Starting phenix.real_space_refine
on Fri May  9 18:56:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cax_16535/05_2025/8cax_16535.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cax_16535/05_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_16535/05_2025/8cax_16535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cax_16535/05_2025/8cax_16535.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cax_16535/05_2025/8cax_16535.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cax_16535/05_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-5687/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: 1.83, per 1000 atoms: 0.53
  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: 0.75
  Conformation dependent library (CDL) restraints added in 396.2 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: 0.52
  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: 0.72

  Time building geometry restraints manager: 0.89 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:             1.170
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     11.960
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.230
-------------------------------------------------------------------------------
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  : 0.427 
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: 0.2210
  time to fit residues: 47.2003
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  : 0.410 
-------------------------------------------------------------------------------
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:    3.9990
   overall best weight:    2.9994

-------------------------------------------------------------------------------
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 = 0.4358 r_free = 0.4358 target = 0.121477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.105196 restraints weight = 8078.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.107596 restraints weight = 3725.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.109343 restraints weight = 2290.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4491

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= 0.159
  Angle     :  0.727   6.477   4680  Z= 0.373
  Chirality :  0.050   0.134    528
  Planarity :  0.006   0.050    594
  Dihedral  :  7.133  45.235    476
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.70 %
    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   0.020   0.002   PHE E 346 
 TYR   0.014   0.002   TYR D 310 
 ARG   0.003   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01827 (   36)
  hydrogen bonds       : angle       4.59128 (  108)
  covalent geometry    : bond        0.00341 ( 3498)
  covalent geometry    : angle       0.72694 ( 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
  143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.9393 (tptm) cc_final: 0.8821 (mmtm)
REVERT: A  371 ILE cc_start: 0.8786 (mt) cc_final: 0.8529 (mp)
REVERT: B  342 GLU cc_start: 0.7883 (mp0) cc_final: 0.7663 (mp0)
REVERT: B  344 LEU cc_start: 0.9180 (mp) cc_final: 0.8963 (mp)
REVERT: B  345 ASP cc_start: 0.8337 (t0) cc_final: 0.8082 (t0)
REVERT: B  346 PHE cc_start: 0.8740 (m-80) cc_final: 0.7516 (p90)
REVERT: B  358 ASP cc_start: 0.8291 (m-30) cc_final: 0.7993 (t0)
REVERT: B  369 LYS cc_start: 0.7959 (mttt) cc_final: 0.7661 (ttmt)
REVERT: C  310 TYR cc_start: 0.6348 (t80) cc_final: 0.5703 (t80)
REVERT: C  336 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7416 (tp40)
REVERT: C  345 ASP cc_start: 0.8058 (m-30) cc_final: 0.7742 (m-30)
REVERT: C  346 PHE cc_start: 0.8617 (m-80) cc_final: 0.7527 (p90)
REVERT: C  371 ILE cc_start: 0.8649 (mt) cc_final: 0.8194 (mp)
REVERT: D  331 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8763 (ttmt)
REVERT: D  372 GLU cc_start: 0.7975 (tt0) cc_final: 0.7296 (mp0)
REVERT: D  376 LEU cc_start: 0.8331 (tp) cc_final: 0.7743 (tt)
REVERT: E  308 ILE cc_start: 0.9047 (mt) cc_final: 0.8814 (mp)
REVERT: E  310 TYR cc_start: 0.6893 (t80) cc_final: 0.6071 (t80)
REVERT: E  369 LYS cc_start: 0.8074 (mttt) cc_final: 0.7735 (ttpt)
REVERT: E  372 GLU cc_start: 0.8282 (tt0) cc_final: 0.7649 (mp0)
REVERT: E  375 LYS cc_start: 0.8549 (tttt) cc_final: 0.8265 (tttm)
REVERT: F  376 LEU cc_start: 0.8443 (tp) cc_final: 0.8168 (tt)
  outliers start: 15
  outliers final: 11
  residues processed: 136
  average time/residue: 0.1707
  time to fit residues: 27.5595
Evaluate side-chains
  113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
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  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:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   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:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    7.7590

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.116448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.099566 restraints weight = 8465.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.101698 restraints weight = 4054.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.103344 restraints weight = 2623.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.5279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   3498  Z= 0.272
  Angle     :  0.816  10.691   4680  Z= 0.404
  Chirality :  0.051   0.137    528
  Planarity :  0.006   0.046    594
  Dihedral  :  6.760  45.075    468
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 20.45 %
    Favored  : 75.51 %
  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: -3.28 (0.26), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.20), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS C 330 
 PHE   0.015   0.001   PHE E 378 
 TYR   0.016   0.004   TYR A 310 
 ARG   0.003   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02364 (   36)
  hydrogen bonds       : angle       4.46163 (  108)
  covalent geometry    : bond        0.00577 ( 3498)
  covalent geometry    : angle       0.81596 ( 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
  118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 ILE cc_start: 0.8820 (mt) cc_final: 0.8490 (mp)
REVERT: B  342 GLU cc_start: 0.7720 (mp0) cc_final: 0.7074 (mp0)
REVERT: B  344 LEU cc_start: 0.9294 (mp) cc_final: 0.8929 (mp)
REVERT: B  345 ASP cc_start: 0.8490 (t0) cc_final: 0.8212 (t0)
REVERT: B  346 PHE cc_start: 0.8905 (m-80) cc_final: 0.7693 (p90)
REVERT: C  310 TYR cc_start: 0.6431 (t80) cc_final: 0.5871 (t80)
REVERT: C  336 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7283 (tp40)
REVERT: C  345 ASP cc_start: 0.7984 (m-30) cc_final: 0.7611 (m-30)
REVERT: C  346 PHE cc_start: 0.8676 (m-80) cc_final: 0.7746 (p90)
REVERT: C  371 ILE cc_start: 0.8592 (mt) cc_final: 0.8002 (mp)
REVERT: D  372 GLU cc_start: 0.8140 (tt0) cc_final: 0.7432 (mp0)
REVERT: D  375 LYS cc_start: 0.8887 (tttm) cc_final: 0.8620 (tttm)
REVERT: D  376 LEU cc_start: 0.8298 (tp) cc_final: 0.8004 (tt)
REVERT: E  308 ILE cc_start: 0.8943 (mt) cc_final: 0.8652 (mp)
REVERT: E  369 LYS cc_start: 0.8186 (mttt) cc_final: 0.7968 (ttmt)
REVERT: E  372 GLU cc_start: 0.8356 (tt0) cc_final: 0.7583 (mp0)
REVERT: E  375 LYS cc_start: 0.8479 (tttt) cc_final: 0.8188 (tttm)
REVERT: E  376 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7873 (mt)
REVERT: F  310 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.5941 (m-80)
REVERT: F  376 LEU cc_start: 0.8335 (tp) cc_final: 0.8067 (tp)
  outliers start: 16
  outliers final: 12
  residues processed: 114
  average time/residue: 0.1272
  time to fit residues: 18.2787
Evaluate side-chains
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  318 VAL
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 E residue  376 LEU
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  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0030
   chunk 7 optimal weight:    0.0060
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.1008

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.117338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.101117 restraints weight = 8422.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.103181 restraints weight = 4147.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.104704 restraints weight = 2636.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.5689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3498  Z= 0.106
  Angle     :  0.739  13.709   4680  Z= 0.331
  Chirality :  0.049   0.131    528
  Planarity :  0.005   0.047    594
  Dihedral  :  6.127  51.458    468
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 21.46 %
    Favored  : 75.76 %
  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: -2.80 (0.28), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.21), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.020   0.001   PHE D 378 
 TYR   0.013   0.002   TYR B 310 
 ARG   0.001   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01231 (   36)
  hydrogen bonds       : angle       4.09331 (  108)
  covalent geometry    : bond        0.00218 ( 3498)
  covalent geometry    : angle       0.73879 ( 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
  125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LYS cc_start: 0.9119 (tptm) cc_final: 0.8532 (tppt)
REVERT: A  371 ILE cc_start: 0.8619 (mt) cc_final: 0.8300 (mp)
REVERT: B  345 ASP cc_start: 0.8482 (t0) cc_final: 0.8277 (t0)
REVERT: B  346 PHE cc_start: 0.8946 (m-80) cc_final: 0.7516 (p90)
REVERT: C  310 TYR cc_start: 0.6027 (t80) cc_final: 0.5382 (t80)
REVERT: C  336 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7176 (tp40)
REVERT: C  345 ASP cc_start: 0.8093 (m-30) cc_final: 0.7631 (t0)
REVERT: C  346 PHE cc_start: 0.8700 (m-80) cc_final: 0.7829 (p90)
REVERT: D  331 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8826 (ttmt)
REVERT: D  372 GLU cc_start: 0.7863 (tt0) cc_final: 0.7222 (mp0)
REVERT: D  376 LEU cc_start: 0.8113 (tp) cc_final: 0.7631 (tt)
REVERT: E  308 ILE cc_start: 0.8817 (mt) cc_final: 0.8595 (mp)
REVERT: E  336 GLN cc_start: 0.7874 (tm130) cc_final: 0.7544 (tm-30)
REVERT: E  369 LYS cc_start: 0.8024 (mttt) cc_final: 0.7743 (ttpt)
REVERT: E  372 GLU cc_start: 0.8151 (tt0) cc_final: 0.7449 (mp0)
REVERT: E  376 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8046 (mt)
REVERT: F  336 GLN cc_start: 0.7670 (tm130) cc_final: 0.7346 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 121
  average time/residue: 0.1432
  time to fit residues: 21.1617
Evaluate side-chains
  103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
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 E residue  376 LEU
Chi-restraints excluded: chain F residue  311 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 7 optimal weight:   40.0000
   chunk 15 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 1 optimal weight:   30.0000
   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**
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 359 ASN
D 359 ASN
** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4327 r_free = 0.4327 target = 0.116972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.099037 restraints weight = 8317.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.101091 restraints weight = 4204.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.102658 restraints weight = 2750.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.6081

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= 0.247
  Angle     :  0.846  14.737   4680  Z= 0.392
  Chirality :  0.050   0.135    528
  Planarity :  0.005   0.040    594
  Dihedral  :  6.511  49.084    468
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 26.52 %
    Favored  : 70.71 %
  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 (0.28), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.21), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS C 330 
 PHE   0.024   0.003   PHE E 378 
 TYR   0.012   0.003   TYR A 310 
 ARG   0.004   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02163 (   36)
  hydrogen bonds       : angle       4.55987 (  108)
  covalent geometry    : bond        0.00522 ( 3498)
  covalent geometry    : angle       0.84576 ( 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
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  342 GLU cc_start: 0.7763 (mp0) cc_final: 0.7109 (mp0)
REVERT: B  344 LEU cc_start: 0.9319 (mp) cc_final: 0.8909 (mp)
REVERT: B  345 ASP cc_start: 0.8478 (t0) cc_final: 0.8055 (t0)
REVERT: B  346 PHE cc_start: 0.8957 (m-80) cc_final: 0.7754 (p90)
REVERT: C  310 TYR cc_start: 0.6578 (t80) cc_final: 0.6015 (t80)
REVERT: C  336 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7281 (tp40)
REVERT: C  345 ASP cc_start: 0.8009 (m-30) cc_final: 0.7592 (m-30)
REVERT: C  346 PHE cc_start: 0.8663 (m-80) cc_final: 0.7737 (p90)
REVERT: D  311 LYS cc_start: 0.3284 (OUTLIER) cc_final: 0.2668 (pptt)
REVERT: D  372 GLU cc_start: 0.8227 (tt0) cc_final: 0.7602 (mp0)
REVERT: D  376 LEU cc_start: 0.8205 (tp) cc_final: 0.7830 (tt)
REVERT: E  308 ILE cc_start: 0.8870 (mt) cc_final: 0.8653 (mp)
REVERT: E  372 GLU cc_start: 0.8331 (tt0) cc_final: 0.7622 (mp0)
REVERT: F  376 LEU cc_start: 0.8160 (tp) cc_final: 0.7386 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 108
  average time/residue: 0.1070
  time to fit residues: 14.9450
Evaluate side-chains
  101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 7 optimal weight:   30.0000
   chunk 27 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    3.5188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.120058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.101692 restraints weight = 8259.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.103908 restraints weight = 4087.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.105405 restraints weight = 2638.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.6404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3498  Z= 0.148
  Angle     :  0.786  14.704   4680  Z= 0.354
  Chirality :  0.050   0.136    528
  Planarity :  0.005   0.042    594
  Dihedral  :  6.250  51.730    468
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 26.26 %
    Favored  : 69.95 %
  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: -2.47 (0.29), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.22), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.020   0.002   PHE F 346 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.005   0.001   ARG D 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01620 (   36)
  hydrogen bonds       : angle       4.40782 (  108)
  covalent geometry    : bond        0.00313 ( 3498)
  covalent geometry    : angle       0.78562 ( 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
  114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  342 GLU cc_start: 0.7864 (mp0) cc_final: 0.7211 (mp0)
REVERT: B  344 LEU cc_start: 0.9277 (mp) cc_final: 0.8864 (mp)
REVERT: B  345 ASP cc_start: 0.8562 (t0) cc_final: 0.8214 (t0)
REVERT: B  346 PHE cc_start: 0.8939 (m-80) cc_final: 0.7574 (p90)
REVERT: C  310 TYR cc_start: 0.6256 (t80) cc_final: 0.5741 (t80)
REVERT: C  336 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7239 (tp40)
REVERT: C  345 ASP cc_start: 0.8066 (m-30) cc_final: 0.7682 (m-30)
REVERT: C  346 PHE cc_start: 0.8642 (m-80) cc_final: 0.7754 (p90)
REVERT: D  311 LYS cc_start: 0.3497 (OUTLIER) cc_final: 0.2950 (pptt)
REVERT: D  372 GLU cc_start: 0.8151 (tt0) cc_final: 0.7505 (mp0)
REVERT: D  376 LEU cc_start: 0.8290 (tp) cc_final: 0.7927 (tt)
REVERT: E  308 ILE cc_start: 0.8868 (mt) cc_final: 0.8645 (mp)
REVERT: E  336 GLN cc_start: 0.7951 (tm130) cc_final: 0.7628 (tm-30)
REVERT: E  372 GLU cc_start: 0.8286 (tt0) cc_final: 0.7686 (mp0)
REVERT: E  376 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7567 (mp)
REVERT: F  328 ILE cc_start: 0.8799 (mm) cc_final: 0.8597 (mp)
REVERT: F  376 LEU cc_start: 0.8366 (tp) cc_final: 0.7596 (mt)
  outliers start: 15
  outliers final: 11
  residues processed: 111
  average time/residue: 0.1041
  time to fit residues: 15.0667
Evaluate side-chains
  105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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 E residue  376 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0570
   chunk 16 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0670
   chunk 3 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    3.6242

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.121953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.105344 restraints weight = 8566.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.107652 restraints weight = 4141.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.109315 restraints weight = 2632.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.6591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3498  Z= 0.146
  Angle     :  0.777  14.126   4680  Z= 0.351
  Chirality :  0.050   0.136    528
  Planarity :  0.004   0.039    594
  Dihedral  :  6.198  53.677    468
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 26.01 %
    Favored  : 70.96 %
  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: -2.32 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.021   0.002   PHE E 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        0.01634 (   36)
  hydrogen bonds       : angle       4.34447 (  108)
  covalent geometry    : bond        0.00310 ( 3498)
  covalent geometry    : angle       0.77682 ( 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
  112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  342 GLU cc_start: 0.7914 (mp0) cc_final: 0.7263 (mp0)
REVERT: B  344 LEU cc_start: 0.9244 (mp) cc_final: 0.8814 (mp)
REVERT: B  345 ASP cc_start: 0.8602 (t0) cc_final: 0.8255 (t0)
REVERT: B  346 PHE cc_start: 0.8952 (m-80) cc_final: 0.7593 (p90)
REVERT: C  310 TYR cc_start: 0.6185 (t80) cc_final: 0.5687 (t80)
REVERT: C  336 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7337 (tp40)
REVERT: C  345 ASP cc_start: 0.8088 (m-30) cc_final: 0.7708 (m-30)
REVERT: C  346 PHE cc_start: 0.8585 (m-80) cc_final: 0.7712 (p90)
REVERT: D  311 LYS cc_start: 0.3512 (OUTLIER) cc_final: 0.2977 (pptt)
REVERT: D  372 GLU cc_start: 0.8104 (tt0) cc_final: 0.7426 (mp0)
REVERT: D  376 LEU cc_start: 0.8339 (tp) cc_final: 0.8070 (tt)
REVERT: E  308 ILE cc_start: 0.8894 (mt) cc_final: 0.8665 (mp)
REVERT: E  336 GLN cc_start: 0.7802 (tm130) cc_final: 0.7568 (tm-30)
REVERT: E  372 GLU cc_start: 0.8235 (tt0) cc_final: 0.7673 (mp0)
REVERT: E  376 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7587 (mp)
REVERT: F  328 ILE cc_start: 0.8744 (mm) cc_final: 0.8541 (mp)
  outliers start: 12
  outliers final: 10
  residues processed: 108
  average time/residue: 0.1054
  time to fit residues: 14.6553
Evaluate side-chains
  105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 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 E residue  376 LEU
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
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:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.118537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.100500 restraints weight = 8350.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.102594 restraints weight = 4146.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.104152 restraints weight = 2698.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.6712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3498  Z= 0.174
  Angle     :  0.799  14.416   4680  Z= 0.363
  Chirality :  0.050   0.136    528
  Planarity :  0.005   0.036    594
  Dihedral  :  6.320  52.900    468
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 26.26 %
    Favored  : 70.45 %
  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: -2.28 (0.30), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.23), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.022   0.001   PHE D 378 
 TYR   0.008   0.002   TYR A 310 
 ARG   0.004   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01794 (   36)
  hydrogen bonds       : angle       4.37828 (  108)
  covalent geometry    : bond        0.00368 ( 3498)
  covalent geometry    : angle       0.79937 ( 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
  110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  342 GLU cc_start: 0.7875 (mp0) cc_final: 0.7226 (mp0)
REVERT: B  345 ASP cc_start: 0.8591 (t0) cc_final: 0.8231 (t0)
REVERT: B  346 PHE cc_start: 0.8967 (m-80) cc_final: 0.7624 (p90)
REVERT: C  310 TYR cc_start: 0.6328 (t80) cc_final: 0.5783 (t80)
REVERT: C  336 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7215 (tp40)
REVERT: C  345 ASP cc_start: 0.8071 (m-30) cc_final: 0.7701 (m-30)
REVERT: C  346 PHE cc_start: 0.8663 (m-80) cc_final: 0.7814 (p90)
REVERT: D  311 LYS cc_start: 0.3441 (OUTLIER) cc_final: 0.2858 (pptt)
REVERT: D  372 GLU cc_start: 0.8114 (tt0) cc_final: 0.7418 (mp0)
REVERT: D  376 LEU cc_start: 0.8270 (tp) cc_final: 0.7987 (tt)
REVERT: E  308 ILE cc_start: 0.8808 (mt) cc_final: 0.8580 (mp)
REVERT: E  336 GLN cc_start: 0.7707 (tm130) cc_final: 0.7481 (tm-30)
REVERT: E  372 GLU cc_start: 0.8219 (tt0) cc_final: 0.7554 (mp0)
REVERT: E  376 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7486 (mp)
REVERT: F  311 LYS cc_start: 0.3692 (OUTLIER) cc_final: 0.2946 (pptt)
REVERT: F  328 ILE cc_start: 0.8687 (mm) cc_final: 0.8484 (mp)
  outliers start: 13
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1312
  time to fit residues: 17.9926
Evaluate side-chains
  107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
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 E residue  376 LEU
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
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:   30.0000
   chunk 8 optimal weight:   30.0000
   chunk 27 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 14 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.9188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.119707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.101495 restraints weight = 8077.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.103659 restraints weight = 4031.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.105235 restraints weight = 2625.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.6873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3498  Z= 0.130
  Angle     :  0.795  14.731   4680  Z= 0.352
  Chirality :  0.050   0.139    528
  Planarity :  0.004   0.037    594
  Dihedral  :  6.134  53.724    468
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 27.02 %
    Favored  : 69.70 %
  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: -2.17 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.022   0.002   PHE E 378 
 TYR   0.006   0.002   TYR A 310 
 ARG   0.003   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01510 (   36)
  hydrogen bonds       : angle       4.24994 (  108)
  covalent geometry    : bond        0.00277 ( 3498)
  covalent geometry    : angle       0.79530 ( 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
  109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7470 (mp0)
REVERT: B  342 GLU cc_start: 0.8010 (mp0) cc_final: 0.7396 (mp0)
REVERT: B  345 ASP cc_start: 0.8634 (t0) cc_final: 0.8276 (t0)
REVERT: B  346 PHE cc_start: 0.8930 (m-80) cc_final: 0.7530 (p90)
REVERT: C  310 TYR cc_start: 0.6140 (t80) cc_final: 0.5684 (t80)
REVERT: C  336 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7333 (tp40)
REVERT: C  345 ASP cc_start: 0.8021 (m-30) cc_final: 0.7664 (m-30)
REVERT: C  346 PHE cc_start: 0.8614 (m-80) cc_final: 0.7777 (p90)
REVERT: C  372 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7656 (mp0)
REVERT: D  311 LYS cc_start: 0.3613 (OUTLIER) cc_final: 0.3054 (pptt)
REVERT: D  372 GLU cc_start: 0.8123 (tt0) cc_final: 0.7548 (mp0)
REVERT: D  376 LEU cc_start: 0.8399 (tp) cc_final: 0.8110 (tt)
REVERT: E  308 ILE cc_start: 0.8854 (mt) cc_final: 0.8617 (mp)
REVERT: E  336 GLN cc_start: 0.7889 (tm130) cc_final: 0.7635 (tm-30)
REVERT: E  372 GLU cc_start: 0.8242 (tt0) cc_final: 0.7624 (mp0)
REVERT: E  376 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7563 (mp)
REVERT: F  311 LYS cc_start: 0.3880 (OUTLIER) cc_final: 0.3161 (pptt)
  outliers start: 13
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1121
  time to fit residues: 15.1145
Evaluate side-chains
  106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
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 E residue  376 LEU
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
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:    1.9990
   chunk 8 optimal weight:   30.0000
   chunk 32 optimal weight:   20.0000
   chunk 23 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 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**
D 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.120022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.103839 restraints weight = 8934.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.106040 restraints weight = 4331.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.107411 restraints weight = 2755.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.6946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3498  Z= 0.211
  Angle     :  0.845  14.689   4680  Z= 0.383
  Chirality :  0.050   0.138    528
  Planarity :  0.005   0.039    594
  Dihedral  :  6.364  51.955    468
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 27.27 %
    Favored  : 69.44 %
  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: -2.25 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C 330 
 PHE   0.023   0.002   PHE F 378 
 TYR   0.010   0.003   TYR F 310 
 ARG   0.004   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01877 (   36)
  hydrogen bonds       : angle       4.40505 (  108)
  covalent geometry    : bond        0.00445 ( 3498)
  covalent geometry    : angle       0.84476 ( 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
  105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: A  372 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7298 (mp0)
REVERT: A  378 PHE cc_start: 0.8349 (t80) cc_final: 0.7749 (t80)
REVERT: B  342 GLU cc_start: 0.7718 (mp0) cc_final: 0.7078 (mp0)
REVERT: C  310 TYR cc_start: 0.6423 (t80) cc_final: 0.5932 (t80)
REVERT: C  336 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7213 (tp40)
REVERT: C  345 ASP cc_start: 0.7931 (m-30) cc_final: 0.7544 (m-30)
REVERT: C  346 PHE cc_start: 0.8644 (m-80) cc_final: 0.7768 (p90)
REVERT: D  311 LYS cc_start: 0.3391 (OUTLIER) cc_final: 0.2874 (pptt)
REVERT: D  372 GLU cc_start: 0.8241 (tt0) cc_final: 0.7450 (mp0)
REVERT: D  376 LEU cc_start: 0.8209 (tp) cc_final: 0.7880 (tt)
REVERT: E  336 GLN cc_start: 0.7489 (tm130) cc_final: 0.7251 (tm-30)
REVERT: E  372 GLU cc_start: 0.8228 (tt0) cc_final: 0.7358 (mp0)
REVERT: E  376 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7914 (mt)
REVERT: F  311 LYS cc_start: 0.3416 (OUTLIER) cc_final: 0.2744 (pptt)
  outliers start: 13
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1187
  time to fit residues: 15.4278
Evaluate side-chains
  102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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 E residue  376 LEU
Chi-restraints excluded: chain F residue  311 LYS
Chi-restraints excluded: chain F residue  318 VAL
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:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:    0.3980
   chunk 16 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   overall best weight:    4.2788

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.114493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.097852 restraints weight = 8833.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.100100 restraints weight = 4235.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.101738 restraints weight = 2672.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.7174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3498  Z= 0.166
  Angle     :  0.842  14.791   4680  Z= 0.377
  Chirality :  0.050   0.142    528
  Planarity :  0.005   0.039    594
  Dihedral  :  6.307  51.978    468
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 27.78 %
    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: -2.26 (0.31), residues: 438
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.24), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 330 
 PHE   0.024   0.002   PHE E 378 
 TYR   0.007   0.002   TYR A 310 
 ARG   0.006   0.001   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01737 (   36)
  hydrogen bonds       : angle       4.24927 (  108)
  covalent geometry    : bond        0.00354 ( 3498)
  covalent geometry    : angle       0.84232 ( 4680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1493.53 seconds
wall clock time: 27 minutes 15.28 seconds (1635.28 seconds total)