Starting phenix.real_space_refine
on Tue Feb 11 11:14:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ic3_4452/02_2025/6ic3_4452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ic3_4452/02_2025/6ic3_4452.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ic3_4452/02_2025/6ic3_4452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ic3_4452/02_2025/6ic3_4452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ic3_4452/02_2025/6ic3_4452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ic3_4452/02_2025/6ic3_4452.cif"
  }
  resolution = 3.3
  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=   0.002
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      16      5.16       5
     C    3400      2.51       5
     N     968      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 684
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
  Restraints were copied for chains:
    C, B, E, D, G, F, H
  Time building chain proxies: 2.47, per 1000 atoms: 0.45
  Number of scatterers: 5472
  At special positions: 0
  Unit cell: (79.116, 92.649, 56.214, 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      16     16.00
     O    1088      8.00
     N     968      7.00
     C    3400      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  89 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 689.4 milliseconds
  

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1280

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27
      removed outlier: 8.197A  pdb=" N   ARG A  25 " --> pdb=" O   SER B  26 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   ARG B  25 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
      removed outlier: 8.155A  pdb=" N   ARG C  25 " --> pdb=" O   SER D  26 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   ARG D  25 " --> pdb=" O   SER E  26 " (cutoff:3.500A)
      removed outlier: 8.224A  pdb=" N   ARG E  25 " --> pdb=" O   SER F  26 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   ARG F  25 " --> pdb=" O   SER G  26 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   ARG G  25 " --> pdb=" O   SER H  26 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43
    Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 49
      removed outlier: 6.231A  pdb=" N   LEU A  47 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LEU B  47 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   LEU C  47 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   LEU D  47 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   LEU E  47 " --> pdb=" O   LEU F  48 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LEU F  47 " --> pdb=" O   LEU G  48 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   LEU G  47 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 63
    Processing sheet with id=AA6, first strand: chain 'A' and resid 82 through 83
      removed outlier: 6.628A  pdb=" N   GLU A  82 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   GLU B  82 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 94 through 95
      removed outlier: 6.819A  pdb=" N   ALA A  94 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ALA B  94 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ALA C  94 " --> pdb=" O   THR D  95 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA D  94 " --> pdb=" O   THR E  95 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ALA E  94 " --> pdb=" O   THR F  95 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ALA F  94 " --> pdb=" O   THR G  95 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ALA G  94 " --> pdb=" O   THR H  95 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35
    Processing sheet with id=AA9, first strand: chain 'D' and resid 82 through 83
      removed outlier: 6.641A  pdb=" N   GLU D  82 " --> pdb=" O   ASP E  83 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLU E  82 " --> pdb=" O   ASP F  83 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   GLU F  82 " --> pdb=" O   ASP G  83 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 33 through 35

    32 hydrogen bonds defined for protein.
    96 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1755
        1.33 -     1.45: 885
        1.45 -     1.56: 2944
        1.56 -     1.68: 0
        1.68 -     1.79: 16
  Bond restraints: 5600
  Sorted by residual:
  bond pdb=" CB  TYR H  88 "
       pdb=" CG  TYR H  88 "
    ideal  model  delta    sigma   weight residual
    1.512  1.476  0.036 2.20e-02 2.07e+03 2.61e+00
  bond pdb=" CB  TYR C  88 "
       pdb=" CG  TYR C  88 "
    ideal  model  delta    sigma   weight residual
    1.512  1.477  0.035 2.20e-02 2.07e+03 2.60e+00
  bond pdb=" CB  TYR E  88 "
       pdb=" CG  TYR E  88 "
    ideal  model  delta    sigma   weight residual
    1.512  1.477  0.035 2.20e-02 2.07e+03 2.58e+00
  bond pdb=" CB  TYR F  88 "
       pdb=" CG  TYR F  88 "
    ideal  model  delta    sigma   weight residual
    1.512  1.477  0.035 2.20e-02 2.07e+03 2.57e+00
  bond pdb=" CB  TYR A  88 "
       pdb=" CG  TYR A  88 "
    ideal  model  delta    sigma   weight residual
    1.512  1.477  0.035 2.20e-02 2.07e+03 2.55e+00
  ... (remaining 5595 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 6823
        1.79 -     3.58: 589
        3.58 -     5.37: 132
        5.37 -     7.17: 24
        7.17 -     8.96: 32
  Bond angle restraints: 7600
  Sorted by residual:
  angle pdb=" N   PHE C  40 "
        pdb=" CA  PHE C  40 "
        pdb=" C   PHE C  40 "
      ideal   model   delta    sigma   weight residual
     109.81  118.43   -8.62 2.21e+00 2.05e-01 1.52e+01
  angle pdb=" N   PHE F  40 "
        pdb=" CA  PHE F  40 "
        pdb=" C   PHE F  40 "
      ideal   model   delta    sigma   weight residual
     109.81  118.43   -8.62 2.21e+00 2.05e-01 1.52e+01
  angle pdb=" N   PHE G  40 "
        pdb=" CA  PHE G  40 "
        pdb=" C   PHE G  40 "
      ideal   model   delta    sigma   weight residual
     109.81  118.41   -8.60 2.21e+00 2.05e-01 1.52e+01
  angle pdb=" N   PHE H  40 "
        pdb=" CA  PHE H  40 "
        pdb=" C   PHE H  40 "
      ideal   model   delta    sigma   weight residual
     109.81  118.40   -8.59 2.21e+00 2.05e-01 1.51e+01
  angle pdb=" N   PHE E  40 "
        pdb=" CA  PHE E  40 "
        pdb=" C   PHE E  40 "
      ideal   model   delta    sigma   weight residual
     109.81  118.39   -8.58 2.21e+00 2.05e-01 1.51e+01
  ... (remaining 7595 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.57: 2512
       11.57 -    23.15: 440
       23.15 -    34.72: 160
       34.72 -    46.29: 107
       46.29 -    57.87: 24
  Dihedral angle restraints: 3243
    sinusoidal: 1211
      harmonic: 2032
  Sorted by residual:
  dihedral pdb=" CA  THR A  70 "
           pdb=" C   THR A  70 "
           pdb=" N   SER A  71 "
           pdb=" CA  SER A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.47  -23.53     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  THR E  70 "
           pdb=" C   THR E  70 "
           pdb=" N   SER E  71 "
           pdb=" CA  SER E  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.48  -23.52     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  THR G  70 "
           pdb=" C   THR G  70 "
           pdb=" N   SER G  71 "
           pdb=" CA  SER G  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.48  -23.52     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 3240 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 324
       0.026 -    0.051: 195
       0.051 -    0.077: 125
       0.077 -    0.103: 81
       0.103 -    0.128: 67
  Chirality restraints: 792
  Sorted by residual:
  chirality pdb=" CG  LEU C  96 "
            pdb=" CB  LEU C  96 "
            pdb=" CD1 LEU C  96 "
            pdb=" CD2 LEU C  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  VAL G 100 "
            pdb=" N   VAL G 100 "
            pdb=" C   VAL G 100 "
            pdb=" CB  VAL G 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CG  LEU F  96 "
            pdb=" CB  LEU F  96 "
            pdb=" CD1 LEU F  96 "
            pdb=" CD2 LEU F  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 789 not shown)

  Planarity restraints: 1000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F  99 "    0.022 2.00e-02 2.50e+03   1.59e-02 6.35e+00
        pdb=" CG  TRP F  99 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP F  99 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP F  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP F  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP F  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP F  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F  99 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP F  99 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  99 "    0.022 2.00e-02 2.50e+03   1.59e-02 6.32e+00
        pdb=" CG  TRP H  99 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  99 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  99 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  99 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  99 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  99 "    0.022 2.00e-02 2.50e+03   1.58e-02 6.25e+00
        pdb=" CG  TRP B  99 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  99 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  99 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  99 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  99 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  99 "    0.003 2.00e-02 2.50e+03
  ... (remaining 997 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 131
        2.59 -     3.17: 4242
        3.17 -     3.75: 8910
        3.75 -     4.32: 11586
        4.32 -     4.90: 23154
  Nonbonded interactions: 48023
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B  22 "
            pdb=" SG  CYS B  89 "
     model   vdw
     2.017 3.760
  nonbonded pdb=" SG  CYS H  22 "
            pdb=" SG  CYS H  89 "
     model   vdw
     2.017 3.760
  nonbonded pdb=" SG  CYS C  22 "
            pdb=" SG  CYS C  89 "
     model   vdw
     2.018 3.760
  nonbonded pdb=" SG  CYS G  22 "
            pdb=" SG  CYS G  89 "
     model   vdw
     2.018 3.760
  nonbonded pdb=" SG  CYS D  22 "
            pdb=" SG  CYS D  89 "
     model   vdw
     2.018 3.760
  ... (remaining 48018 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'H'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.540
  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:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     14.830
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
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      :  0.010   0.043   5600  Z= 0.659
  Angle     :  1.262   8.957   7600  Z= 0.668
  Chirality :  0.056   0.128    792
  Planarity :  0.009   0.051   1000
  Dihedral  : 16.173  57.866   1960
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.85 %
    Favored  : 83.15 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.11 %
    Favored  : 87.50 %
  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: -5.61 (0.19), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.27 (0.15), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.006   TRP F  99 
 PHE   0.020   0.005   PHE E  63 
 TYR   0.013   0.003   TYR D  50 
 ARG   0.001   0.000   ARG B  55 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 227
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8805 (mttt) cc_final: 0.8293 (mtpt)
REVERT: A   36 TRP cc_start: 0.8826 (t-100) cc_final: 0.8563 (t-100)
REVERT: A   80 GLN cc_start: 0.8796 (tt0) cc_final: 0.8535 (tt0)
REVERT: B   35 LYS cc_start: 0.8338 (mttt) cc_final: 0.7694 (ttmm)
REVERT: B   36 TRP cc_start: 0.8876 (t-100) cc_final: 0.8423 (t-100)
REVERT: B   37 TYR cc_start: 0.8376 (t80) cc_final: 0.7268 (t80)
REVERT: B   50 TYR cc_start: 0.8478 (t80) cc_final: 0.8157 (t80)
REVERT: B   80 GLN cc_start: 0.8619 (tt0) cc_final: 0.8009 (tt0)
REVERT: C   40 PHE cc_start: 0.8537 (m-80) cc_final: 0.8273 (m-10)
REVERT: C   46 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8809 (ptpt)
REVERT: D   53 ASP cc_start: 0.8613 (p0) cc_final: 0.7869 (p0)
REVERT: D   80 GLN cc_start: 0.8757 (tt0) cc_final: 0.8274 (tt0)
REVERT: D   82 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8006 (mt-10)
REVERT: D   87 TYR cc_start: 0.8378 (t80) cc_final: 0.8068 (t80)
REVERT: E   36 TRP cc_start: 0.8881 (t-100) cc_final: 0.8388 (t-100)
REVERT: E   46 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8613 (ptpp)
REVERT: E   80 GLN cc_start: 0.8605 (tt0) cc_final: 0.7975 (tt0)
REVERT: E   87 TYR cc_start: 0.8327 (t80) cc_final: 0.8095 (t80)
REVERT: F   36 TRP cc_start: 0.8781 (t-100) cc_final: 0.8530 (t-100)
REVERT: F   50 TYR cc_start: 0.8498 (t80) cc_final: 0.8186 (t80)
REVERT: G   40 PHE cc_start: 0.8521 (m-80) cc_final: 0.8290 (m-10)
REVERT: G   46 LYS cc_start: 0.8945 (ptpt) cc_final: 0.8676 (ptpp)
REVERT: G   80 GLN cc_start: 0.8735 (tt0) cc_final: 0.8205 (tm-30)
REVERT: G   82 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7842 (mt-10)
REVERT: G   84 GLU cc_start: 0.8245 (mp0) cc_final: 0.8018 (mp0)
REVERT: G   87 TYR cc_start: 0.8457 (t80) cc_final: 0.8169 (t80)
REVERT: H   46 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8781 (ptpt)
  outliers start: 8
  outliers final: 3
  residues processed: 235
  average time/residue: 0.2309
  time to fit residues: 65.5469
Evaluate side-chains
  190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 187
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain G residue   70 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4167 r_free = 0.4167 target = 0.090647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.080095 restraints weight = 15461.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 4.18
r_work: 0.3753 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5600  Z= 0.298
  Angle     :  0.828   8.062   7600  Z= 0.400
  Chirality :  0.044   0.135    792
  Planarity :  0.008   0.060   1000
  Dihedral  :  6.557  29.586    795
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.57 %
    Favored  : 73.96 %
  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: -5.31 (0.20), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.04 (0.15), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  99 
 PHE   0.011   0.003   PHE D 101 
 TYR   0.018   0.002   TYR A  88 
 ARG   0.009   0.001   ARG A  55 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 196
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8320 (tp)
REVERT: A   35 LYS cc_start: 0.8727 (mttt) cc_final: 0.8176 (mtpt)
REVERT: A   36 TRP cc_start: 0.8922 (t-100) cc_final: 0.8283 (t-100)
REVERT: A   53 ASP cc_start: 0.8895 (p0) cc_final: 0.8083 (p0)
REVERT: B   36 TRP cc_start: 0.8872 (t-100) cc_final: 0.8061 (t-100)
REVERT: B   53 ASP cc_start: 0.8736 (p0) cc_final: 0.7542 (p0)
REVERT: B   80 GLN cc_start: 0.8856 (tt0) cc_final: 0.8364 (tt0)
REVERT: B   84 GLU cc_start: 0.8073 (mp0) cc_final: 0.7740 (mp0)
REVERT: C   17 ARG cc_start: 0.8277 (mtt180) cc_final: 0.8057 (mtp180)
REVERT: C   40 PHE cc_start: 0.8636 (m-80) cc_final: 0.8348 (m-10)
REVERT: C   67 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8197 (mttt)
REVERT: C   83 ASP cc_start: 0.8312 (t0) cc_final: 0.7953 (t0)
REVERT: C  101 PHE cc_start: 0.6823 (m-80) cc_final: 0.6297 (m-80)
REVERT: D   40 PHE cc_start: 0.8599 (m-10) cc_final: 0.8383 (m-10)
REVERT: D   53 ASP cc_start: 0.8782 (p0) cc_final: 0.7597 (p0)
REVERT: D   80 GLN cc_start: 0.8894 (tt0) cc_final: 0.8651 (tt0)
REVERT: D   87 TYR cc_start: 0.8607 (t80) cc_final: 0.7911 (t80)
REVERT: E   36 TRP cc_start: 0.8883 (t-100) cc_final: 0.8119 (t-100)
REVERT: E   46 LYS cc_start: 0.8249 (ptpt) cc_final: 0.7965 (ptpp)
REVERT: E   82 GLU cc_start: 0.8471 (mp0) cc_final: 0.8126 (mp0)
REVERT: E   84 GLU cc_start: 0.8024 (mp0) cc_final: 0.7745 (mp0)
REVERT: E   87 TYR cc_start: 0.8670 (t80) cc_final: 0.8304 (t80)
REVERT: F   43 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8682 (m)
REVERT: F   82 GLU cc_start: 0.8679 (mt-10) cc_final: 0.7930 (mp0)
REVERT: G   36 TRP cc_start: 0.8679 (t-100) cc_final: 0.8309 (t-100)
REVERT: G   46 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7880 (ptpp)
REVERT: G   53 ASP cc_start: 0.8782 (p0) cc_final: 0.7605 (p0)
REVERT: G   63 PHE cc_start: 0.8660 (t80) cc_final: 0.8087 (t80)
REVERT: G   80 GLN cc_start: 0.8790 (tt0) cc_final: 0.8376 (tm-30)
REVERT: G   82 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: G   84 GLU cc_start: 0.7800 (mp0) cc_final: 0.7407 (mp0)
REVERT: G   86 ASP cc_start: 0.8529 (m-30) cc_final: 0.8319 (m-30)
REVERT: H   37 TYR cc_start: 0.7874 (t80) cc_final: 0.7447 (t80)
REVERT: H   40 PHE cc_start: 0.8584 (m-10) cc_final: 0.8241 (m-10)
REVERT: H   46 LYS cc_start: 0.8370 (ptpt) cc_final: 0.7792 (ptpt)
REVERT: H   53 ASP cc_start: 0.8812 (p0) cc_final: 0.7820 (p0)
  outliers start: 20
  outliers final: 5
  residues processed: 205
  average time/residue: 0.1433
  time to fit residues: 39.2514
Evaluate side-chains
  189 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 182
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain B residue   29 ILE
Chi-restraints excluded: chain F residue   43 THR
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 71 optimal weight:    0.3980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4143 r_free = 0.4143 target = 0.088133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.078335 restraints weight = 15782.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 4.04
r_work: 0.3746 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5600  Z= 0.288
  Angle     :  0.789   6.898   7600  Z= 0.380
  Chirality :  0.042   0.141    792
  Planarity :  0.006   0.050   1000
  Dihedral  :  5.982  23.061    792
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.92 %
    Favored  : 87.08 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 24.13 %
    Favored  : 73.61 %
  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: -5.15 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  99 
 PHE   0.013   0.002   PHE G  40 
 TYR   0.017   0.002   TYR G  87 
 ARG   0.004   0.000   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A   29 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8399 (tp)
REVERT: A   35 LYS cc_start: 0.8737 (mttt) cc_final: 0.8209 (mtpt)
REVERT: A   36 TRP cc_start: 0.8963 (t-100) cc_final: 0.8010 (t-100)
REVERT: A   53 ASP cc_start: 0.8883 (p0) cc_final: 0.8440 (p0)
REVERT: B   36 TRP cc_start: 0.8862 (t-100) cc_final: 0.7999 (t-100)
REVERT: B   50 TYR cc_start: 0.8188 (t80) cc_final: 0.7911 (t80)
REVERT: B   76 VAL cc_start: 0.8657 (t) cc_final: 0.8298 (p)
REVERT: B   80 GLN cc_start: 0.8948 (tt0) cc_final: 0.8708 (mt0)
REVERT: B   82 GLU cc_start: 0.8304 (mp0) cc_final: 0.8014 (mp0)
REVERT: C   17 ARG cc_start: 0.8299 (mtt180) cc_final: 0.8080 (mtp180)
REVERT: C   40 PHE cc_start: 0.8685 (m-80) cc_final: 0.8356 (m-10)
REVERT: C   53 ASP cc_start: 0.8921 (p0) cc_final: 0.8709 (p0)
REVERT: C   67 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8425 (mttt)
REVERT: C   82 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8071 (mp0)
REVERT: C   87 TYR cc_start: 0.8708 (t80) cc_final: 0.8089 (t80)
REVERT: C  101 PHE cc_start: 0.6836 (m-80) cc_final: 0.6629 (m-80)
REVERT: D   53 ASP cc_start: 0.8819 (p0) cc_final: 0.7616 (p0)
REVERT: D   80 GLN cc_start: 0.8875 (tt0) cc_final: 0.8423 (tt0)
REVERT: D   82 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7949 (mp0)
REVERT: D   87 TYR cc_start: 0.8514 (t80) cc_final: 0.8137 (t80)
REVERT: E   36 TRP cc_start: 0.8949 (t-100) cc_final: 0.8191 (t-100)
REVERT: E   46 LYS cc_start: 0.8272 (ptpt) cc_final: 0.7961 (ptpp)
REVERT: E   82 GLU cc_start: 0.8530 (mp0) cc_final: 0.8181 (mp0)
REVERT: E   84 GLU cc_start: 0.8039 (mp0) cc_final: 0.7750 (mp0)
REVERT: F   17 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7860 (mtp180)
REVERT: F   43 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8607 (m)
REVERT: F   82 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8119 (mp0)
REVERT: G   22 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7965 (p)
REVERT: G   36 TRP cc_start: 0.8707 (t-100) cc_final: 0.8354 (t-100)
REVERT: G   40 PHE cc_start: 0.8448 (m-10) cc_final: 0.8181 (m-10)
REVERT: G   46 LYS cc_start: 0.8389 (ptpt) cc_final: 0.8057 (ptpp)
REVERT: G   53 ASP cc_start: 0.8833 (p0) cc_final: 0.7608 (p0)
REVERT: G   80 GLN cc_start: 0.8828 (tt0) cc_final: 0.8395 (tm-30)
REVERT: G   82 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8144 (mt-10)
REVERT: G   84 GLU cc_start: 0.7800 (mp0) cc_final: 0.7358 (mp0)
REVERT: G   86 ASP cc_start: 0.8413 (m-30) cc_final: 0.8130 (m-30)
REVERT: H   22 CYS cc_start: 0.8847 (p) cc_final: 0.8530 (t)
REVERT: H   40 PHE cc_start: 0.8662 (m-10) cc_final: 0.8326 (m-10)
REVERT: H   46 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7820 (ptmt)
REVERT: H   53 ASP cc_start: 0.8868 (p0) cc_final: 0.7910 (p0)
  outliers start: 13
  outliers final: 5
  residues processed: 200
  average time/residue: 0.1470
  time to fit residues: 39.0383
Evaluate side-chains
  195 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 187
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain F residue   43 THR
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   22 CYS
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.3956 r_free = 0.3956 target = 0.079058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.068990 restraints weight = 17715.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 4.11
r_work: 0.3572 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.074   5600  Z= 0.693
  Angle     :  1.045   8.030   7600  Z= 0.529
  Chirality :  0.048   0.230    792
  Planarity :  0.007   0.042   1000
  Dihedral  :  7.375  27.166    792
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 25.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.19 %
    Favored  : 77.81 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.83 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.50 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.18 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP H  99 
 PHE   0.019   0.003   PHE H 101 
 TYR   0.025   0.003   TYR D  88 
 ARG   0.004   0.001   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8856 (mttt) cc_final: 0.8243 (mtpt)
REVERT: A   36 TRP cc_start: 0.9064 (t-100) cc_final: 0.8714 (t-100)
REVERT: A   53 ASP cc_start: 0.8771 (p0) cc_final: 0.8418 (p0)
REVERT: A   82 GLU cc_start: 0.8434 (tt0) cc_final: 0.7507 (tm-30)
REVERT: B   22 CYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8501 (p)
REVERT: B   35 LYS cc_start: 0.8013 (mttt) cc_final: 0.7338 (ttmm)
REVERT: B   50 TYR cc_start: 0.8171 (t80) cc_final: 0.7812 (t80)
REVERT: B   79 LEU cc_start: 0.9149 (mm) cc_final: 0.8914 (mm)
REVERT: B   80 GLN cc_start: 0.9040 (tt0) cc_final: 0.8755 (mt0)
REVERT: B   82 GLU cc_start: 0.8368 (mp0) cc_final: 0.8148 (mp0)
REVERT: B   84 GLU cc_start: 0.8261 (mp0) cc_final: 0.7869 (mp0)
REVERT: C   22 CYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8402 (p)
REVERT: C   40 PHE cc_start: 0.8792 (m-80) cc_final: 0.8446 (m-10)
REVERT: C   67 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8466 (mttt)
REVERT: C   84 GLU cc_start: 0.8468 (mp0) cc_final: 0.8059 (mp0)
REVERT: C   89 CYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6486 (m)
REVERT: D   40 PHE cc_start: 0.8917 (m-10) cc_final: 0.8587 (m-10)
REVERT: D   53 ASP cc_start: 0.8896 (p0) cc_final: 0.7525 (p0)
REVERT: D   80 GLN cc_start: 0.9021 (tt0) cc_final: 0.8650 (tt0)
REVERT: D   82 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8100 (mp0)
REVERT: D   84 GLU cc_start: 0.8250 (mp0) cc_final: 0.7889 (mp0)
REVERT: E   46 LYS cc_start: 0.8296 (ptpt) cc_final: 0.8025 (ptpp)
REVERT: E   82 GLU cc_start: 0.8556 (mp0) cc_final: 0.8294 (mp0)
REVERT: E   83 ASP cc_start: 0.7989 (t0) cc_final: 0.7773 (t0)
REVERT: E   86 ASP cc_start: 0.8720 (m-30) cc_final: 0.8487 (m-30)
REVERT: G   22 CYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8285 (p)
REVERT: G   46 LYS cc_start: 0.8312 (ptpt) cc_final: 0.8050 (ptpp)
REVERT: G   53 ASP cc_start: 0.8943 (p0) cc_final: 0.7557 (p0)
REVERT: G   80 GLN cc_start: 0.8950 (tt0) cc_final: 0.8748 (tp40)
REVERT: G   82 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8444 (mt-10)
REVERT: G   84 GLU cc_start: 0.8164 (mp0) cc_final: 0.7882 (mp0)
REVERT: G   86 ASP cc_start: 0.8569 (m-30) cc_final: 0.8235 (m-30)
REVERT: H   40 PHE cc_start: 0.8591 (m-10) cc_final: 0.8343 (m-10)
REVERT: H   46 LYS cc_start: 0.7961 (ptpt) cc_final: 0.7456 (ptpt)
REVERT: H   88 TYR cc_start: 0.8280 (m-80) cc_final: 0.8045 (m-80)
  outliers start: 23
  outliers final: 12
  residues processed: 187
  average time/residue: 0.1420
  time to fit residues: 35.8606
Evaluate side-chains
  176 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 TYR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   53 ASP
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   89 CYS
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain E residue   53 ASP
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain F residue   74 LEU
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   22 CYS
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4116 r_free = 0.4116 target = 0.086684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.076110 restraints weight = 15655.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 4.00
r_work: 0.3729 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5600  Z= 0.269
  Angle     :  0.793   7.309   7600  Z= 0.383
  Chirality :  0.045   0.220    792
  Planarity :  0.006   0.048   1000
  Dihedral  :  6.270  25.346    792
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.00 %
    Favored  : 71.53 %
  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: -5.37 (0.20), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.09 (0.15), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  92 
 PHE   0.013   0.002   PHE G  40 
 TYR   0.008   0.001   TYR A  88 
 ARG   0.003   0.000   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.582 
Fit side-chains
REVERT: A   36 TRP cc_start: 0.8905 (t-100) cc_final: 0.8507 (t-100)
REVERT: A   53 ASP cc_start: 0.8901 (p0) cc_final: 0.7738 (p0)
REVERT: A   55 ARG cc_start: 0.8523 (ttm110) cc_final: 0.6951 (mtt-85)
REVERT: B   50 TYR cc_start: 0.8147 (t80) cc_final: 0.7767 (t80)
REVERT: B   53 ASP cc_start: 0.8723 (p0) cc_final: 0.7154 (p0)
REVERT: B   63 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8118 (t80)
REVERT: B   87 TYR cc_start: 0.8936 (t80) cc_final: 0.8476 (t80)
REVERT: C   40 PHE cc_start: 0.8678 (m-80) cc_final: 0.8251 (m-10)
REVERT: C   53 ASP cc_start: 0.8801 (p0) cc_final: 0.8522 (p0)
REVERT: C   67 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8366 (mttt)
REVERT: C   84 GLU cc_start: 0.8437 (mp0) cc_final: 0.7910 (mp0)
REVERT: D   40 PHE cc_start: 0.8684 (m-10) cc_final: 0.8406 (m-10)
REVERT: D   53 ASP cc_start: 0.8847 (p0) cc_final: 0.7444 (p0)
REVERT: D   63 PHE cc_start: 0.8700 (t80) cc_final: 0.7650 (t80)
REVERT: D   80 GLN cc_start: 0.8870 (tt0) cc_final: 0.8424 (tt0)
REVERT: D   82 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8071 (mp0)
REVERT: D   84 GLU cc_start: 0.8202 (mp0) cc_final: 0.7743 (mp0)
REVERT: E   36 TRP cc_start: 0.8973 (t-100) cc_final: 0.8130 (t-100)
REVERT: E   46 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7853 (ptpp)
REVERT: E   53 ASP cc_start: 0.8929 (p0) cc_final: 0.7990 (p0)
REVERT: E   63 PHE cc_start: 0.8634 (t80) cc_final: 0.7813 (t80)
REVERT: E   82 GLU cc_start: 0.8493 (mp0) cc_final: 0.8178 (mp0)
REVERT: E   86 ASP cc_start: 0.8613 (m-30) cc_final: 0.8398 (m-30)
REVERT: F   17 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7851 (mtp180)
REVERT: F   63 PHE cc_start: 0.8726 (t80) cc_final: 0.7968 (t80)
REVERT: F   82 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8160 (mp0)
REVERT: G   36 TRP cc_start: 0.8729 (t-100) cc_final: 0.8278 (t-100)
REVERT: G   40 PHE cc_start: 0.8486 (m-10) cc_final: 0.8114 (m-10)
REVERT: G   46 LYS cc_start: 0.8309 (ptpt) cc_final: 0.8055 (ptpp)
REVERT: G   53 ASP cc_start: 0.8744 (p0) cc_final: 0.7402 (p0)
REVERT: G   80 GLN cc_start: 0.8899 (tt0) cc_final: 0.8634 (tp40)
REVERT: G   82 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8378 (mt-10)
REVERT: G   84 GLU cc_start: 0.8116 (mp0) cc_final: 0.7692 (mp0)
REVERT: G   86 ASP cc_start: 0.8526 (m-30) cc_final: 0.8322 (m-30)
REVERT: H   39 GLN cc_start: 0.7972 (tt0) cc_final: 0.7503 (mt0)
REVERT: H   40 PHE cc_start: 0.8685 (m-10) cc_final: 0.8426 (m-80)
REVERT: H   46 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7516 (ptpt)
REVERT: H   53 ASP cc_start: 0.8823 (p0) cc_final: 0.8503 (p0)
REVERT: H   83 ASP cc_start: 0.7928 (t0) cc_final: 0.7714 (t0)
  outliers start: 20
  outliers final: 7
  residues processed: 196
  average time/residue: 0.1541
  time to fit residues: 40.3529
Evaluate side-chains
  182 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 174
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4012 r_free = 0.4012 target = 0.081130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.070873 restraints weight = 16732.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 4.07
r_work: 0.3618 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058   5600  Z= 0.532
  Angle     :  0.947   7.588   7600  Z= 0.468
  Chirality :  0.046   0.150    792
  Planarity :  0.006   0.038   1000
  Dihedral  :  6.651  26.132    792
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.37 %
    Favored  : 79.63 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.60 %
    Favored  : 70.49 %
  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: -5.45 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.14 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP H  99 
 PHE   0.013   0.003   PHE G  40 
 TYR   0.016   0.002   TYR A  88 
 ARG   0.003   0.001   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 170
  time to evaluate  : 0.604 
Fit side-chains
REVERT: A   36 TRP cc_start: 0.9051 (t-100) cc_final: 0.8718 (t-100)
REVERT: A   53 ASP cc_start: 0.8812 (p0) cc_final: 0.7871 (p0)
REVERT: A   55 ARG cc_start: 0.8531 (ttm110) cc_final: 0.7066 (mtt-85)
REVERT: A   82 GLU cc_start: 0.8664 (tt0) cc_final: 0.7834 (tm-30)
REVERT: B   50 TYR cc_start: 0.8162 (t80) cc_final: 0.7755 (t80)
REVERT: B   53 ASP cc_start: 0.8701 (p0) cc_final: 0.8387 (p0)
REVERT: C   40 PHE cc_start: 0.8719 (m-80) cc_final: 0.8312 (m-10)
REVERT: C   53 ASP cc_start: 0.8848 (p0) cc_final: 0.8634 (p0)
REVERT: C   67 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8415 (mttt)
REVERT: C   84 GLU cc_start: 0.8530 (mp0) cc_final: 0.7986 (mp0)
REVERT: D   40 PHE cc_start: 0.8946 (m-10) cc_final: 0.8613 (m-10)
REVERT: D   53 ASP cc_start: 0.8889 (p0) cc_final: 0.7413 (p0)
REVERT: D   82 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8152 (mp0)
REVERT: D   84 GLU cc_start: 0.8282 (mp0) cc_final: 0.7854 (mp0)
REVERT: E   46 LYS cc_start: 0.8235 (ptpt) cc_final: 0.7979 (ptpp)
REVERT: E   53 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8098 (p0)
REVERT: E   82 GLU cc_start: 0.8626 (mp0) cc_final: 0.8292 (mp0)
REVERT: E   86 ASP cc_start: 0.8888 (m-30) cc_final: 0.8572 (m-30)
REVERT: F   63 PHE cc_start: 0.9006 (t80) cc_final: 0.8519 (t80)
REVERT: F   82 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8277 (mp0)
REVERT: F   84 GLU cc_start: 0.8183 (mp0) cc_final: 0.7944 (mp0)
REVERT: G   23 SER cc_start: 0.9016 (m) cc_final: 0.8629 (p)
REVERT: G   40 PHE cc_start: 0.8566 (m-10) cc_final: 0.8266 (m-10)
REVERT: G   46 LYS cc_start: 0.8388 (ptpt) cc_final: 0.8122 (ptpp)
REVERT: G   53 ASP cc_start: 0.8873 (p0) cc_final: 0.7463 (p0)
REVERT: G   80 GLN cc_start: 0.8942 (tt0) cc_final: 0.8603 (tp40)
REVERT: G   82 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8328 (mt-10)
REVERT: G   84 GLU cc_start: 0.8247 (mp0) cc_final: 0.7822 (mp0)
REVERT: G   86 ASP cc_start: 0.8601 (m-30) cc_final: 0.8369 (m-30)
REVERT: H   39 GLN cc_start: 0.7925 (tt0) cc_final: 0.7568 (mt0)
REVERT: H   40 PHE cc_start: 0.8741 (m-10) cc_final: 0.8455 (m-80)
REVERT: H   46 LYS cc_start: 0.8002 (ptpt) cc_final: 0.7467 (ptpt)
REVERT: H   53 ASP cc_start: 0.8853 (p0) cc_final: 0.8533 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 174
  average time/residue: 0.1412
  time to fit residues: 32.9118
Evaluate side-chains
  171 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain E residue   53 ASP
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4126 r_free = 0.4126 target = 0.083770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.073237 restraints weight = 15749.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 4.07
r_work: 0.3719 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5600  Z= 0.256
  Angle     :  0.795   7.688   7600  Z= 0.379
  Chirality :  0.044   0.152    792
  Planarity :  0.005   0.041   1000
  Dihedral  :  5.926  26.087    792
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 26.91 %
    Favored  : 70.49 %
  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: -5.25 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.99 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  92 
 PHE   0.019   0.002   PHE E  40 
 TYR   0.011   0.001   TYR B  87 
 ARG   0.003   0.000   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 182
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.8924 (t-100) cc_final: 0.8559 (t-100)
REVERT: A   53 ASP cc_start: 0.8899 (p0) cc_final: 0.7735 (p0)
REVERT: A   55 ARG cc_start: 0.8580 (ttm110) cc_final: 0.7177 (mtt-85)
REVERT: B   50 TYR cc_start: 0.8121 (t80) cc_final: 0.7678 (t80)
REVERT: B   53 ASP cc_start: 0.8705 (p0) cc_final: 0.7121 (p0)
REVERT: B   63 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8088 (t80)
REVERT: B   76 VAL cc_start: 0.8680 (t) cc_final: 0.8311 (p)
REVERT: C   40 PHE cc_start: 0.8703 (m-80) cc_final: 0.8334 (m-10)
REVERT: C   53 ASP cc_start: 0.8819 (p0) cc_final: 0.7269 (p0)
REVERT: C   67 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8333 (mttt)
REVERT: C   82 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8165 (mp0)
REVERT: C   84 GLU cc_start: 0.8440 (mp0) cc_final: 0.7774 (mp0)
REVERT: C   86 ASP cc_start: 0.8688 (m-30) cc_final: 0.8375 (m-30)
REVERT: D   40 PHE cc_start: 0.8712 (m-80) cc_final: 0.8440 (m-10)
REVERT: D   53 ASP cc_start: 0.8759 (p0) cc_final: 0.7290 (p0)
REVERT: D   63 PHE cc_start: 0.8691 (t80) cc_final: 0.7750 (t80)
REVERT: D   82 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8091 (mp0)
REVERT: D   84 GLU cc_start: 0.8250 (mp0) cc_final: 0.7881 (mp0)
REVERT: E   36 TRP cc_start: 0.8983 (t-100) cc_final: 0.8336 (t-100)
REVERT: E   46 LYS cc_start: 0.7981 (ptpt) cc_final: 0.7756 (ptpp)
REVERT: E   53 ASP cc_start: 0.8928 (p0) cc_final: 0.7651 (p0)
REVERT: E   63 PHE cc_start: 0.8645 (t80) cc_final: 0.7475 (t80)
REVERT: E   82 GLU cc_start: 0.8511 (mp0) cc_final: 0.8087 (mp0)
REVERT: E   86 ASP cc_start: 0.8827 (m-30) cc_final: 0.8548 (m-30)
REVERT: F   17 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7876 (mtp180)
REVERT: F   36 TRP cc_start: 0.9152 (t-100) cc_final: 0.8615 (t-100)
REVERT: F   63 PHE cc_start: 0.8698 (t80) cc_final: 0.7771 (t80)
REVERT: F   82 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8126 (mp0)
REVERT: G   23 SER cc_start: 0.8761 (m) cc_final: 0.8258 (p)
REVERT: G   36 TRP cc_start: 0.8798 (t-100) cc_final: 0.8368 (t-100)
REVERT: G   37 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7826 (t80)
REVERT: G   40 PHE cc_start: 0.8506 (m-10) cc_final: 0.8052 (m-10)
REVERT: G   46 LYS cc_start: 0.8335 (ptpt) cc_final: 0.8117 (ptpp)
REVERT: G   53 ASP cc_start: 0.8781 (p0) cc_final: 0.7424 (p0)
REVERT: G   62 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7533 (mtm-85)
REVERT: G   80 GLN cc_start: 0.8884 (tt0) cc_final: 0.8554 (tp40)
REVERT: G   82 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: G   84 GLU cc_start: 0.8046 (mp0) cc_final: 0.7637 (mp0)
REVERT: H   39 GLN cc_start: 0.8153 (tt0) cc_final: 0.7761 (mt0)
REVERT: H   40 PHE cc_start: 0.8708 (m-10) cc_final: 0.8441 (m-80)
REVERT: H   46 LYS cc_start: 0.7965 (ptpt) cc_final: 0.7417 (ptpt)
REVERT: H   53 ASP cc_start: 0.8831 (p0) cc_final: 0.8533 (p0)
REVERT: H   83 ASP cc_start: 0.8020 (t0) cc_final: 0.7815 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 190
  average time/residue: 0.1502
  time to fit residues: 37.8437
Evaluate side-chains
  183 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 173
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   37 TYR
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain G residue   63 PHE
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 38 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4123 r_free = 0.4123 target = 0.084402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.073543 restraints weight = 15972.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 4.18
r_work: 0.3694 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.4385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5600  Z= 0.288
  Angle     :  0.807   8.362   7600  Z= 0.383
  Chirality :  0.044   0.155    792
  Planarity :  0.005   0.041   1000
  Dihedral  :  5.809  27.292    792
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.03 %
    Favored  : 84.97 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 28.99 %
    Favored  : 69.10 %
  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: -5.17 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.94 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  92 
 PHE   0.013   0.002   PHE E  40 
 TYR   0.012   0.001   TYR B  87 
 ARG   0.003   0.000   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.9003 (t-100) cc_final: 0.8637 (t-100)
REVERT: A   53 ASP cc_start: 0.8891 (p0) cc_final: 0.7610 (p0)
REVERT: A   55 ARG cc_start: 0.8541 (ttm110) cc_final: 0.7070 (mtt-85)
REVERT: B   53 ASP cc_start: 0.8752 (p0) cc_final: 0.7218 (p0)
REVERT: B   63 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8191 (t80)
REVERT: C   23 SER cc_start: 0.8837 (m) cc_final: 0.8386 (p)
REVERT: C   40 PHE cc_start: 0.8739 (m-80) cc_final: 0.8363 (m-10)
REVERT: C   53 ASP cc_start: 0.8860 (p0) cc_final: 0.7345 (p0)
REVERT: C   67 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8364 (mttt)
REVERT: C   82 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8207 (mp0)
REVERT: C   84 GLU cc_start: 0.8463 (mp0) cc_final: 0.7783 (mp0)
REVERT: D   40 PHE cc_start: 0.8781 (m-80) cc_final: 0.8521 (m-10)
REVERT: D   53 ASP cc_start: 0.8735 (p0) cc_final: 0.7222 (p0)
REVERT: D   63 PHE cc_start: 0.8773 (t80) cc_final: 0.7752 (t80)
REVERT: D   82 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8084 (mp0)
REVERT: D   84 GLU cc_start: 0.8266 (mp0) cc_final: 0.7835 (mp0)
REVERT: E   36 TRP cc_start: 0.8936 (t-100) cc_final: 0.8286 (t-100)
REVERT: E   46 LYS cc_start: 0.8062 (ptpt) cc_final: 0.7835 (ptpp)
REVERT: E   53 ASP cc_start: 0.8940 (p0) cc_final: 0.7706 (p0)
REVERT: E   63 PHE cc_start: 0.8754 (t80) cc_final: 0.7648 (t80)
REVERT: E   82 GLU cc_start: 0.8572 (mp0) cc_final: 0.8294 (mp0)
REVERT: E   86 ASP cc_start: 0.8895 (m-30) cc_final: 0.8607 (m-30)
REVERT: F   17 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7851 (mtp180)
REVERT: F   63 PHE cc_start: 0.8880 (t80) cc_final: 0.8038 (t80)
REVERT: F   82 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8217 (mp0)
REVERT: G   23 SER cc_start: 0.8779 (m) cc_final: 0.8372 (p)
REVERT: G   36 TRP cc_start: 0.8851 (t-100) cc_final: 0.8367 (t-100)
REVERT: G   37 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7963 (t80)
REVERT: G   40 PHE cc_start: 0.8567 (m-10) cc_final: 0.8177 (m-10)
REVERT: G   46 LYS cc_start: 0.8379 (ptpt) cc_final: 0.8125 (ptpp)
REVERT: G   53 ASP cc_start: 0.8794 (p0) cc_final: 0.7495 (p0)
REVERT: G   80 GLN cc_start: 0.8939 (tt0) cc_final: 0.8601 (tp40)
REVERT: G   82 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8396 (mt-10)
REVERT: G   84 GLU cc_start: 0.8137 (mp0) cc_final: 0.7675 (mp0)
REVERT: H   39 GLN cc_start: 0.8196 (tt0) cc_final: 0.7805 (mt0)
REVERT: H   40 PHE cc_start: 0.8719 (m-10) cc_final: 0.8452 (m-80)
REVERT: H   46 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7483 (ptpt)
REVERT: H   53 ASP cc_start: 0.8844 (p0) cc_final: 0.8544 (p0)
REVERT: H   83 ASP cc_start: 0.8068 (t0) cc_final: 0.7786 (t0)
REVERT: H   88 TYR cc_start: 0.8376 (m-80) cc_final: 0.7965 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 181
  average time/residue: 0.1518
  time to fit residues: 36.4675
Evaluate side-chains
  181 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 171
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   37 TYR
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   63 PHE
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4118 r_free = 0.4118 target = 0.083980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.073073 restraints weight = 15994.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 4.20
r_work: 0.3688 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.4463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5600  Z= 0.295
  Angle     :  0.808   8.469   7600  Z= 0.383
  Chirality :  0.045   0.193    792
  Planarity :  0.005   0.040   1000
  Dihedral  :  5.779  28.027    792
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.34 %
    Favored  : 86.66 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 28.47 %
    Favored  : 69.27 %
  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: -5.12 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.90 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  92 
 PHE   0.011   0.002   PHE E  40 
 TYR   0.012   0.001   TYR B  88 
 ARG   0.003   0.000   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.9020 (t-100) cc_final: 0.8646 (t-100)
REVERT: A   53 ASP cc_start: 0.8826 (p0) cc_final: 0.7629 (p0)
REVERT: A   55 ARG cc_start: 0.8457 (ttm110) cc_final: 0.6976 (mtt-85)
REVERT: B   53 ASP cc_start: 0.8727 (p0) cc_final: 0.6750 (p0)
REVERT: B   63 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8191 (t80)
REVERT: C   29 ILE cc_start: 0.8782 (mt) cc_final: 0.8430 (mm)
REVERT: C   40 PHE cc_start: 0.8730 (m-80) cc_final: 0.8344 (m-10)
REVERT: C   53 ASP cc_start: 0.8844 (p0) cc_final: 0.7300 (p0)
REVERT: C   67 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8366 (mttt)
REVERT: C   82 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8203 (mp0)
REVERT: C   84 GLU cc_start: 0.8450 (mp0) cc_final: 0.7806 (mp0)
REVERT: D   40 PHE cc_start: 0.8752 (m-80) cc_final: 0.8480 (m-10)
REVERT: D   53 ASP cc_start: 0.8728 (p0) cc_final: 0.7210 (p0)
REVERT: D   63 PHE cc_start: 0.8799 (t80) cc_final: 0.7828 (t80)
REVERT: D   82 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8077 (mp0)
REVERT: D   84 GLU cc_start: 0.8284 (mp0) cc_final: 0.7730 (mp0)
REVERT: E   36 TRP cc_start: 0.8958 (t-100) cc_final: 0.8317 (t-100)
REVERT: E   46 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7827 (ptpp)
REVERT: E   53 ASP cc_start: 0.8924 (p0) cc_final: 0.7697 (p0)
REVERT: E   63 PHE cc_start: 0.8732 (t80) cc_final: 0.7630 (t80)
REVERT: E   82 GLU cc_start: 0.8567 (mp0) cc_final: 0.8257 (mp0)
REVERT: E   84 GLU cc_start: 0.8142 (mp0) cc_final: 0.7933 (mp0)
REVERT: E   86 ASP cc_start: 0.8829 (m-30) cc_final: 0.8518 (m-30)
REVERT: F   17 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7880 (mtp180)
REVERT: F   63 PHE cc_start: 0.8844 (t80) cc_final: 0.7951 (t80)
REVERT: F   82 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8231 (mp0)
REVERT: F   84 GLU cc_start: 0.7985 (mp0) cc_final: 0.7779 (mp0)
REVERT: G   23 SER cc_start: 0.8809 (m) cc_final: 0.8385 (p)
REVERT: G   36 TRP cc_start: 0.8783 (t-100) cc_final: 0.8326 (t-100)
REVERT: G   37 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8014 (t80)
REVERT: G   40 PHE cc_start: 0.8567 (m-10) cc_final: 0.8157 (m-10)
REVERT: G   46 LYS cc_start: 0.8354 (ptpt) cc_final: 0.8112 (ptpp)
REVERT: G   53 ASP cc_start: 0.8796 (p0) cc_final: 0.7433 (p0)
REVERT: G   62 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7527 (mtm-85)
REVERT: G   80 GLN cc_start: 0.8933 (tt0) cc_final: 0.8602 (tp40)
REVERT: G   82 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8293 (mt-10)
REVERT: G   84 GLU cc_start: 0.8178 (mp0) cc_final: 0.7659 (mp0)
REVERT: H   39 GLN cc_start: 0.8226 (tt0) cc_final: 0.7863 (mt0)
REVERT: H   40 PHE cc_start: 0.8746 (m-10) cc_final: 0.8470 (m-80)
REVERT: H   46 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7536 (ptpt)
REVERT: H   53 ASP cc_start: 0.8851 (p0) cc_final: 0.8554 (p0)
REVERT: H   83 ASP cc_start: 0.8034 (t0) cc_final: 0.7805 (t0)
REVERT: H   88 TYR cc_start: 0.8406 (m-80) cc_final: 0.7979 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 183
  average time/residue: 0.1540
  time to fit residues: 37.6563
Evaluate side-chains
  185 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 173
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   37 TYR
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain G residue   63 PHE
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4131 r_free = 0.4131 target = 0.084827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.073902 restraints weight = 16002.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 4.22
r_work: 0.3687 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5600  Z= 0.277
  Angle     :  0.803   8.641   7600  Z= 0.380
  Chirality :  0.044   0.146    792
  Planarity :  0.005   0.039   1000
  Dihedral  :  5.675  27.281    792
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.33 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 28.82 %
    Favored  : 68.75 %
  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: -5.05 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  92 
 PHE   0.010   0.001   PHE G  40 
 TYR   0.010   0.001   TYR B  88 
 ARG   0.003   0.000   ARG B  25 

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A   36 TRP cc_start: 0.8968 (t-100) cc_final: 0.8598 (t-100)
REVERT: A   53 ASP cc_start: 0.8789 (p0) cc_final: 0.7643 (p0)
REVERT: A   55 ARG cc_start: 0.8508 (ttm110) cc_final: 0.7209 (mtt-85)
REVERT: A   63 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7657 (t80)
REVERT: B   46 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7780 (ptpp)
REVERT: B   53 ASP cc_start: 0.8663 (p0) cc_final: 0.6741 (p0)
REVERT: B   63 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7964 (t80)
REVERT: C   23 SER cc_start: 0.8845 (m) cc_final: 0.8295 (p)
REVERT: C   40 PHE cc_start: 0.8701 (m-80) cc_final: 0.8317 (m-10)
REVERT: C   53 ASP cc_start: 0.8783 (p0) cc_final: 0.7268 (p0)
REVERT: C   67 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8323 (mttt)
REVERT: C   82 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8181 (mp0)
REVERT: C   84 GLU cc_start: 0.8343 (mp0) cc_final: 0.7674 (mp0)
REVERT: D   40 PHE cc_start: 0.8746 (m-80) cc_final: 0.8481 (m-10)
REVERT: D   53 ASP cc_start: 0.8650 (p0) cc_final: 0.7148 (p0)
REVERT: D   63 PHE cc_start: 0.8759 (t80) cc_final: 0.7766 (t80)
REVERT: D   82 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8173 (mp0)
REVERT: D   84 GLU cc_start: 0.8195 (mp0) cc_final: 0.7693 (mp0)
REVERT: E   36 TRP cc_start: 0.8918 (t-100) cc_final: 0.8176 (t-100)
REVERT: E   46 LYS cc_start: 0.7958 (ptpt) cc_final: 0.7708 (ptpp)
REVERT: E   53 ASP cc_start: 0.8931 (p0) cc_final: 0.7693 (p0)
REVERT: E   63 PHE cc_start: 0.8697 (t80) cc_final: 0.7566 (t80)
REVERT: E   82 GLU cc_start: 0.8488 (mp0) cc_final: 0.8039 (mp0)
REVERT: E   84 GLU cc_start: 0.8110 (mp0) cc_final: 0.7816 (mp0)
REVERT: E   86 ASP cc_start: 0.8756 (m-30) cc_final: 0.8401 (m-30)
REVERT: F   17 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7841 (mtp180)
REVERT: F   36 TRP cc_start: 0.9186 (t-100) cc_final: 0.8717 (t-100)
REVERT: F   63 PHE cc_start: 0.8798 (t80) cc_final: 0.7846 (t80)
REVERT: F   82 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8179 (mp0)
REVERT: F   84 GLU cc_start: 0.7902 (mp0) cc_final: 0.7680 (mp0)
REVERT: G   23 SER cc_start: 0.8806 (m) cc_final: 0.8275 (p)
REVERT: G   36 TRP cc_start: 0.8784 (t-100) cc_final: 0.8295 (t-100)
REVERT: G   37 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7929 (t80)
REVERT: G   40 PHE cc_start: 0.8528 (m-10) cc_final: 0.8107 (m-80)
REVERT: G   46 LYS cc_start: 0.8235 (ptpt) cc_final: 0.7986 (ptpp)
REVERT: G   53 ASP cc_start: 0.8755 (p0) cc_final: 0.7427 (p0)
REVERT: G   62 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7467 (mtm-85)
REVERT: G   80 GLN cc_start: 0.8914 (tt0) cc_final: 0.8583 (tp40)
REVERT: G   82 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8285 (mt-10)
REVERT: G   84 GLU cc_start: 0.8105 (mp0) cc_final: 0.7612 (mp0)
REVERT: H   39 GLN cc_start: 0.8205 (tt0) cc_final: 0.7911 (mt0)
REVERT: H   40 PHE cc_start: 0.8738 (m-10) cc_final: 0.8514 (m-80)
REVERT: H   46 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7736 (ptmt)
REVERT: H   53 ASP cc_start: 0.8836 (p0) cc_final: 0.8541 (p0)
REVERT: H   83 ASP cc_start: 0.8115 (t0) cc_final: 0.7891 (t0)
REVERT: H   88 TYR cc_start: 0.8334 (m-80) cc_final: 0.7971 (m-80)
  outliers start: 14
  outliers final: 8
  residues processed: 186
  average time/residue: 0.1599
  time to fit residues: 39.2310
Evaluate side-chains
  190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   37 TYR
Chi-restraints excluded: chain G residue   43 THR
Chi-restraints excluded: chain G residue   62 ARG
Chi-restraints excluded: chain G residue   63 PHE
Chi-restraints excluded: chain G residue   79 LEU
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   79 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0050
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
** B  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 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 = 0.4124 r_free = 0.4124 target = 0.084004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.072861 restraints weight = 15982.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 4.25
r_work: 0.3674 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5600  Z= 0.286
  Angle     :  0.807   8.633   7600  Z= 0.381
  Chirality :  0.044   0.158    792
  Planarity :  0.005   0.039   1000
  Dihedral  :  5.634  26.833    792
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.34 %
    Favored  : 86.66 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 29.34 %
    Favored  : 68.58 %
  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: -5.00 (0.22), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.80 (0.17), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  92 
 PHE   0.009   0.001   PHE G  40 
 TYR   0.010   0.001   TYR B  88 
 ARG   0.003   0.000   ARG B  25 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2574.64 seconds
wall clock time: 46 minutes 51.22 seconds (2811.22 seconds total)