645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.146494 restraints weight = 7117.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.151711 restraints weight = 4206.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.155277 restraints weight = 2880.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.4919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5686  Z= 0.163
  Angle     :  0.564   7.091   7743  Z= 0.299
  Chirality :  0.045   0.174    853
  Planarity :  0.004   0.029    995
  Dihedral  :  4.518  31.210    780
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 21.49 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.70 (0.76), residues: 47
  sheet:  0.46 (0.41), residues: 156
  loop : -0.67 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  80 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.030   0.002   PHE B 219 
 TYR   0.032   0.002   TYR C 194 
 ARG   0.005   0.001   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03008 (  150)
  hydrogen bonds       : angle       5.75180 (  369)
  SS BOND              : bond        0.00192 (    8)
  SS BOND              : angle       0.62657 (   16)
  covalent geometry    : bond        0.00382 ( 5678)
  covalent geometry    : angle       0.56435 ( 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
  193 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 161
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   35 ASP cc_start: 0.3901 (OUTLIER) cc_final: 0.3388 (t70)
REVERT: E   71 LYS cc_start: 0.8222 (ptmt) cc_final: 0.7910 (mttm)
REVERT: E   82 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3479 (tt)
REVERT: E  105 ASN cc_start: 0.8537 (m-40) cc_final: 0.8061 (m-40)
REVERT: E  113 TYR cc_start: 0.8311 (m-80) cc_final: 0.7773 (m-10)
REVERT: E  205 LEU cc_start: 0.7071 (mp) cc_final: 0.6821 (mm)
REVERT: E  246 ARG cc_start: 0.7554 (ptp-170) cc_final: 0.6942 (mtp85)
REVERT: B   64 TYR cc_start: 0.8596 (m-80) cc_final: 0.8276 (m-80)
REVERT: B   72 GLU cc_start: 0.8544 (mp0) cc_final: 0.8032 (mp0)
REVERT: B   74 ASP cc_start: 0.8142 (p0) cc_final: 0.7829 (p0)
REVERT: B   81 LYS cc_start: 0.8724 (mttp) cc_final: 0.8500 (mmtp)
REVERT: B   84 ASP cc_start: 0.7726 (t0) cc_final: 0.7438 (t0)
REVERT: B   87 LYS cc_start: 0.8291 (pttt) cc_final: 0.7659 (ptpt)
REVERT: B   96 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7543 (ttp)
REVERT: B  129 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7265 (mm-30)
REVERT: B  132 MET cc_start: 0.9013 (mtt) cc_final: 0.8424 (mtt)
REVERT: B  154 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7774 (mtmm)
REVERT: B  158 THR cc_start: 0.8979 (p) cc_final: 0.8661 (t)
REVERT: B  213 MET cc_start: 0.7854 (mtt) cc_final: 0.7329 (mpp)
REVERT: B  215 ARG cc_start: 0.6925 (ttp-170) cc_final: 0.4609 (mmt180)
REVERT: B  226 PHE cc_start: 0.8664 (m-10) cc_final: 0.8439 (m-10)
REVERT: B  256 ARG cc_start: 0.7839 (ppt90) cc_final: 0.6164 (mtt-85)
REVERT: C   44 MET cc_start: 0.7990 (mmt) cc_final: 0.7672 (tpp)
REVERT: C   61 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7978 (mtmt)
REVERT: C  134 TYR cc_start: 0.8267 (t80) cc_final: 0.7886 (t80)
REVERT: A   98 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7562 (mtt90)
REVERT: A  254 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8411 (mmm160)
REVERT: A  286 LYS cc_start: 0.8666 (pttm) cc_final: 0.8342 (pttm)
  outliers start: 32
  outliers final: 21
  residues processed: 179
  average time/residue: 0.1750
  time to fit residues: 40.2741
Evaluate side-chains
  174 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain E residue  271 ASN
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   96 MET
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  154 LYS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 17 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:    0.4980
   chunk 26 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.216643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.149784 restraints weight = 7082.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.154614 restraints weight = 4382.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158427 restraints weight = 3056.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.5111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5686  Z= 0.140
  Angle     :  0.579   9.117   7743  Z= 0.304
  Chirality :  0.045   0.161    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.475  26.093    780
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 22.62 %
    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: -0.60 (0.29), residues: 699
  helix: -0.48 (0.76), residues: 47
  sheet:  0.50 (0.42), residues: 155
  loop : -0.71 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  78 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.025   0.001   PHE B 219 
 TYR   0.024   0.002   TYR B 100 
 ARG   0.006   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03090 (  150)
  hydrogen bonds       : angle       5.69890 (  369)
  SS BOND              : bond        0.00255 (    8)
  SS BOND              : angle       0.69461 (   16)
  covalent geometry    : bond        0.00330 ( 5678)
  covalent geometry    : angle       0.57859 ( 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
  183 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 154
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   35 ASP cc_start: 0.4024 (OUTLIER) cc_final: 0.3391 (t70)
REVERT: E   71 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7898 (mttm)
REVERT: E   82 LEU cc_start: 0.3815 (OUTLIER) cc_final: 0.3200 (tt)
REVERT: E  105 ASN cc_start: 0.8535 (m-40) cc_final: 0.8052 (m-40)
REVERT: E  113 TYR cc_start: 0.8164 (m-80) cc_final: 0.7587 (m-10)
REVERT: E  157 PHE cc_start: 0.4870 (p90) cc_final: 0.4539 (p90)
REVERT: E  205 LEU cc_start: 0.7219 (mp) cc_final: 0.6974 (mm)
REVERT: B   64 TYR cc_start: 0.8517 (m-80) cc_final: 0.8174 (m-80)
REVERT: B   72 GLU cc_start: 0.8555 (mp0) cc_final: 0.8022 (mp0)
REVERT: B   74 ASP cc_start: 0.8094 (p0) cc_final: 0.7762 (p0)
REVERT: B   81 LYS cc_start: 0.8657 (mttp) cc_final: 0.8005 (mmtp)
REVERT: B   84 ASP cc_start: 0.7692 (t0) cc_final: 0.7401 (t0)
REVERT: B   87 LYS cc_start: 0.8266 (pttt) cc_final: 0.7587 (ptpt)
REVERT: B   96 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7621 (ttp)
REVERT: B  129 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7236 (mm-30)
REVERT: B  132 MET cc_start: 0.8954 (mtt) cc_final: 0.8557 (mtt)
REVERT: B  158 THR cc_start: 0.8910 (p) cc_final: 0.8679 (t)
REVERT: B  213 MET cc_start: 0.7610 (mtt) cc_final: 0.6853 (mtt)
REVERT: B  215 ARG cc_start: 0.6844 (ttp-170) cc_final: 0.4658 (mmt180)
REVERT: B  226 PHE cc_start: 0.8639 (m-10) cc_final: 0.8415 (m-10)
REVERT: B  256 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6184 (mtt-85)
REVERT: C   44 MET cc_start: 0.8052 (mmt) cc_final: 0.7682 (tpp)
REVERT: C   61 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7983 (mtmt)
REVERT: C  134 TYR cc_start: 0.8157 (t80) cc_final: 0.7731 (t80)
REVERT: A   98 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7533 (mtt90)
REVERT: A  254 ARG cc_start: 0.8893 (mmm160) cc_final: 0.8344 (mmm160)
REVERT: A  265 ASN cc_start: 0.8560 (m-40) cc_final: 0.8269 (m-40)
REVERT: A  286 LYS cc_start: 0.8618 (pttm) cc_final: 0.8417 (ptpp)
  outliers start: 29
  outliers final: 23
  residues processed: 168
  average time/residue: 0.1772
  time to fit residues: 38.3025
Evaluate side-chains
  175 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
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  109 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  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   96 MET
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0470
   chunk 9 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0070
   chunk 54 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
B  95 ASN
** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 HIS
** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.218652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.152137 restraints weight = 7091.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.157060 restraints weight = 4240.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.160407 restraints weight = 2921.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.5246

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= 0.129
  Angle     :  0.575   9.556   7743  Z= 0.300
  Chirality :  0.045   0.165    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.349  20.495    780
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 21.49 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.30), residues: 699
  helix: -0.17 (0.81), residues: 47
  sheet:  0.61 (0.43), residues: 149
  loop : -0.72 (0.25), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  78 
 HIS   0.007   0.001   HIS B 109 
 PHE   0.027   0.001   PHE B 219 
 TYR   0.024   0.002   TYR B 100 
 ARG   0.006   0.000   ARG E 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02942 (  150)
  hydrogen bonds       : angle       5.64308 (  369)
  SS BOND              : bond        0.00265 (    8)
  SS BOND              : angle       0.61275 (   16)
  covalent geometry    : bond        0.00302 ( 5678)
  covalent geometry    : angle       0.57513 ( 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
  191 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 158
  time to evaluate  : 0.578 
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: 0.8238 (ptmt) cc_final: 0.7912 (mttm)
REVERT: E   82 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.3299 (tt)
REVERT: E  105 ASN cc_start: 0.8492 (m-40) cc_final: 0.8044 (m-40)
REVERT: E  205 LEU cc_start: 0.7140 (mp) cc_final: 0.6874 (mm)
REVERT: E  246 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.7023 (mtp85)
REVERT: B   64 TYR cc_start: 0.8501 (m-80) cc_final: 0.8239 (m-80)
REVERT: B   72 GLU cc_start: 0.8596 (mp0) cc_final: 0.8100 (mp0)
REVERT: B   74 ASP cc_start: 0.8074 (p0) cc_final: 0.7767 (p0)
REVERT: B   84 ASP cc_start: 0.7627 (t0) cc_final: 0.7368 (t0)
REVERT: B   87 LYS cc_start: 0.8240 (pttt) cc_final: 0.7667 (ptpt)
REVERT: B   95 ASN cc_start: 0.8758 (m-40) cc_final: 0.8557 (m-40)
REVERT: B   96 MET cc_start: 0.8062 (ttp) cc_final: 0.7630 (ttp)
REVERT: B  129 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7145 (mm-30)
REVERT: B  132 MET cc_start: 0.8929 (mtt) cc_final: 0.8651 (mtt)
REVERT: B  158 THR cc_start: 0.8984 (p) cc_final: 0.8767 (t)
REVERT: B  213 MET cc_start: 0.7479 (mtt) cc_final: 0.6778 (mtt)
REVERT: B  215 ARG cc_start: 0.6571 (ttp-170) cc_final: 0.4521 (mmt180)
REVERT: B  226 PHE cc_start: 0.8637 (m-10) cc_final: 0.8415 (m-10)
REVERT: B  256 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6179 (mtt-85)
REVERT: C   44 MET cc_start: 0.7972 (mmt) cc_final: 0.7670 (tpp)
REVERT: C  134 TYR cc_start: 0.8168 (t80) cc_final: 0.7771 (t80)
REVERT: A   98 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7421 (mtt90)
REVERT: A  265 ASN cc_start: 0.8525 (m-40) cc_final: 0.8313 (m-40)
  outliers start: 33
  outliers final: 25
  residues processed: 174
  average time/residue: 0.1768
  time to fit residues: 39.8883
Evaluate side-chains
  171 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  203 PHE
Chi-restraints excluded: chain E residue  266 TYR
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LYS
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 B residue  256 ARG
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 57 optimal weight:    0.4980
   chunk 14 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0970
   chunk 63 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.5378

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.218303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.150746 restraints weight = 7156.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155881 restraints weight = 4294.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.159034 restraints weight = 2947.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
moved from start:          0.5430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5686  Z= 0.131
  Angle     :  0.592   9.447   7743  Z= 0.310
  Chirality :  0.045   0.152    853
  Planarity :  0.004   0.035    995
  Dihedral  :  4.362  18.211    780
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 22.78 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.53 (0.30), residues: 699
  helix:  0.06 (0.83), residues: 47
  sheet:  0.65 (0.43), residues: 149
  loop : -0.74 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B  78 
 HIS   0.006   0.001   HIS B 109 
 PHE   0.029   0.001   PHE B 219 
 TYR   0.023   0.002   TYR B 100 
 ARG   0.005   0.001   ARG E 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  150)
  hydrogen bonds       : angle       5.65801 (  369)
  SS BOND              : bond        0.00254 (    8)
  SS BOND              : angle       0.60781 (   16)
  covalent geometry    : bond        0.00311 ( 5678)
  covalent geometry    : angle       0.59207 ( 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
  178 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.621 
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: 0.8213 (ptmt) cc_final: 0.7918 (mttm)
REVERT: E   82 LEU cc_start: 0.3959 (OUTLIER) cc_final: 0.3397 (tt)
REVERT: E  105 ASN cc_start: 0.8449 (m-40) cc_final: 0.8001 (m-40)
REVERT: E  205 LEU cc_start: 0.7221 (mp) cc_final: 0.6962 (mm)
REVERT: B   64 TYR cc_start: 0.8493 (m-80) cc_final: 0.8193 (m-80)
REVERT: B   74 ASP cc_start: 0.8090 (p0) cc_final: 0.7756 (p0)
REVERT: B   78 TRP cc_start: 0.8355 (m-90) cc_final: 0.8127 (m-90)
REVERT: B   84 ASP cc_start: 0.7637 (t0) cc_final: 0.7367 (t0)
REVERT: B   87 LYS cc_start: 0.8262 (pttt) cc_final: 0.7612 (ptpt)
REVERT: B   96 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7828 (ttp)
REVERT: B  129 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7153 (mm-30)
REVERT: B  132 MET cc_start: 0.8936 (mtt) cc_final: 0.8679 (mtt)
REVERT: B  158 THR cc_start: 0.9033 (p) cc_final: 0.8805 (t)
REVERT: B  213 MET cc_start: 0.7548 (mtt) cc_final: 0.6898 (mtt)
REVERT: B  215 ARG cc_start: 0.6538 (ttp-170) cc_final: 0.4617 (mmt180)
REVERT: B  226 PHE cc_start: 0.8644 (m-10) cc_final: 0.8438 (m-10)
REVERT: B  256 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6143 (mtt-85)
REVERT: C   44 MET cc_start: 0.7985 (mmt) cc_final: 0.7544 (tpp)
REVERT: C  134 TYR cc_start: 0.8194 (t80) cc_final: 0.7778 (t80)
REVERT: A   98 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7408 (mtt90)
REVERT: A  265 ASN cc_start: 0.8591 (m-40) cc_final: 0.8376 (m-40)
  outliers start: 30
  outliers final: 25
  residues processed: 163
  average time/residue: 0.1791
  time to fit residues: 37.1954
Evaluate side-chains
  169 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  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   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain A residue  113 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0670
   chunk 27 optimal weight:    0.4980
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.0720

-------------------------------------------------------------------------------
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**
** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.217107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.148436 restraints weight = 7305.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.153347 restraints weight = 4421.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.156832 restraints weight = 3066.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.5591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5686  Z= 0.185
  Angle     :  0.643   9.482   7743  Z= 0.338
  Chirality :  0.046   0.170    853
  Planarity :  0.004   0.030    995
  Dihedral  :  4.606  18.968    780
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 23.59 %
    Favored  : 71.08 %
  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: -0.68 (0.30), residues: 699
  helix: -0.23 (0.81), residues: 47
  sheet:  0.44 (0.42), residues: 152
  loop : -0.79 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  78 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.027   0.002   PHE B 219 
 TYR   0.033   0.002   TYR C 194 
 ARG   0.008   0.001   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03130 (  150)
  hydrogen bonds       : angle       5.86318 (  369)
  SS BOND              : bond        0.00248 (    8)
  SS BOND              : angle       0.57657 (   16)
  covalent geometry    : bond        0.00435 ( 5678)
  covalent geometry    : angle       0.64328 ( 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
  177 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.589 
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: 0.8225 (ptmt) cc_final: 0.7911 (mttm)
REVERT: E   82 LEU cc_start: 0.4001 (OUTLIER) cc_final: 0.3459 (tt)
REVERT: E  105 ASN cc_start: 0.8468 (m-40) cc_final: 0.8108 (m-40)
REVERT: E  157 PHE cc_start: 0.4440 (p90) cc_final: 0.3360 (p90)
REVERT: E  205 LEU cc_start: 0.7206 (mp) cc_final: 0.6913 (mm)
REVERT: B   72 GLU cc_start: 0.8526 (mp0) cc_final: 0.8313 (mp0)
REVERT: B   74 ASP cc_start: 0.8196 (p0) cc_final: 0.7842 (p0)
REVERT: B   84 ASP cc_start: 0.7733 (t0) cc_final: 0.7375 (t0)
REVERT: B   87 LYS cc_start: 0.8311 (pttt) cc_final: 0.7658 (ptpt)
REVERT: B   96 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7861 (ttp)
REVERT: B  129 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7215 (mm-30)
REVERT: B  132 MET cc_start: 0.9000 (mtt) cc_final: 0.8552 (mtt)
REVERT: B  158 THR cc_start: 0.9025 (p) cc_final: 0.8727 (t)
REVERT: B  213 MET cc_start: 0.7665 (mtt) cc_final: 0.7040 (mtt)
REVERT: B  215 ARG cc_start: 0.6618 (ttp-170) cc_final: 0.4766 (mmt180)
REVERT: B  256 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6215 (mtt-85)
REVERT: C   44 MET cc_start: 0.8023 (mmt) cc_final: 0.7659 (tpp)
REVERT: C  134 TYR cc_start: 0.8232 (t80) cc_final: 0.7874 (t80)
REVERT: A   98 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7465 (mtt90)
REVERT: A  100 MET cc_start: 0.5748 (mtm) cc_final: 0.5404 (ttp)
REVERT: A  265 ASN cc_start: 0.8602 (m-40) cc_final: 0.8328 (m-40)
  outliers start: 33
  outliers final: 26
  residues processed: 162
  average time/residue: 0.1788
  time to fit residues: 37.0220
Evaluate side-chains
  174 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  119 PHE
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  162 SER
Chi-restraints excluded: chain E residue  180 ILE
Chi-restraints excluded: chain E residue  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   88 ASP
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   96 MET
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  113 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  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 B residue  256 ARG
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  199 VAL
Chi-restraints excluded: chain C residue  210 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 36 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.218545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.150567 restraints weight = 7383.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.155884 restraints weight = 4512.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.159553 restraints weight = 3099.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.5770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5686  Z= 0.149
  Angle     :  0.641   9.499   7743  Z= 0.332
  Chirality :  0.045   0.152    853
  Planarity :  0.006   0.126    995
  Dihedral  :  4.591  19.288    780
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 24.23 %
    Favored  : 70.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.30), residues: 699
  helix:  0.04 (0.83), residues: 47
  sheet:  0.43 (0.43), residues: 152
  loop : -0.76 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B  78 
 HIS   0.005   0.001   HIS C  97 
 PHE   0.034   0.002   PHE B 226 
 TYR   0.041   0.002   TYR E 127 
 ARG   0.026   0.001   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  150)
  hydrogen bonds       : angle       5.78226 (  369)
  SS BOND              : bond        0.00218 (    8)
  SS BOND              : angle       0.63194 (   16)
  covalent geometry    : bond        0.00351 ( 5678)
  covalent geometry    : angle       0.64084 ( 7727)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2982.22 seconds
wall clock time: 52 minutes 0.56 seconds (3120.56 seconds total)