Starting phenix.real_space_refine
on Sun Apr 27 10:39:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ic3_4452/04_2025/6ic3_4452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ic3_4452/04_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_4452/04_2025/6ic3_4452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ic3_4452/04_2025/6ic3_4452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ic3_4452/04_2025/6ic3_4452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ic3_4452/04_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-5669/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: 2.86, per 1000 atoms: 0.52
  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=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  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: 1.25
  Conformation dependent library (CDL) restraints added in 697.8 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: 0.82
  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: 1.59

  Time building geometry restraints manager: 1.50 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: 128
       46.29 -    57.87: 24
  Dihedral angle restraints: 3264
    sinusoidal: 1232
      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 3261 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:
        2.28 -     2.80: 1655
        2.80 -     3.33: 4706
        3.33 -     3.85: 9392
        3.85 -     4.38: 10364
        4.38 -     4.90: 21885
  Nonbonded interactions: 48002
  Sorted by model distance:
  nonbonded pdb=" O   ASN G  52 "
            pdb=" ND2 ASN H  52 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" O   THR H  70 "
            pdb=" OG1 THR H  70 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   THR B  70 "
            pdb=" OG1 THR B  70 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   THR F  70 "
            pdb=" OG1 THR F  70 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   THR E  70 "
            pdb=" OG1 THR E  70 "
     model   vdw
     2.307 3.040
  ... (remaining 47997 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     16.660
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.260
-------------------------------------------------------------------------------
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   5608  Z= 0.469
  Angle     :  1.263   8.957   7616  Z= 0.669
  Chirality :  0.056   0.128    792
  Planarity :  0.009   0.051   1000
  Dihedral  : 16.173  57.866   1960
  Min Nonbonded Distance : 2.277

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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14707 (   32)
  hydrogen bonds       : angle       9.15383 (   96)
  SS BOND              : bond        0.01339 (    8)
  SS BOND              : angle       1.60469 (   16)
  covalent geometry    : bond        0.00973 ( 5600)
  covalent geometry    : angle       1.26208 ( 7600)

*********************** 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  : 0.558 
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: 0.2173
  time to fit residues: 61.7750
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  : 0.574 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.087944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.077196 restraints weight = 15033.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 4.02
r_work: 0.3736 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5608  Z= 0.185
  Angle     :  0.827   8.224   7616  Z= 0.398
  Chirality :  0.044   0.136    792
  Planarity :  0.008   0.058   1000
  Dihedral  :  6.664  33.505    795
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.66 %
    Favored  : 75.87 %
  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: -5.26 (0.20), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.00 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  99 
 PHE   0.012   0.002   PHE D 101 
 TYR   0.019   0.002   TYR A  88 
 ARG   0.009   0.001   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02074 (   32)
  hydrogen bonds       : angle       4.74504 (   96)
  SS BOND              : bond        0.00301 (    8)
  SS BOND              : angle       1.25817 (   16)
  covalent geometry    : bond        0.00427 ( 5600)
  covalent geometry    : angle       0.82613 ( 7600)

*********************** 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
  215 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8355 (tp)
REVERT: A   35 LYS cc_start: 0.8748 (mttt) cc_final: 0.8213 (mtpt)
REVERT: A   36 TRP cc_start: 0.8924 (t-100) cc_final: 0.7986 (t-100)
REVERT: A   53 ASP cc_start: 0.8866 (p0) cc_final: 0.8020 (p0)
REVERT: B   36 TRP cc_start: 0.8867 (t-100) cc_final: 0.8161 (t-100)
REVERT: B   37 TYR cc_start: 0.8739 (t80) cc_final: 0.7177 (t80)
REVERT: B   52 ASN cc_start: 0.7990 (t0) cc_final: 0.7785 (t0)
REVERT: B   53 ASP cc_start: 0.8675 (p0) cc_final: 0.7396 (p0)
REVERT: B   80 GLN cc_start: 0.8933 (tt0) cc_final: 0.8715 (tt0)
REVERT: B   84 GLU cc_start: 0.8146 (mp0) cc_final: 0.7943 (mp0)
REVERT: C   17 ARG cc_start: 0.8292 (mtt180) cc_final: 0.8070 (mtp180)
REVERT: C   40 PHE cc_start: 0.8623 (m-80) cc_final: 0.8315 (m-10)
REVERT: C   67 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8205 (mttt)
REVERT: C   83 ASP cc_start: 0.8200 (t0) cc_final: 0.7808 (t0)
REVERT: C  101 PHE cc_start: 0.6831 (m-80) cc_final: 0.6329 (m-80)
REVERT: D   40 PHE cc_start: 0.8585 (m-10) cc_final: 0.8340 (m-10)
REVERT: D   53 ASP cc_start: 0.8776 (p0) cc_final: 0.7556 (p0)
REVERT: D   80 GLN cc_start: 0.8874 (tt0) cc_final: 0.8647 (tt0)
REVERT: D   87 TYR cc_start: 0.8483 (t80) cc_final: 0.7936 (t80)
REVERT: E   36 TRP cc_start: 0.8900 (t-100) cc_final: 0.8172 (t-100)
REVERT: E   46 LYS cc_start: 0.8303 (ptpt) cc_final: 0.8089 (ptpp)
REVERT: E   82 GLU cc_start: 0.8468 (mp0) cc_final: 0.8134 (mp0)
REVERT: E   87 TYR cc_start: 0.8472 (t80) cc_final: 0.8163 (t80)
REVERT: F   53 ASP cc_start: 0.8720 (p0) cc_final: 0.7799 (p0)
REVERT: F   82 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7956 (mp0)
REVERT: F   86 ASP cc_start: 0.8477 (m-30) cc_final: 0.8126 (m-30)
REVERT: G   36 TRP cc_start: 0.8625 (t-100) cc_final: 0.8271 (t-100)
REVERT: G   46 LYS cc_start: 0.8277 (ptpt) cc_final: 0.7989 (ptpp)
REVERT: G   53 ASP cc_start: 0.8789 (p0) cc_final: 0.7522 (p0)
REVERT: G   63 PHE cc_start: 0.8673 (t80) cc_final: 0.8101 (t80)
REVERT: G   80 GLN cc_start: 0.8777 (tt0) cc_final: 0.8358 (tm-30)
REVERT: G   82 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8158 (mt-10)
REVERT: G   84 GLU cc_start: 0.7773 (mp0) cc_final: 0.7386 (mp0)
REVERT: G   86 ASP cc_start: 0.8303 (m-30) cc_final: 0.8066 (m-30)
REVERT: G   87 TYR cc_start: 0.8495 (t80) cc_final: 0.8200 (t80)
REVERT: H   37 TYR cc_start: 0.7877 (t80) cc_final: 0.7472 (t80)
REVERT: H   40 PHE cc_start: 0.8622 (m-10) cc_final: 0.8279 (m-10)
REVERT: H   46 LYS cc_start: 0.8433 (ptpt) cc_final: 0.7868 (ptpt)
REVERT: H   53 ASP cc_start: 0.8809 (p0) cc_final: 0.7833 (p0)
  outliers start: 20
  outliers final: 5
  residues processed: 205
  average time/residue: 0.1483
  time to fit residues: 40.8671
Evaluate side-chains
  188 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 182
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
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   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:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0570
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.6900

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.088271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.077451 restraints weight = 14952.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 4.10
r_work: 0.3767 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5608  Z= 0.150
  Angle     :  0.769   7.213   7616  Z= 0.366
  Chirality :  0.043   0.182    792
  Planarity :  0.006   0.048   1000
  Dihedral  :  5.793  22.319    792
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.64 %
    Favored  : 87.36 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 21.53 %
    Favored  : 77.08 %
  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: -5.02 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  99 
 PHE   0.012   0.002   PHE A  40 
 TYR   0.019   0.001   TYR B  87 
 ARG   0.003   0.000   ARG B  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01192 (   32)
  hydrogen bonds       : angle       4.24387 (   96)
  SS BOND              : bond        0.00106 (    8)
  SS BOND              : angle       0.93566 (   16)
  covalent geometry    : bond        0.00362 ( 5600)
  covalent geometry    : angle       0.76873 ( 7600)

*********************** 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: 8
    poor density    : 199
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8341 (tp)
REVERT: A   35 LYS cc_start: 0.8672 (mttt) cc_final: 0.8112 (mtpt)
REVERT: A   36 TRP cc_start: 0.8903 (t-100) cc_final: 0.8629 (t-100)
REVERT: A   53 ASP cc_start: 0.8920 (p0) cc_final: 0.8009 (p0)
REVERT: B   36 TRP cc_start: 0.8809 (t-100) cc_final: 0.8507 (t-100)
REVERT: B   50 TYR cc_start: 0.8238 (t80) cc_final: 0.8002 (t80)
REVERT: B   53 ASP cc_start: 0.8696 (p0) cc_final: 0.7426 (p0)
REVERT: B   76 VAL cc_start: 0.8620 (t) cc_final: 0.8257 (p)
REVERT: B   82 GLU cc_start: 0.8197 (mp0) cc_final: 0.7993 (mp0)
REVERT: B   87 TYR cc_start: 0.8752 (t80) cc_final: 0.8537 (t80)
REVERT: C   17 ARG cc_start: 0.8234 (mtt180) cc_final: 0.8008 (mtp180)
REVERT: C   40 PHE cc_start: 0.8639 (m-80) cc_final: 0.8280 (m-10)
REVERT: C   53 ASP cc_start: 0.8917 (p0) cc_final: 0.8684 (p0)
REVERT: C   67 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8398 (mttt)
REVERT: C   82 GLU cc_start: 0.8631 (mt-10) cc_final: 0.7915 (mp0)
REVERT: C   84 GLU cc_start: 0.8029 (mp0) cc_final: 0.7553 (mp0)
REVERT: C  101 PHE cc_start: 0.6808 (m-80) cc_final: 0.6240 (m-80)
REVERT: D   53 ASP cc_start: 0.8834 (p0) cc_final: 0.7664 (p0)
REVERT: D   80 GLN cc_start: 0.8806 (tt0) cc_final: 0.8406 (tt0)
REVERT: D   82 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7881 (mp0)
REVERT: D   84 GLU cc_start: 0.8049 (mp0) cc_final: 0.7777 (mp0)
REVERT: E   35 LYS cc_start: 0.7489 (mttt) cc_final: 0.6941 (mtpt)
REVERT: E   36 TRP cc_start: 0.8877 (t-100) cc_final: 0.8053 (t-100)
REVERT: E   46 LYS cc_start: 0.8157 (ptpt) cc_final: 0.7895 (ptpp)
REVERT: E   82 GLU cc_start: 0.8489 (mp0) cc_final: 0.8197 (mp0)
REVERT: E   84 GLU cc_start: 0.7933 (mp0) cc_final: 0.7713 (mp0)
REVERT: E   87 TYR cc_start: 0.8373 (t80) cc_final: 0.8042 (t80)
REVERT: F   17 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7773 (mtp180)
REVERT: F   36 TRP cc_start: 0.8770 (t-100) cc_final: 0.8128 (t-100)
REVERT: F   53 ASP cc_start: 0.8714 (p0) cc_final: 0.7894 (p0)
REVERT: F   82 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8068 (mp0)
REVERT: F   86 ASP cc_start: 0.8401 (m-30) cc_final: 0.8170 (m-30)
REVERT: G   36 TRP cc_start: 0.8620 (t-100) cc_final: 0.8262 (t-100)
REVERT: G   40 PHE cc_start: 0.8345 (m-10) cc_final: 0.8100 (m-10)
REVERT: G   46 LYS cc_start: 0.8282 (ptpt) cc_final: 0.8018 (ptpp)
REVERT: G   53 ASP cc_start: 0.8790 (p0) cc_final: 0.7591 (p0)
REVERT: G   80 GLN cc_start: 0.8769 (tt0) cc_final: 0.8300 (tm-30)
REVERT: G   82 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8164 (mt-10)
REVERT: G   84 GLU cc_start: 0.7622 (mp0) cc_final: 0.7208 (mp0)
REVERT: G   87 TYR cc_start: 0.8397 (t80) cc_final: 0.8150 (t80)
REVERT: H   40 PHE cc_start: 0.8597 (m-10) cc_final: 0.8224 (m-10)
REVERT: H   46 LYS cc_start: 0.8222 (ptpt) cc_final: 0.7835 (ptmt)
REVERT: H   53 ASP cc_start: 0.8855 (p0) cc_final: 0.7913 (p0)
REVERT: H   83 ASP cc_start: 0.7517 (t0) cc_final: 0.7267 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 201
  average time/residue: 0.1521
  time to fit residues: 40.0682
Evaluate side-chains
  192 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 186
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain C residue   29 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.081590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.071525 restraints weight = 16828.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 4.08
r_work: 0.3613 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   5608  Z= 0.312
  Angle     :  0.871   6.999   7616  Z= 0.434
  Chirality :  0.044   0.149    792
  Planarity :  0.006   0.045   1000
  Dihedral  :  6.385  24.809    792
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 20.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.13 %
    Favored  : 82.87 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 24.48 %
    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: -5.22 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP H  99 
 PHE   0.013   0.002   PHE H 101 
 TYR   0.019   0.002   TYR A  88 
 ARG   0.003   0.001   ARG B  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02318 (   32)
  hydrogen bonds       : angle       4.27756 (   96)
  SS BOND              : bond        0.00515 (    8)
  SS BOND              : angle       1.18603 (   16)
  covalent geometry    : bond        0.00679 ( 5600)
  covalent geometry    : angle       0.87071 ( 7600)

*********************** 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
  196 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 187
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8695 (mttt) cc_final: 0.8130 (mtpt)
REVERT: A   36 TRP cc_start: 0.8933 (t-100) cc_final: 0.8531 (t-100)
REVERT: A   53 ASP cc_start: 0.8650 (p0) cc_final: 0.8290 (p0)
REVERT: B   50 TYR cc_start: 0.7999 (t80) cc_final: 0.7684 (t80)
REVERT: B   82 GLU cc_start: 0.8256 (mp0) cc_final: 0.7630 (mp0)
REVERT: C   40 PHE cc_start: 0.8667 (m-80) cc_final: 0.8386 (m-10)
REVERT: C   67 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8387 (mttt)
REVERT: C   82 GLU cc_start: 0.8721 (mt-10) cc_final: 0.7918 (mp0)
REVERT: C   84 GLU cc_start: 0.8232 (mp0) cc_final: 0.7597 (mp0)
REVERT: C   88 TYR cc_start: 0.8760 (m-80) cc_final: 0.8473 (m-80)
REVERT: D   53 ASP cc_start: 0.8835 (p0) cc_final: 0.7577 (p0)
REVERT: D   80 GLN cc_start: 0.8907 (tt0) cc_final: 0.8546 (tt0)
REVERT: D   82 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8003 (mp0)
REVERT: D   84 GLU cc_start: 0.8049 (mp0) cc_final: 0.7595 (mp0)
REVERT: E   46 LYS cc_start: 0.7885 (ptpt) cc_final: 0.7629 (ptpp)
REVERT: E   53 ASP cc_start: 0.8435 (p0) cc_final: 0.7460 (p0)
REVERT: E   76 VAL cc_start: 0.9121 (t) cc_final: 0.8841 (p)
REVERT: E   82 GLU cc_start: 0.8419 (mp0) cc_final: 0.8071 (mp0)
REVERT: F   36 TRP cc_start: 0.9044 (t-100) cc_final: 0.8397 (t-100)
REVERT: F   63 PHE cc_start: 0.8791 (t80) cc_final: 0.8276 (t80)
REVERT: F   82 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8128 (mp0)
REVERT: F   86 ASP cc_start: 0.8333 (m-30) cc_final: 0.8004 (m-30)
REVERT: F   88 TYR cc_start: 0.8899 (m-80) cc_final: 0.8601 (m-80)
REVERT: G   36 TRP cc_start: 0.8695 (t-100) cc_final: 0.8174 (t-100)
REVERT: G   46 LYS cc_start: 0.8092 (ptpt) cc_final: 0.7811 (ptpp)
REVERT: G   53 ASP cc_start: 0.8747 (p0) cc_final: 0.7588 (p0)
REVERT: G   84 GLU cc_start: 0.7919 (mp0) cc_final: 0.7615 (mp0)
REVERT: H   40 PHE cc_start: 0.8519 (m-10) cc_final: 0.8250 (m-10)
REVERT: H   46 LYS cc_start: 0.7838 (ptpt) cc_final: 0.7361 (ptpt)
  outliers start: 9
  outliers final: 6
  residues processed: 190
  average time/residue: 0.1352
  time to fit residues: 34.5227
Evaluate side-chains
  182 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 176
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain F residue   79 LEU
Chi-restraints excluded: chain G residue   79 LEU
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:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4107 r_free = 0.4107 target = 0.085129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.075463 restraints weight = 15744.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 3.91
r_work: 0.3725 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5608  Z= 0.176
  Angle     :  0.774   8.139   7616  Z= 0.371
  Chirality :  0.044   0.155    792
  Planarity :  0.006   0.045   1000
  Dihedral  :  5.758  22.700    792
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.52 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 26.39 %
    Favored  : 72.05 %
  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   0.013   0.002   TRP B  92 
 PHE   0.011   0.002   PHE A  40 
 TYR   0.014   0.001   TYR B  87 
 ARG   0.003   0.000   ARG B  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01381 (   32)
  hydrogen bonds       : angle       3.77560 (   96)
  SS BOND              : bond        0.00189 (    8)
  SS BOND              : angle       0.91396 (   16)
  covalent geometry    : bond        0.00411 ( 5600)
  covalent geometry    : angle       0.77326 ( 7600)

*********************** 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
  194 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 185
  time to evaluate  : 0.559 
Fit side-chains
REVERT: A   29 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8513 (tp)
REVERT: A   35 LYS cc_start: 0.8779 (mttt) cc_final: 0.8198 (mtpt)
REVERT: A   36 TRP cc_start: 0.9028 (t-100) cc_final: 0.8045 (t-100)
REVERT: A   47 LEU cc_start: 0.8752 (tt) cc_final: 0.8541 (tt)
REVERT: A   53 ASP cc_start: 0.8893 (p0) cc_final: 0.7852 (p0)
REVERT: A   55 ARG cc_start: 0.8472 (ttm110) cc_final: 0.6871 (mtt-85)
REVERT: B   29 ILE cc_start: 0.8985 (pt) cc_final: 0.8542 (mt)
REVERT: B   36 TRP cc_start: 0.8853 (t-100) cc_final: 0.7485 (t-100)
REVERT: B   50 TYR cc_start: 0.8207 (t80) cc_final: 0.7787 (t80)
REVERT: B   53 ASP cc_start: 0.8710 (p0) cc_final: 0.8342 (p0)
REVERT: B   63 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7995 (t80)
REVERT: B   80 GLN cc_start: 0.9100 (mt0) cc_final: 0.8657 (mm-40)
REVERT: B   82 GLU cc_start: 0.8387 (mp0) cc_final: 0.8055 (mp0)
REVERT: C   40 PHE cc_start: 0.8702 (m-80) cc_final: 0.8376 (m-10)
REVERT: C   67 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8433 (mttt)
REVERT: C   82 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8061 (mp0)
REVERT: C   84 GLU cc_start: 0.8420 (mp0) cc_final: 0.7783 (mp0)
REVERT: D   53 ASP cc_start: 0.8868 (p0) cc_final: 0.7602 (p0)
REVERT: D   63 PHE cc_start: 0.8640 (t80) cc_final: 0.7632 (t80)
REVERT: D   80 GLN cc_start: 0.8881 (tt0) cc_final: 0.8284 (tt0)
REVERT: D   82 GLU cc_start: 0.8686 (mt-10) cc_final: 0.7962 (mp0)
REVERT: D   84 GLU cc_start: 0.8168 (mp0) cc_final: 0.7742 (mp0)
REVERT: E   29 ILE cc_start: 0.8968 (pt) cc_final: 0.8750 (mt)
REVERT: E   36 TRP cc_start: 0.9091 (t-100) cc_final: 0.8276 (t-100)
REVERT: E   37 TYR cc_start: 0.8616 (t80) cc_final: 0.7102 (t80)
REVERT: E   53 ASP cc_start: 0.8534 (p0) cc_final: 0.7534 (p0)
REVERT: E   63 PHE cc_start: 0.8615 (t80) cc_final: 0.7724 (t80)
REVERT: E   76 VAL cc_start: 0.9252 (t) cc_final: 0.9006 (p)
REVERT: E   82 GLU cc_start: 0.8489 (mp0) cc_final: 0.8156 (mp0)
REVERT: E   84 GLU cc_start: 0.8175 (mp0) cc_final: 0.7912 (mp0)
REVERT: F   17 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7914 (mtp180)
REVERT: F   82 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8190 (mp0)
REVERT: F   86 ASP cc_start: 0.8343 (m-30) cc_final: 0.8126 (m-30)
REVERT: G   36 TRP cc_start: 0.8837 (t-100) cc_final: 0.8212 (t-100)
REVERT: G   40 PHE cc_start: 0.8404 (m-10) cc_final: 0.8030 (m-10)
REVERT: G   46 LYS cc_start: 0.8452 (ptpt) cc_final: 0.8139 (ptpp)
REVERT: G   53 ASP cc_start: 0.8856 (p0) cc_final: 0.7671 (p0)
REVERT: G   82 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8471 (mt-10)
REVERT: G   84 GLU cc_start: 0.8164 (mp0) cc_final: 0.7636 (mp0)
REVERT: H   39 GLN cc_start: 0.8105 (tt0) cc_final: 0.7624 (mt0)
REVERT: H   40 PHE cc_start: 0.8681 (m-10) cc_final: 0.8470 (m-80)
REVERT: H   53 ASP cc_start: 0.8855 (p0) cc_final: 0.7867 (p0)
REVERT: H   83 ASP cc_start: 0.7961 (t0) cc_final: 0.7679 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 188
  average time/residue: 0.1366
  time to fit residues: 34.2967
Evaluate side-chains
  185 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 177
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain E residue   79 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0470
   chunk 68 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.8280

-------------------------------------------------------------------------------
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 = 0.4126 r_free = 0.4126 target = 0.085489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.076290 restraints weight = 15729.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 3.84
r_work: 0.3734 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5608  Z= 0.165
  Angle     :  0.773   8.018   7616  Z= 0.365
  Chirality :  0.043   0.151    792
  Planarity :  0.005   0.041   1000
  Dihedral  :  5.532  24.815    792
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.17 %
    Favored  : 84.83 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 26.22 %
    Favored  : 72.05 %
  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: -5.14 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.91 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  92 
 PHE   0.013   0.002   PHE G  40 
 TYR   0.021   0.001   TYR G  87 
 ARG   0.003   0.000   ARG F  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01455 (   32)
  hydrogen bonds       : angle       3.68454 (   96)
  SS BOND              : bond        0.00162 (    8)
  SS BOND              : angle       0.85351 (   16)
  covalent geometry    : bond        0.00391 ( 5600)
  covalent geometry    : angle       0.77292 ( 7600)

*********************** 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
  192 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 182
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A   29 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8470 (tp)
REVERT: A   35 LYS cc_start: 0.8726 (mttt) cc_final: 0.8111 (mtpt)
REVERT: A   36 TRP cc_start: 0.8852 (t-100) cc_final: 0.7897 (t-100)
REVERT: A   55 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7709 (mtt90)
REVERT: B   36 TRP cc_start: 0.8779 (t-100) cc_final: 0.7393 (t-100)
REVERT: B   63 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7939 (t80)
REVERT: B   80 GLN cc_start: 0.9138 (mt0) cc_final: 0.8673 (mm-40)
REVERT: B   82 GLU cc_start: 0.8289 (mp0) cc_final: 0.7848 (mp0)
REVERT: C   17 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8045 (mtp180)
REVERT: C   40 PHE cc_start: 0.8638 (m-80) cc_final: 0.8399 (m-10)
REVERT: C   67 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8316 (mttt)
REVERT: C   82 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8008 (mp0)
REVERT: C   84 GLU cc_start: 0.8288 (mp0) cc_final: 0.7632 (mp0)
REVERT: D   53 ASP cc_start: 0.8769 (p0) cc_final: 0.7503 (p0)
REVERT: D   63 PHE cc_start: 0.8664 (t80) cc_final: 0.7579 (t80)
REVERT: D   80 GLN cc_start: 0.8867 (tt0) cc_final: 0.8290 (tt0)
REVERT: D   82 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7942 (mp0)
REVERT: D   84 GLU cc_start: 0.8027 (mp0) cc_final: 0.7575 (mp0)
REVERT: E   36 TRP cc_start: 0.9024 (t-100) cc_final: 0.8136 (t-100)
REVERT: E   37 TYR cc_start: 0.8469 (t80) cc_final: 0.6893 (t80)
REVERT: E   53 ASP cc_start: 0.8420 (p0) cc_final: 0.7357 (p0)
REVERT: E   63 PHE cc_start: 0.8615 (t80) cc_final: 0.7358 (t80)
REVERT: E   82 GLU cc_start: 0.8403 (mp0) cc_final: 0.8064 (mp0)
REVERT: F   17 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7841 (mtp180)
REVERT: F   63 PHE cc_start: 0.8681 (t80) cc_final: 0.7708 (t80)
REVERT: F   82 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8130 (mp0)
REVERT: G   36 TRP cc_start: 0.8771 (t-100) cc_final: 0.8129 (t-100)
REVERT: G   40 PHE cc_start: 0.8174 (m-10) cc_final: 0.7895 (m-10)
REVERT: G   46 LYS cc_start: 0.8233 (ptpt) cc_final: 0.7926 (ptpp)
REVERT: G   53 ASP cc_start: 0.8781 (p0) cc_final: 0.7603 (p0)
REVERT: G   82 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8433 (mt-10)
REVERT: G   84 GLU cc_start: 0.8009 (mp0) cc_final: 0.7502 (mp0)
REVERT: H   39 GLN cc_start: 0.8066 (tt0) cc_final: 0.7522 (mt0)
REVERT: H   40 PHE cc_start: 0.8636 (m-10) cc_final: 0.8329 (m-10)
REVERT: H   46 LYS cc_start: 0.7935 (ptpt) cc_final: 0.7425 (ptpt)
REVERT: H   53 ASP cc_start: 0.8786 (p0) cc_final: 0.7803 (p0)
REVERT: H   83 ASP cc_start: 0.7878 (t0) cc_final: 0.7618 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 186
  average time/residue: 0.1456
  time to fit residues: 35.8426
Evaluate side-chains
  188 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 180
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.083682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.074010 restraints weight = 15884.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 3.85
r_work: 0.3690 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5608  Z= 0.202
  Angle     :  0.797   8.131   7616  Z= 0.381
  Chirality :  0.044   0.163    792
  Planarity :  0.005   0.045   1000
  Dihedral  :  5.666  25.441    792
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.47 %
    Favored  : 85.53 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.95 %
    Favored  : 70.14 %
  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: -5.18 (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   0.012   0.002   TRP H  92 
 PHE   0.030   0.002   PHE D  40 
 TYR   0.025   0.002   TYR G  87 
 ARG   0.002   0.000   ARG B  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01725 (   32)
  hydrogen bonds       : angle       3.71138 (   96)
  SS BOND              : bond        0.00361 (    8)
  SS BOND              : angle       1.16456 (   16)
  covalent geometry    : bond        0.00461 ( 5600)
  covalent geometry    : angle       0.79627 ( 7600)

*********************** 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
  193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 182
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8767 (mttt) cc_final: 0.8182 (mtpt)
REVERT: A   36 TRP cc_start: 0.8900 (t-100) cc_final: 0.7946 (t-100)
REVERT: A   55 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7727 (mtt90)
REVERT: B   36 TRP cc_start: 0.8824 (t-100) cc_final: 0.7397 (t-100)
REVERT: B   63 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7970 (t80)
REVERT: B   80 GLN cc_start: 0.9131 (mt0) cc_final: 0.8818 (mm-40)
REVERT: B   82 GLU cc_start: 0.8318 (mp0) cc_final: 0.7973 (mp0)
REVERT: C   17 ARG cc_start: 0.8343 (mtt180) cc_final: 0.8113 (mtp180)
REVERT: C   40 PHE cc_start: 0.8660 (m-80) cc_final: 0.8431 (m-10)
REVERT: C   67 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8321 (mttt)
REVERT: C   82 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8094 (mp0)
REVERT: C   84 GLU cc_start: 0.8381 (mp0) cc_final: 0.7695 (mp0)
REVERT: D   53 ASP cc_start: 0.8758 (p0) cc_final: 0.7458 (p0)
REVERT: D   63 PHE cc_start: 0.8656 (t80) cc_final: 0.7564 (t80)
REVERT: D   80 GLN cc_start: 0.8917 (tt0) cc_final: 0.8541 (tt0)
REVERT: D   82 GLU cc_start: 0.8645 (mt-10) cc_final: 0.7989 (mp0)
REVERT: D   84 GLU cc_start: 0.8082 (mp0) cc_final: 0.7639 (mp0)
REVERT: E   29 ILE cc_start: 0.8846 (pt) cc_final: 0.8643 (mt)
REVERT: E   37 TYR cc_start: 0.8533 (t80) cc_final: 0.6990 (t80)
REVERT: E   53 ASP cc_start: 0.8417 (p0) cc_final: 0.7362 (p0)
REVERT: E   63 PHE cc_start: 0.8641 (t80) cc_final: 0.7456 (t80)
REVERT: E   82 GLU cc_start: 0.8443 (mp0) cc_final: 0.8131 (mp0)
REVERT: E   84 GLU cc_start: 0.8044 (mp0) cc_final: 0.7718 (mp0)
REVERT: F   17 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7884 (mtp180)
REVERT: F   63 PHE cc_start: 0.8755 (t80) cc_final: 0.7798 (t80)
REVERT: F   82 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8150 (mp0)
REVERT: G   36 TRP cc_start: 0.8752 (t-100) cc_final: 0.8078 (t-100)
REVERT: G   40 PHE cc_start: 0.8203 (m-10) cc_final: 0.7670 (m-80)
REVERT: G   46 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7944 (ptpp)
REVERT: G   53 ASP cc_start: 0.8896 (p0) cc_final: 0.7599 (p0)
REVERT: G   82 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8443 (mt-10)
REVERT: G   84 GLU cc_start: 0.8087 (mp0) cc_final: 0.7626 (mp0)
REVERT: H   39 GLN cc_start: 0.8060 (tt0) cc_final: 0.7707 (mt0)
REVERT: H   46 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7434 (ptpt)
REVERT: H   53 ASP cc_start: 0.8821 (p0) cc_final: 0.8537 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 185
  average time/residue: 0.1493
  time to fit residues: 36.6028
Evaluate side-chains
  185 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 175
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain F residue   79 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   chunk 34 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.084072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.075057 restraints weight = 15986.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 3.80
r_work: 0.3706 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5608  Z= 0.180
  Angle     :  0.791   8.146   7616  Z= 0.377
  Chirality :  0.044   0.193    792
  Planarity :  0.005   0.044   1000
  Dihedral  :  5.665  25.820    792
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 27.78 %
    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: -5.16 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E  36 
 PHE   0.024   0.002   PHE D  40 
 TYR   0.023   0.001   TYR G  87 
 ARG   0.003   0.000   ARG G  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01665 (   32)
  hydrogen bonds       : angle       3.65287 (   96)
  SS BOND              : bond        0.00200 (    8)
  SS BOND              : angle       1.01675 (   16)
  covalent geometry    : bond        0.00420 ( 5600)
  covalent geometry    : angle       0.79020 ( 7600)

*********************** 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
  195 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 185
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8782 (mttt) cc_final: 0.8186 (mtpt)
REVERT: A   36 TRP cc_start: 0.8875 (t-100) cc_final: 0.7916 (t-100)
REVERT: A   55 ARG cc_start: 0.8450 (ttm110) cc_final: 0.7838 (mtt90)
REVERT: B   36 TRP cc_start: 0.8790 (t-100) cc_final: 0.7426 (t-100)
REVERT: B   63 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8050 (t80)
REVERT: B   80 GLN cc_start: 0.9132 (mt0) cc_final: 0.8822 (mm-40)
REVERT: B   82 GLU cc_start: 0.8305 (mp0) cc_final: 0.7934 (mp0)
REVERT: C   17 ARG cc_start: 0.8297 (mtt180) cc_final: 0.8049 (mtp180)
REVERT: C   40 PHE cc_start: 0.8628 (m-80) cc_final: 0.8376 (m-10)
REVERT: C   67 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8312 (mttt)
REVERT: C   82 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8060 (mp0)
REVERT: C   84 GLU cc_start: 0.8359 (mp0) cc_final: 0.7647 (mp0)
REVERT: D   53 ASP cc_start: 0.8716 (p0) cc_final: 0.7399 (p0)
REVERT: D   63 PHE cc_start: 0.8667 (t80) cc_final: 0.7614 (t80)
REVERT: D   80 GLN cc_start: 0.8905 (tt0) cc_final: 0.8475 (tt0)
REVERT: D   82 GLU cc_start: 0.8645 (mt-10) cc_final: 0.7935 (mp0)
REVERT: D   84 GLU cc_start: 0.8067 (mp0) cc_final: 0.7587 (mp0)
REVERT: E   29 ILE cc_start: 0.9039 (pt) cc_final: 0.8665 (mt)
REVERT: E   36 TRP cc_start: 0.9015 (t-100) cc_final: 0.7874 (t-100)
REVERT: E   53 ASP cc_start: 0.8401 (p0) cc_final: 0.7196 (p0)
REVERT: E   63 PHE cc_start: 0.8650 (t80) cc_final: 0.7457 (t80)
REVERT: E   82 GLU cc_start: 0.8401 (mp0) cc_final: 0.7983 (mp0)
REVERT: E   84 GLU cc_start: 0.8044 (mp0) cc_final: 0.7638 (mp0)
REVERT: F   17 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7844 (mtp180)
REVERT: F   53 ASP cc_start: 0.8666 (p0) cc_final: 0.8254 (p0)
REVERT: F   63 PHE cc_start: 0.8748 (t80) cc_final: 0.7809 (t80)
REVERT: F   82 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8143 (mp0)
REVERT: F   84 GLU cc_start: 0.7955 (mp0) cc_final: 0.7689 (mp0)
REVERT: G   40 PHE cc_start: 0.8378 (m-10) cc_final: 0.7831 (m-10)
REVERT: G   46 LYS cc_start: 0.8265 (ptpt) cc_final: 0.7964 (ptpp)
REVERT: G   53 ASP cc_start: 0.8903 (p0) cc_final: 0.7601 (p0)
REVERT: G   82 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8452 (mt-10)
REVERT: G   84 GLU cc_start: 0.8148 (mp0) cc_final: 0.7617 (mp0)
REVERT: H   37 TYR cc_start: 0.7526 (t80) cc_final: 0.6679 (t80)
REVERT: H   40 PHE cc_start: 0.8496 (m-80) cc_final: 0.8009 (m-80)
REVERT: H   46 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7475 (ptpt)
REVERT: H   53 ASP cc_start: 0.8813 (p0) cc_final: 0.8527 (p0)
REVERT: H   83 ASP cc_start: 0.7820 (t0) cc_final: 0.7553 (t0)
REVERT: H   88 TYR cc_start: 0.7336 (m-80) cc_final: 0.6998 (t80)
  outliers start: 10
  outliers final: 9
  residues processed: 187
  average time/residue: 0.1425
  time to fit residues: 35.5580
Evaluate side-chains
  190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 180
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain F residue   79 LEU
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:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.080288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.071022 restraints weight = 16489.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 3.91
r_work: 0.3617 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   5608  Z= 0.252
  Angle     :  0.856   8.889   7616  Z= 0.412
  Chirality :  0.045   0.194    792
  Planarity :  0.005   0.045   1000
  Dihedral  :  6.007  27.156    792
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.99 %
    Favored  : 83.01 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 28.47 %
    Favored  : 69.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.23 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.98 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  36 
 PHE   0.030   0.003   PHE D  40 
 TYR   0.026   0.002   TYR G  87 
 ARG   0.002   0.000   ARG G  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02066 (   32)
  hydrogen bonds       : angle       3.81218 (   96)
  SS BOND              : bond        0.00376 (    8)
  SS BOND              : angle       1.14036 (   16)
  covalent geometry    : bond        0.00561 ( 5600)
  covalent geometry    : angle       0.85481 ( 7600)

*********************** 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
  194 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.8898 (t-100) cc_final: 0.7906 (t-100)
REVERT: A   53 ASP cc_start: 0.8802 (p0) cc_final: 0.7626 (p0)
REVERT: A   55 ARG cc_start: 0.8406 (ttm110) cc_final: 0.7085 (mtt-85)
REVERT: B   36 TRP cc_start: 0.8838 (t-100) cc_final: 0.7379 (t-100)
REVERT: B   53 ASP cc_start: 0.8632 (p0) cc_final: 0.8354 (p0)
REVERT: B   63 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8088 (t80)
REVERT: B   80 GLN cc_start: 0.9157 (mt0) cc_final: 0.8792 (mm-40)
REVERT: B   82 GLU cc_start: 0.8339 (mp0) cc_final: 0.7961 (mp0)
REVERT: C   40 PHE cc_start: 0.8671 (m-80) cc_final: 0.8457 (m-10)
REVERT: C   67 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8344 (mttt)
REVERT: C   82 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8059 (mp0)
REVERT: C   84 GLU cc_start: 0.8326 (mp0) cc_final: 0.7610 (mp0)
REVERT: D   53 ASP cc_start: 0.8641 (p0) cc_final: 0.7257 (p0)
REVERT: D   63 PHE cc_start: 0.8719 (t80) cc_final: 0.7577 (t80)
REVERT: D   82 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7971 (mp0)
REVERT: D   84 GLU cc_start: 0.8081 (mp0) cc_final: 0.7514 (mp0)
REVERT: E   63 PHE cc_start: 0.8624 (t80) cc_final: 0.7689 (t80)
REVERT: E   82 GLU cc_start: 0.8446 (mp0) cc_final: 0.8185 (mp0)
REVERT: E   83 ASP cc_start: 0.8139 (t0) cc_final: 0.7917 (t0)
REVERT: E   84 GLU cc_start: 0.8070 (mp0) cc_final: 0.7799 (mp0)
REVERT: F   17 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7867 (mtp180)
REVERT: F   53 ASP cc_start: 0.8709 (p0) cc_final: 0.8495 (p0)
REVERT: F   63 PHE cc_start: 0.8839 (t80) cc_final: 0.8030 (t80)
REVERT: F   82 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8173 (mp0)
REVERT: F   84 GLU cc_start: 0.8044 (mp0) cc_final: 0.7763 (mp0)
REVERT: G   40 PHE cc_start: 0.8409 (m-10) cc_final: 0.7939 (m-10)
REVERT: G   46 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7971 (ptpp)
REVERT: G   53 ASP cc_start: 0.8910 (p0) cc_final: 0.7616 (p0)
REVERT: G   82 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8470 (mt-10)
REVERT: G   84 GLU cc_start: 0.8220 (mp0) cc_final: 0.7712 (mp0)
REVERT: H   37 TYR cc_start: 0.7449 (t80) cc_final: 0.6609 (t80)
REVERT: H   40 PHE cc_start: 0.8537 (m-80) cc_final: 0.8032 (m-80)
REVERT: H   46 LYS cc_start: 0.7750 (ptpt) cc_final: 0.7336 (ptpt)
REVERT: H   53 ASP cc_start: 0.8700 (p0) cc_final: 0.8364 (p0)
REVERT: H   83 ASP cc_start: 0.7727 (t0) cc_final: 0.7507 (t0)
REVERT: H   84 GLU cc_start: 0.8665 (mp0) cc_final: 0.8392 (mp0)
  outliers start: 12
  outliers final: 10
  residues processed: 186
  average time/residue: 0.1356
  time to fit residues: 34.2895
Evaluate side-chains
  192 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 181
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain F residue   79 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.3980
   chunk 6 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0870
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.083572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.073102 restraints weight = 15536.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 3.95
r_work: 0.3764 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5608  Z= 0.141
  Angle     :  0.791   9.399   7616  Z= 0.371
  Chirality :  0.045   0.275    792
  Planarity :  0.005   0.039   1000
  Dihedral  :  5.550  27.120    792
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 28.99 %
    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: -5.09 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.88 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  36 
 PHE   0.030   0.002   PHE D  40 
 TYR   0.019   0.001   TYR G  87 
 ARG   0.002   0.000   ARG D  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01426 (   32)
  hydrogen bonds       : angle       3.66229 (   96)
  SS BOND              : bond        0.00051 (    8)
  SS BOND              : angle       0.80201 (   16)
  covalent geometry    : bond        0.00352 ( 5600)
  covalent geometry    : angle       0.79053 ( 7600)

********************** 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
  193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 183
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.8954 (t-100) cc_final: 0.8496 (t-100)
REVERT: A   55 ARG cc_start: 0.8452 (ttm110) cc_final: 0.7746 (mtt90)
REVERT: A   63 PHE cc_start: 0.8005 (t80) cc_final: 0.7660 (t80)
REVERT: B   53 ASP cc_start: 0.8833 (p0) cc_final: 0.7657 (p0)
REVERT: B   63 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7812 (t80)
REVERT: B   80 GLN cc_start: 0.9162 (mt0) cc_final: 0.8815 (mm-40)
REVERT: B   82 GLU cc_start: 0.8392 (mp0) cc_final: 0.8044 (mp0)
REVERT: C   17 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8135 (mtp180)
REVERT: C   40 PHE cc_start: 0.8618 (m-80) cc_final: 0.8351 (m-10)
REVERT: C   53 ASP cc_start: 0.8653 (p0) cc_final: 0.7605 (p0)
REVERT: C   63 PHE cc_start: 0.8785 (t80) cc_final: 0.8271 (t80)
REVERT: C   67 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8313 (mttt)
REVERT: C   82 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8107 (mp0)
REVERT: C   84 GLU cc_start: 0.8428 (mp0) cc_final: 0.7745 (mp0)
REVERT: D   53 ASP cc_start: 0.8772 (p0) cc_final: 0.7363 (p0)
REVERT: D   63 PHE cc_start: 0.8700 (t80) cc_final: 0.7801 (t80)
REVERT: D   80 GLN cc_start: 0.8895 (tt0) cc_final: 0.8414 (tt0)
REVERT: D   82 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8079 (mp0)
REVERT: D   83 ASP cc_start: 0.8273 (t0) cc_final: 0.8068 (t0)
REVERT: D   84 GLU cc_start: 0.8142 (mp0) cc_final: 0.7681 (mp0)
REVERT: E   53 ASP cc_start: 0.8648 (p0) cc_final: 0.7269 (p0)
REVERT: E   63 PHE cc_start: 0.8709 (t80) cc_final: 0.7604 (t80)
REVERT: E   82 GLU cc_start: 0.8530 (mp0) cc_final: 0.8203 (mp0)
REVERT: E   84 GLU cc_start: 0.8060 (mp0) cc_final: 0.7729 (mp0)
REVERT: E   86 ASP cc_start: 0.8723 (m-30) cc_final: 0.8434 (m-30)
REVERT: F   17 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7918 (mtp180)
REVERT: F   36 TRP cc_start: 0.9022 (t-100) cc_final: 0.8522 (t-100)
REVERT: F   53 ASP cc_start: 0.8818 (p0) cc_final: 0.8259 (p0)
REVERT: F   63 PHE cc_start: 0.8741 (t80) cc_final: 0.7858 (t80)
REVERT: F   82 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8158 (mp0)
REVERT: G   40 PHE cc_start: 0.8507 (m-10) cc_final: 0.8088 (m-80)
REVERT: G   46 LYS cc_start: 0.8355 (ptpt) cc_final: 0.8046 (ptpp)
REVERT: G   53 ASP cc_start: 0.8955 (p0) cc_final: 0.7664 (p0)
REVERT: G   82 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8161 (mp0)
REVERT: G   84 GLU cc_start: 0.8226 (mp0) cc_final: 0.7705 (mp0)
REVERT: H   40 PHE cc_start: 0.8635 (m-80) cc_final: 0.8372 (m-80)
REVERT: H   46 LYS cc_start: 0.8267 (ptpt) cc_final: 0.7685 (ptpt)
REVERT: H   53 ASP cc_start: 0.8863 (p0) cc_final: 0.7847 (p0)
REVERT: H   83 ASP cc_start: 0.8072 (t0) cc_final: 0.7844 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 186
  average time/residue: 0.1605
  time to fit residues: 40.3775
Evaluate side-chains
  185 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 177
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   63 PHE
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain F residue   79 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   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 = 0.4097 r_free = 0.4097 target = 0.082710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.072929 restraints weight = 15922.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 3.87
r_work: 0.3721 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.4267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5608  Z= 0.189
  Angle     :  0.814   8.753   7616  Z= 0.387
  Chirality :  0.045   0.262    792
  Planarity :  0.005   0.044   1000
  Dihedral  :  5.659  30.345    792
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.47 %
    Favored  : 85.53 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 29.34 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -5.11 (0.21), residues: 712
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.16), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP E  36 
 PHE   0.027   0.002   PHE D  40 
 TYR   0.027   0.002   TYR B  87 
 ARG   0.002   0.000   ARG D  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01705 (   32)
  hydrogen bonds       : angle       3.71404 (   96)
  SS BOND              : bond        0.00202 (    8)
  SS BOND              : angle       0.91966 (   16)
  covalent geometry    : bond        0.00441 ( 5600)
  covalent geometry    : angle       0.81337 ( 7600)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2646.00 seconds
wall clock time: 46 minutes 17.48 seconds (2777.48 seconds total)