Starting phenix.real_space_refine
on Wed Jun  4 16:17:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cax_16535/06_2025/8cax_16535.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cax_16535/06_2025/8cax_16535.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cax_16535/06_2025/8cax_16535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cax_16535/06_2025/8cax_16535.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cax_16535/06_2025/8cax_16535.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cax_16535/06_2025/8cax_16535.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2160      2.51       5
     N     636      2.21       5
     O     642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3444
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 3.06, per 1000 atoms: 0.89
  Number of scatterers: 3444
  At special positions: 0
  Unit cell: (130.192, 119.48, 37.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     642      8.00
     N     636      7.00
     C    2160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 444.8 milliseconds
  

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 22.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 308
      removed outlier: 6.833A  pdb=" N   GLN A 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLN E 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.927A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL E 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 321 through 325
      removed outlier: 8.973A  pdb=" N   CYS A 322 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   LEU B 325 " --> pdb=" O   CYS A 322 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   SER A 324 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   SER E 324 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU A 325 " --> pdb=" O   SER E 324 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   SER F 324 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU E 325 " --> pdb=" O   SER F 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 339
      removed outlier: 6.439A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 346
      removed outlier: 6.125A  pdb=" N   GLU A 342 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   ASP B 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LYS A 343 " --> pdb=" O   GLU E 342 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LYS E 343 " --> pdb=" O   GLU F 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351
      removed outlier: 6.351A  pdb=" N   VAL A 350 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 357
      removed outlier: 6.131A  pdb=" N   ILE A 354 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU B 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   SER A 356 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 308
      removed outlier: 6.833A  pdb=" N   GLN C 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.927A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 321 through 325
      removed outlier: 6.728A  pdb=" N   SER D 324 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU C 325 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 339
    Processing sheet with id=AB3, first strand: chain 'C' and resid 342 through 346
      removed outlier: 6.838A  pdb=" N   LYS C 343 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 350 through 351
    Processing sheet with id=AB5, first strand: chain 'C' and resid 354 through 357

    36 hydrogen bonds defined for protein.
    108 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 990
        1.34 -     1.46: 739
        1.46 -     1.58: 1763
        1.58 -     1.70: 0
        1.70 -     1.82: 6
  Bond restraints: 3498
  Sorted by residual:
  bond pdb=" CG  HIS B 330 "
       pdb=" CD2 HIS B 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.311  0.043 1.10e-02 8.26e+03 1.50e+01
  bond pdb=" CG  HIS F 330 "
       pdb=" CD2 HIS F 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.312  0.042 1.10e-02 8.26e+03 1.49e+01
  bond pdb=" CG  HIS D 330 "
       pdb=" CD2 HIS D 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.312  0.042 1.10e-02 8.26e+03 1.48e+01
  bond pdb=" CG  HIS E 330 "
       pdb=" CD2 HIS E 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.312  0.042 1.10e-02 8.26e+03 1.46e+01
  bond pdb=" CG  HIS C 330 "
       pdb=" CD2 HIS C 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.312  0.042 1.10e-02 8.26e+03 1.45e+01
  ... (remaining 3493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 4091
        2.25 -     4.50: 481
        4.50 -     6.76: 90
        6.76 -     9.01: 12
        9.01 -    11.26: 6
  Bond angle restraints: 4680
  Sorted by residual:
  angle pdb=" C   HIS C 362 "
        pdb=" CA  HIS C 362 "
        pdb=" CB  HIS C 362 "
      ideal   model   delta    sigma   weight residual
     109.84  121.10  -11.26 1.63e+00 3.76e-01 4.77e+01
  angle pdb=" C   HIS D 362 "
        pdb=" CA  HIS D 362 "
        pdb=" CB  HIS D 362 "
      ideal   model   delta    sigma   weight residual
     109.84  121.09  -11.25 1.63e+00 3.76e-01 4.76e+01
  angle pdb=" C   HIS E 362 "
        pdb=" CA  HIS E 362 "
        pdb=" CB  HIS E 362 "
      ideal   model   delta    sigma   weight residual
     109.84  121.09  -11.25 1.63e+00 3.76e-01 4.76e+01
  angle pdb=" C   HIS B 362 "
        pdb=" CA  HIS B 362 "
        pdb=" CB  HIS B 362 "
      ideal   model   delta    sigma   weight residual
     109.84  121.07  -11.23 1.63e+00 3.76e-01 4.75e+01
  angle pdb=" C   HIS A 362 "
        pdb=" CA  HIS A 362 "
        pdb=" CB  HIS A 362 "
      ideal   model   delta    sigma   weight residual
     109.84  121.07  -11.23 1.63e+00 3.76e-01 4.75e+01
  ... (remaining 4675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.41: 1619
       11.41 -    22.81: 350
       22.81 -    34.21: 113
       34.21 -    45.62: 42
       45.62 -    57.02: 12
  Dihedral angle restraints: 2136
    sinusoidal: 894
      harmonic: 1242
  Sorted by residual:
  dihedral pdb=" CA  GLY B 326 "
           pdb=" C   GLY B 326 "
           pdb=" N   ASN B 327 "
           pdb=" CA  ASN B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.47   36.53     0      5.00e+00 4.00e-02 5.34e+01
  dihedral pdb=" CA  GLY E 326 "
           pdb=" C   GLY E 326 "
           pdb=" N   ASN E 327 "
           pdb=" CA  ASN E 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.49   36.51     0      5.00e+00 4.00e-02 5.33e+01
  dihedral pdb=" CA  GLY D 326 "
           pdb=" C   GLY D 326 "
           pdb=" N   ASN D 327 "
           pdb=" CA  ASN D 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.50   36.50     0      5.00e+00 4.00e-02 5.33e+01
  ... (remaining 2133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 193
       0.045 -    0.089: 137
       0.089 -    0.134: 99
       0.134 -    0.179: 87
       0.179 -    0.223: 12
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" CA  HIS B 362 "
            pdb=" N   HIS B 362 "
            pdb=" C   HIS B 362 "
            pdb=" CB  HIS B 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  HIS E 362 "
            pdb=" N   HIS E 362 "
            pdb=" C   HIS E 362 "
            pdb=" CB  HIS E 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  HIS D 362 "
            pdb=" N   HIS D 362 "
            pdb=" C   HIS D 362 "
            pdb=" CB  HIS D 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 525 not shown)

  Planarity restraints: 594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 310 "    0.024 2.00e-02 2.50e+03   1.57e-02 4.95e+00
        pdb=" CG  TYR E 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 310 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 310 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 310 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 310 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E 310 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 310 "    0.024 2.00e-02 2.50e+03   1.57e-02 4.91e+00
        pdb=" CG  TYR B 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 310 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 310 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 310 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 310 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 310 "    0.024 2.00e-02 2.50e+03   1.56e-02 4.89e+00
        pdb=" CG  TYR A 310 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 310 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 310 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 310 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 310 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 310 "    0.003 2.00e-02 2.50e+03
  ... (remaining 591 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 648
        2.80 -     3.32: 3342
        3.32 -     3.85: 5056
        3.85 -     4.37: 6045
        4.37 -     4.90: 11475
  Nonbonded interactions: 26566
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 316 "
            pdb=" NZ  LYS B 370 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER D 316 "
            pdb=" NZ  LYS D 370 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER F 316 "
            pdb=" NZ  LYS F 370 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER A 316 "
            pdb=" NZ  LYS A 370 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER E 316 "
            pdb=" NZ  LYS E 370 "
     model   vdw
     2.271 3.120
  ... (remaining 26561 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             2.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.150
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
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      :  0.009   0.043   3498  Z= 0.576
  Angle     :  1.646  11.259   4680  Z= 1.069
  Chirality :  0.092   0.223    528
  Planarity :  0.009   0.040    594
  Dihedral  : 14.826  57.023   1344
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  :  7.58 %
    Favored  : 87.88 %
  Cbeta Deviations :  1.52 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.41 %

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: -3.97 (0.25), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.19), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.005   HIS E 330 
 PHE   0.015   0.003   PHE D 378 
 TYR   0.036   0.010   TYR E 310 
 ARG   0.004   0.001   ARG D 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17422 (   36)
  hydrogen bonds       : angle       8.12086 (  108)
  covalent geometry    : bond        0.00872 ( 3498)
  covalent geometry    : angle       1.64637 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LYS cc_start: 0.9051 (tttt) cc_final: 0.8834 (tttp)
REVERT: B  310 TYR cc_start: 0.8145 (t80) cc_final: 0.7858 (t80)
REVERT: B  346 PHE cc_start: 0.8797 (m-80) cc_final: 0.7886 (p90)
REVERT: B  369 LYS cc_start: 0.8704 (mttt) cc_final: 0.8488 (ttmt)
REVERT: C  310 TYR cc_start: 0.8172 (t80) cc_final: 0.7787 (t80)
REVERT: C  345 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8053 (t0)
REVERT: C  346 PHE cc_start: 0.8834 (m-80) cc_final: 0.8070 (p90)
REVERT: D  349 ARG cc_start: 0.8905 (mtt180) cc_final: 0.8204 (pmt-80)
REVERT: D  372 GLU cc_start: 0.8531 (tt0) cc_final: 0.8157 (mp0)
REVERT: D  375 LYS cc_start: 0.9126 (tttt) cc_final: 0.8838 (tttp)
REVERT: E  308 ILE cc_start: 0.9394 (mt) cc_final: 0.9117 (mp)
REVERT: E  310 TYR cc_start: 0.8050 (t80) cc_final: 0.7797 (t80)
REVERT: E  369 LYS cc_start: 0.8715 (mttt) cc_final: 0.8504 (ttpt)
REVERT: E  372 GLU cc_start: 0.8734 (tt0) cc_final: 0.8312 (mp0)
REVERT: E  375 LYS cc_start: 0.9018 (tttt) cc_final: 0.8741 (tttm)
REVERT: E  378 PHE cc_start: 0.8799 (t80) cc_final: 0.8491 (t80)
REVERT: F  343 LYS cc_start: 0.9041 (mttm) cc_final: 0.8508 (tmmt)
REVERT: F  349 ARG cc_start: 0.8745 (mtt180) cc_final: 0.7988 (ptt-90)
  outliers start: 18
  outliers final: 6
  residues processed: 189
  average time/residue: 0.2241
  time to fit residues: 48.0325
Evaluate side-chains
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  345 ASP
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain F residue  345 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.0010
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    2.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 368 ASN
B 374 HIS
C 362 HIS
D 330 HIS
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 336 GLN
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.121822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.105469 restraints weight = 8033.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.107916 restraints weight = 3696.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.109629 restraints weight = 2263.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.4476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3498  Z= 0.157
  Angle     :  0.725   6.491   4680  Z= 0.373
  Chirality :  0.050   0.136    528
  Planarity :  0.006   0.051    594
  Dihedral  :  7.104  44.977    476
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 19.95 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.49 (0.27), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.65 (0.21), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 330 
 PHE   0.019   0.002   PHE E 346 
 TYR   0.015   0.002   TYR D 310 
 ARG   0.003   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01904 (   36)
  hydrogen bonds       : angle       4.61667 (  108)
  covalent geometry    : bond        0.00337 ( 3498)
  covalent geometry    : angle       0.72548 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.9403 (tptm) cc_final: 0.8814 (mmtm)
REVERT: A  371 ILE cc_start: 0.8786 (mt) cc_final: 0.8564 (mp)
REVERT: B  342 GLU cc_start: 0.7891 (mp0) cc_final: 0.7683 (mp0)
REVERT: B  345 ASP cc_start: 0.8356 (t0) cc_final: 0.8098 (t0)
REVERT: B  346 PHE cc_start: 0.8744 (m-80) cc_final: 0.7516 (p90)
REVERT: B  358 ASP cc_start: 0.8259 (m-30) cc_final: 0.7974 (t0)
REVERT: B  369 LYS cc_start: 0.7931 (mttt) cc_final: 0.7647 (ttmt)
REVERT: C  310 TYR cc_start: 0.6359 (t80) cc_final: 0.5453 (t80)
REVERT: C  336 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7418 (tp40)
REVERT: C  345 ASP cc_start: 0.8052 (m-30) cc_final: 0.7687 (m-30)
REVERT: C  346 PHE cc_start: 0.8615 (m-80) cc_final: 0.7526 (p90)
REVERT: C  371 ILE cc_start: 0.8643 (mt) cc_final: 0.8190 (mp)
REVERT: D  315 LEU cc_start: 0.8249 (mp) cc_final: 0.8012 (mp)
REVERT: D  331 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8761 (ttmt)
REVERT: D  372 GLU cc_start: 0.7967 (tt0) cc_final: 0.7292 (mp0)
REVERT: D  376 LEU cc_start: 0.8333 (tp) cc_final: 0.7511 (mt)
REVERT: E  308 ILE cc_start: 0.9053 (mt) cc_final: 0.8822 (mp)
REVERT: E  310 TYR cc_start: 0.6872 (t80) cc_final: 0.6177 (t80)
REVERT: E  369 LYS cc_start: 0.8064 (mttt) cc_final: 0.7725 (ttpt)
REVERT: E  372 GLU cc_start: 0.8301 (tt0) cc_final: 0.7655 (mp0)
REVERT: E  375 LYS cc_start: 0.8538 (tttt) cc_final: 0.8294 (tttm)
  outliers start: 14
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1594
  time to fit residues: 26.2095
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  324 SER
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  324 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.0270
   chunk 34 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 22 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:   30.0000
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 25 optimal weight:    7.9990
   overall best weight:    6.8046

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 330 HIS
F 336 GLN
** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.114398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.097526 restraints weight = 8416.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.099792 restraints weight = 4041.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.101340 restraints weight = 2528.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.5341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   3498  Z= 0.245
  Angle     :  0.799  11.727   4680  Z= 0.391
  Chirality :  0.051   0.137    528
  Planarity :  0.006   0.044    594
  Dihedral  :  6.683  45.498    468
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.95 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.21 (0.27), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.20), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS C 330 
 PHE   0.009   0.001   PHE F 378 
 TYR   0.021   0.004   TYR B 310 
 ARG   0.003   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02334 (   36)
  hydrogen bonds       : angle       4.42118 (  108)
  covalent geometry    : bond        0.00517 ( 3498)
  covalent geometry    : angle       0.79865 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 ILE cc_start: 0.8742 (mt) cc_final: 0.8364 (mp)
REVERT: B  342 GLU cc_start: 0.7612 (mp0) cc_final: 0.6980 (mp0)
REVERT: B  345 ASP cc_start: 0.8419 (t0) cc_final: 0.8202 (t0)
REVERT: B  346 PHE cc_start: 0.8953 (m-80) cc_final: 0.7683 (p90)
REVERT: C  310 TYR cc_start: 0.6418 (t80) cc_final: 0.5770 (t80)
REVERT: C  336 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7184 (tp40)
REVERT: C  345 ASP cc_start: 0.8002 (m-30) cc_final: 0.7661 (m-30)
REVERT: C  346 PHE cc_start: 0.8714 (m-80) cc_final: 0.7786 (p90)
REVERT: C  371 ILE cc_start: 0.8482 (mt) cc_final: 0.7830 (mp)
REVERT: D  331 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8768 (ttmt)
REVERT: D  372 GLU cc_start: 0.8035 (tt0) cc_final: 0.7278 (mp0)
REVERT: D  376 LEU cc_start: 0.8191 (tp) cc_final: 0.7806 (tt)
REVERT: E  308 ILE cc_start: 0.8870 (mt) cc_final: 0.8619 (mp)
REVERT: E  310 TYR cc_start: 0.7094 (t80) cc_final: 0.6408 (t80)
REVERT: E  369 LYS cc_start: 0.8051 (mttt) cc_final: 0.7785 (ttpt)
REVERT: E  372 GLU cc_start: 0.8319 (tt0) cc_final: 0.7493 (mp0)
REVERT: E  375 LYS cc_start: 0.8288 (tttt) cc_final: 0.7939 (tttm)
  outliers start: 15
  outliers final: 12
  residues processed: 117
  average time/residue: 0.1345
  time to fit residues: 19.5392
Evaluate side-chains
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 22 optimal weight:   30.0000
   chunk 25 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 359 ASN
D 359 ASN
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 GLN
F 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.118296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.101454 restraints weight = 8387.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.103803 restraints weight = 3985.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.105481 restraints weight = 2460.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.5771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3498  Z= 0.187
  Angle     :  0.780  14.144   4680  Z= 0.362
  Chirality :  0.050   0.134    528
  Planarity :  0.005   0.043    594
  Dihedral  :  6.529  49.660    468
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.74 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.95 (0.27), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.21), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C 330 
 PHE   0.020   0.002   PHE E 378 
 TYR   0.010   0.003   TYR B 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01965 (   36)
  hydrogen bonds       : angle       4.34275 (  108)
  covalent geometry    : bond        0.00397 ( 3498)
  covalent geometry    : angle       0.78015 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ASP cc_start: 0.8392 (m-30) cc_final: 0.8119 (m-30)
REVERT: B  342 GLU cc_start: 0.7783 (mp0) cc_final: 0.7114 (mp0)
REVERT: B  345 ASP cc_start: 0.8434 (t0) cc_final: 0.8132 (t0)
REVERT: B  346 PHE cc_start: 0.8942 (m-80) cc_final: 0.7693 (p90)
REVERT: C  310 TYR cc_start: 0.6506 (t80) cc_final: 0.5877 (t80)
REVERT: C  336 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7129 (tp40)
REVERT: C  345 ASP cc_start: 0.7988 (m-30) cc_final: 0.7621 (m-30)
REVERT: C  346 PHE cc_start: 0.8689 (m-80) cc_final: 0.7790 (p90)
REVERT: C  371 ILE cc_start: 0.8522 (mt) cc_final: 0.7899 (mp)
REVERT: D  311 LYS cc_start: 0.3302 (OUTLIER) cc_final: 0.2753 (pptt)
REVERT: D  372 GLU cc_start: 0.8109 (tt0) cc_final: 0.7368 (mp0)
REVERT: D  376 LEU cc_start: 0.8065 (tp) cc_final: 0.7606 (tt)
REVERT: E  308 ILE cc_start: 0.8894 (mt) cc_final: 0.8647 (mp)
REVERT: E  310 TYR cc_start: 0.7068 (t80) cc_final: 0.6327 (t80)
REVERT: E  369 LYS cc_start: 0.8193 (mttt) cc_final: 0.7917 (ttpt)
REVERT: E  372 GLU cc_start: 0.8233 (tt0) cc_final: 0.7496 (mp0)
REVERT: E  375 LYS cc_start: 0.8330 (tttt) cc_final: 0.8007 (tttt)
  outliers start: 12
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1223
  time to fit residues: 18.0846
Evaluate side-chains
  112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 25 optimal weight:    0.0170
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 1 optimal weight:   30.0000
   overall best weight:    4.2026

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.121615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.105211 restraints weight = 8587.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.107497 restraints weight = 4080.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.109284 restraints weight = 2539.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.6091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3498  Z= 0.162
  Angle     :  0.761  14.835   4680  Z= 0.350
  Chirality :  0.050   0.134    528
  Planarity :  0.005   0.040    594
  Dihedral  :  6.294  51.437    468
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.75 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.68 (0.28), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.22), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C 330 
 PHE   0.015   0.001   PHE A 378 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01697 (   36)
  hydrogen bonds       : angle       4.19781 (  108)
  covalent geometry    : bond        0.00341 ( 3498)
  covalent geometry    : angle       0.76075 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
REVERT: B  342 GLU cc_start: 0.7805 (mp0) cc_final: 0.7123 (mp0)
REVERT: B  344 LEU cc_start: 0.9319 (mp) cc_final: 0.8949 (mp)
REVERT: B  345 ASP cc_start: 0.8572 (t0) cc_final: 0.8178 (t0)
REVERT: B  346 PHE cc_start: 0.8909 (m-80) cc_final: 0.7583 (p90)
REVERT: C  310 TYR cc_start: 0.6385 (t80) cc_final: 0.5909 (t80)
REVERT: C  336 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7276 (tp40)
REVERT: C  345 ASP cc_start: 0.8079 (m-30) cc_final: 0.7739 (m-30)
REVERT: C  346 PHE cc_start: 0.8610 (m-80) cc_final: 0.7780 (p90)
REVERT: D  311 LYS cc_start: 0.3483 (OUTLIER) cc_final: 0.2909 (pptt)
REVERT: D  372 GLU cc_start: 0.8162 (tt0) cc_final: 0.7539 (mp0)
REVERT: D  376 LEU cc_start: 0.8283 (tp) cc_final: 0.7938 (tt)
REVERT: E  308 ILE cc_start: 0.8957 (mt) cc_final: 0.8669 (mp)
REVERT: E  310 TYR cc_start: 0.6981 (t80) cc_final: 0.6266 (t80)
REVERT: E  336 GLN cc_start: 0.8057 (tm130) cc_final: 0.7823 (tm-30)
REVERT: E  369 LYS cc_start: 0.8330 (mttt) cc_final: 0.8064 (ttpt)
REVERT: E  372 GLU cc_start: 0.8303 (tt0) cc_final: 0.7644 (mp0)
REVERT: E  375 LYS cc_start: 0.8371 (tttt) cc_final: 0.8090 (tttt)
  outliers start: 14
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1290
  time to fit residues: 18.6240
Evaluate side-chains
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0570
   chunk 7 optimal weight:   30.0000
   chunk 27 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   chunk 40 optimal weight:    0.3980
   chunk 4 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    4.2904

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 329 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.121363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.102789 restraints weight = 8212.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.104848 restraints weight = 4186.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.106424 restraints weight = 2770.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.6450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3498  Z= 0.165
  Angle     :  0.807  15.336   4680  Z= 0.361
  Chirality :  0.050   0.132    528
  Planarity :  0.005   0.040    594
  Dihedral  :  6.278  52.749    468
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 27.02 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.60 (0.29), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.22), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.022   0.001   PHE E 378 
 TYR   0.009   0.002   TYR A 310 
 ARG   0.004   0.001   ARG D 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01733 (   36)
  hydrogen bonds       : angle       4.10024 (  108)
  covalent geometry    : bond        0.00352 ( 3498)
  covalent geometry    : angle       0.80733 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: B  342 GLU cc_start: 0.7875 (mp0) cc_final: 0.7204 (mp0)
REVERT: B  345 ASP cc_start: 0.8566 (t0) cc_final: 0.8260 (t0)
REVERT: B  346 PHE cc_start: 0.8901 (m-80) cc_final: 0.7597 (p90)
REVERT: C  310 TYR cc_start: 0.6374 (t80) cc_final: 0.5842 (t80)
REVERT: C  336 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7293 (tp40)
REVERT: C  345 ASP cc_start: 0.8076 (m-30) cc_final: 0.7738 (m-30)
REVERT: C  346 PHE cc_start: 0.8661 (m-80) cc_final: 0.7803 (p90)
REVERT: D  311 LYS cc_start: 0.3435 (OUTLIER) cc_final: 0.2910 (pptt)
REVERT: D  372 GLU cc_start: 0.8216 (tt0) cc_final: 0.7583 (mp0)
REVERT: D  376 LEU cc_start: 0.8360 (tp) cc_final: 0.8027 (tt)
REVERT: E  308 ILE cc_start: 0.8991 (mt) cc_final: 0.8715 (mp)
REVERT: E  310 TYR cc_start: 0.6944 (t80) cc_final: 0.6316 (t80)
REVERT: E  336 GLN cc_start: 0.8133 (tm130) cc_final: 0.7894 (tm-30)
REVERT: E  369 LYS cc_start: 0.8426 (mttt) cc_final: 0.8116 (ttpt)
REVERT: E  372 GLU cc_start: 0.8300 (tt0) cc_final: 0.7725 (mp0)
REVERT: E  375 LYS cc_start: 0.8396 (tttt) cc_final: 0.8076 (tttm)
REVERT: F  376 LEU cc_start: 0.7883 (tt) cc_final: 0.7587 (tt)
  outliers start: 15
  outliers final: 13
  residues processed: 115
  average time/residue: 0.1253
  time to fit residues: 18.1968
Evaluate side-chains
  112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  379 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    4.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 374 HIS
D 362 HIS
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.119518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.101466 restraints weight = 8274.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.103577 restraints weight = 4214.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.105146 restraints weight = 2759.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.6638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3498  Z= 0.167
  Angle     :  0.793  12.787   4680  Z= 0.362
  Chirality :  0.050   0.139    528
  Planarity :  0.005   0.038    594
  Dihedral  :  6.270  52.354    468
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 27.02 %
    Favored  : 68.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.55 (0.29), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.22), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.022   0.002   PHE D 378 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01715 (   36)
  hydrogen bonds       : angle       4.10544 (  108)
  covalent geometry    : bond        0.00355 ( 3498)
  covalent geometry    : angle       0.79293 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: B  342 GLU cc_start: 0.7883 (mp0) cc_final: 0.7208 (mp0)
REVERT: B  345 ASP cc_start: 0.8628 (t0) cc_final: 0.8259 (t0)
REVERT: B  346 PHE cc_start: 0.8906 (m-80) cc_final: 0.7584 (p90)
REVERT: C  310 TYR cc_start: 0.6288 (t80) cc_final: 0.5826 (t80)
REVERT: C  336 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7306 (tp40)
REVERT: C  345 ASP cc_start: 0.8033 (m-30) cc_final: 0.7697 (m-30)
REVERT: C  346 PHE cc_start: 0.8647 (m-80) cc_final: 0.7814 (p90)
REVERT: D  311 LYS cc_start: 0.3458 (OUTLIER) cc_final: 0.2876 (pptt)
REVERT: D  372 GLU cc_start: 0.8170 (tt0) cc_final: 0.7492 (mp0)
REVERT: D  376 LEU cc_start: 0.8425 (tp) cc_final: 0.8126 (tt)
REVERT: E  308 ILE cc_start: 0.8984 (mt) cc_final: 0.8714 (mp)
REVERT: E  310 TYR cc_start: 0.6853 (t80) cc_final: 0.6148 (t80)
REVERT: E  369 LYS cc_start: 0.8422 (mttt) cc_final: 0.8156 (ttpt)
REVERT: E  372 GLU cc_start: 0.8245 (tt0) cc_final: 0.7693 (mp0)
REVERT: E  375 LYS cc_start: 0.8365 (tttt) cc_final: 0.8033 (tttm)
REVERT: F  310 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5808 (m-80)
REVERT: F  311 LYS cc_start: 0.3908 (OUTLIER) cc_final: 0.2908 (pptt)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1329
  time to fit residues: 17.8253
Evaluate side-chains
  112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  310 TYR
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  379 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 HIS
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 374 HIS
E 336 GLN
F 336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.116439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.098933 restraints weight = 8600.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.100952 restraints weight = 4293.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.102409 restraints weight = 2798.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.6842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3498  Z= 0.239
  Angle     :  0.862  14.488   4680  Z= 0.399
  Chirality :  0.051   0.140    528
  Planarity :  0.005   0.040    594
  Dihedral  :  6.628  50.168    468
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 28.28 %
    Favored  : 67.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.69 (0.29), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.22), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.023   0.002   PHE E 378 
 TYR   0.012   0.003   TYR D 310 
 ARG   0.004   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02095 (   36)
  hydrogen bonds       : angle       4.40679 (  108)
  covalent geometry    : bond        0.00504 ( 3498)
  covalent geometry    : angle       0.86173 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.415 
Fit side-chains
REVERT: B  342 GLU cc_start: 0.7819 (mp0) cc_final: 0.7155 (mp0)
REVERT: C  310 TYR cc_start: 0.6502 (t80) cc_final: 0.6148 (t80)
REVERT: C  336 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7254 (tp40)
REVERT: C  345 ASP cc_start: 0.8024 (m-30) cc_final: 0.7661 (m-30)
REVERT: C  346 PHE cc_start: 0.8654 (m-80) cc_final: 0.7816 (p90)
REVERT: D  310 TYR cc_start: 0.6902 (t80) cc_final: 0.6142 (m-80)
REVERT: D  311 LYS cc_start: 0.3525 (OUTLIER) cc_final: 0.2820 (pptt)
REVERT: D  372 GLU cc_start: 0.8298 (tt0) cc_final: 0.7595 (mp0)
REVERT: D  376 LEU cc_start: 0.8504 (tp) cc_final: 0.8178 (tp)
REVERT: E  308 ILE cc_start: 0.8925 (mt) cc_final: 0.8668 (mp)
REVERT: E  310 TYR cc_start: 0.6946 (t80) cc_final: 0.6344 (t80)
REVERT: E  336 GLN cc_start: 0.8155 (tm130) cc_final: 0.7824 (tm-30)
REVERT: E  369 LYS cc_start: 0.8379 (mttt) cc_final: 0.8148 (ttmt)
REVERT: E  372 GLU cc_start: 0.8301 (tt0) cc_final: 0.7652 (mp0)
REVERT: E  375 LYS cc_start: 0.8348 (tttt) cc_final: 0.7975 (tttm)
REVERT: F  310 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.5925 (m-80)
REVERT: F  311 LYS cc_start: 0.3607 (OUTLIER) cc_final: 0.2669 (pptt)
  outliers start: 17
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1237
  time to fit residues: 16.6948
Evaluate side-chains
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  310 TYR
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  379 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 8 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 40 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.118379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.100726 restraints weight = 8360.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.102724 restraints weight = 4257.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.104187 restraints weight = 2811.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.7093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3498  Z= 0.201
  Angle     :  0.874  14.437   4680  Z= 0.394
  Chirality :  0.052   0.143    528
  Planarity :  0.005   0.041    594
  Dihedral  :  6.553  50.947    468
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 29.04 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.68 (0.29), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.22), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.018   0.002   PHE D 378 
 TYR   0.010   0.002   TYR D 310 
 ARG   0.005   0.001   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01863 (   36)
  hydrogen bonds       : angle       4.34844 (  108)
  covalent geometry    : bond        0.00426 ( 3498)
  covalent geometry    : angle       0.87366 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.475 
Fit side-chains
REVERT: B  342 GLU cc_start: 0.7757 (mp0) cc_final: 0.7080 (mp0)
REVERT: B  345 ASP cc_start: 0.8716 (t0) cc_final: 0.8406 (t0)
REVERT: B  346 PHE cc_start: 0.9006 (m-80) cc_final: 0.7624 (p90)
REVERT: C  310 TYR cc_start: 0.6534 (t80) cc_final: 0.6207 (t80)
REVERT: C  336 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7158 (tp40)
REVERT: C  345 ASP cc_start: 0.7964 (m-30) cc_final: 0.7595 (m-30)
REVERT: C  346 PHE cc_start: 0.8709 (m-80) cc_final: 0.7858 (p90)
REVERT: D  310 TYR cc_start: 0.7021 (t80) cc_final: 0.6200 (m-80)
REVERT: D  311 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.2975 (pptt)
REVERT: D  372 GLU cc_start: 0.8116 (tt0) cc_final: 0.7447 (mp0)
REVERT: D  376 LEU cc_start: 0.8374 (tp) cc_final: 0.7968 (tp)
REVERT: E  308 ILE cc_start: 0.8851 (mt) cc_final: 0.8591 (mp)
REVERT: E  310 TYR cc_start: 0.6993 (t80) cc_final: 0.6395 (t80)
REVERT: E  369 LYS cc_start: 0.8225 (mttt) cc_final: 0.7964 (ttpt)
REVERT: E  372 GLU cc_start: 0.8233 (tt0) cc_final: 0.7469 (mp0)
REVERT: E  375 LYS cc_start: 0.8192 (tttt) cc_final: 0.7842 (tttm)
REVERT: F  310 TYR cc_start: 0.6373 (OUTLIER) cc_final: 0.5858 (m-80)
REVERT: F  311 LYS cc_start: 0.3573 (OUTLIER) cc_final: 0.2739 (pptt)
  outliers start: 16
  outliers final: 13
  residues processed: 104
  average time/residue: 0.1201
  time to fit residues: 16.0956
Evaluate side-chains
  109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  310 TYR
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    6.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.116855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.099083 restraints weight = 8527.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.101107 restraints weight = 4292.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.102557 restraints weight = 2808.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.7286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3498  Z= 0.223
  Angle     :  0.889  14.808   4680  Z= 0.407
  Chirality :  0.052   0.142    528
  Planarity :  0.005   0.043    594
  Dihedral  :  6.632  50.641    468
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 28.03 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.78 (0.29), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 330 
 PHE   0.022   0.002   PHE E 378 
 TYR   0.009   0.003   TYR D 310 
 ARG   0.005   0.001   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01976 (   36)
  hydrogen bonds       : angle       4.39141 (  108)
  covalent geometry    : bond        0.00473 ( 3498)
  covalent geometry    : angle       0.88908 ( 4680)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  378 PHE cc_start: 0.8309 (t80) cc_final: 0.7858 (t80)
REVERT: B  342 GLU cc_start: 0.7857 (mp0) cc_final: 0.7175 (mp0)
REVERT: B  345 ASP cc_start: 0.8759 (t0) cc_final: 0.8288 (t0)
REVERT: B  346 PHE cc_start: 0.8971 (m-80) cc_final: 0.7626 (p90)
REVERT: C  310 TYR cc_start: 0.6505 (t80) cc_final: 0.5831 (m-80)
REVERT: C  336 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7164 (tp40)
REVERT: C  345 ASP cc_start: 0.8024 (m-30) cc_final: 0.7646 (m-30)
REVERT: C  346 PHE cc_start: 0.8657 (m-80) cc_final: 0.7778 (p90)
REVERT: D  310 TYR cc_start: 0.6866 (t80) cc_final: 0.6044 (m-80)
REVERT: D  311 LYS cc_start: 0.3615 (OUTLIER) cc_final: 0.2977 (pptt)
REVERT: D  372 GLU cc_start: 0.8282 (tt0) cc_final: 0.7648 (mp0)
REVERT: D  376 LEU cc_start: 0.8519 (tp) cc_final: 0.7226 (tp)
REVERT: E  308 ILE cc_start: 0.8892 (mt) cc_final: 0.8592 (mp)
REVERT: E  310 TYR cc_start: 0.6834 (t80) cc_final: 0.5861 (m-80)
REVERT: E  369 LYS cc_start: 0.8377 (mttt) cc_final: 0.8100 (ttpt)
REVERT: E  372 GLU cc_start: 0.8260 (tt0) cc_final: 0.7476 (mp0)
REVERT: E  375 LYS cc_start: 0.8417 (tttt) cc_final: 0.8056 (tttm)
REVERT: F  310 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6054 (m-80)
REVERT: F  311 LYS cc_start: 0.3508 (OUTLIER) cc_final: 0.2593 (pptt)
  outliers start: 16
  outliers final: 13
  residues processed: 105
  average time/residue: 0.1198
  time to fit residues: 16.1765
Evaluate side-chains
  109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain F residue  310 TYR
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
Chi-restraints excluded: chain F residue  356 SER
Chi-restraints excluded: chain F residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 22 optimal weight:   20.0000
   chunk 40 optimal weight:    0.5980
   chunk 23 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    5.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.118475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.100694 restraints weight = 8457.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.102730 restraints weight = 4305.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.104147 restraints weight = 2826.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.7338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3498  Z= 0.190
  Angle     :  0.856  13.782   4680  Z= 0.389
  Chirality :  0.052   0.142    528
  Planarity :  0.005   0.041    594
  Dihedral  :  6.534  51.656    468
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 27.78 %
    Favored  : 68.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.76 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.018   0.001   PHE D 378 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.004   0.001   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01807 (   36)
  hydrogen bonds       : angle       4.36054 (  108)
  covalent geometry    : bond        0.00404 ( 3498)
  covalent geometry    : angle       0.85594 ( 4680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1550.02 seconds
wall clock time: 27 minutes 58.22 seconds (1678.22 seconds total)