Starting phenix.real_space_refine
on Sat May 17 03:19:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gel_29974/05_2025/8gel_29974.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gel_29974/05_2025/8gel_29974.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gel_29974/05_2025/8gel_29974.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gel_29974/05_2025/8gel_29974.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gel_29974/05_2025/8gel_29974.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gel_29974/05_2025/8gel_29974.cif"
  }
  resolution = 3.9
  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=   0.005
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      52      5.16       5
     C    9824      2.51       5
     N    2620      2.21       5
     O    3060      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15556
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3889
          Classifications: {'peptide': 498}
          Link IDs: {'TRANS': 497}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 7.61, per 1000 atoms: 0.49
  Number of scatterers: 15556
  At special positions: 0
  Unit cell: (127.875, 127.875, 90.75, 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      52     16.00
     O    3060      8.00
     N    2620      7.00
     C    9824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.53
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3920

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      96.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 43
      removed outlier: 3.847A  pdb=" N   GLU A  42 " --> pdb=" O   GLU A  38 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASP A  43 " --> pdb=" O   LYS A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 89
      removed outlier: 4.183A  pdb=" N   ASN A  55 " --> pdb=" O   ASN A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 131
      removed outlier: 3.727A  pdb=" N   ILE A  96 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 170
    Processing helix  chain 'A' and resid 173 through 210
      removed outlier: 3.815A  pdb=" N   ARG A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 213
      No H-bonds generated for 'chain 'A' and resid 211 through 213'
    Processing helix  chain 'A' and resid 214 through 253
    Processing helix  chain 'A' and resid 256 through 294
      removed outlier: 4.510A  pdb=" N   GLU A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 335
    Processing helix  chain 'A' and resid 338 through 375
    Processing helix  chain 'A' and resid 378 through 422
      removed outlier: 3.601A  pdb=" N   VAL A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 464
    Processing helix  chain 'A' and resid 466 through 500
    Processing helix  chain 'B' and resid 2 through 43
      removed outlier: 3.848A  pdb=" N   GLU B  42 " --> pdb=" O   GLU B  38 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASP B  43 " --> pdb=" O   LYS B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 89
      removed outlier: 4.183A  pdb=" N   ASN B  55 " --> pdb=" O   ASN B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 131
      removed outlier: 3.728A  pdb=" N   ILE B  96 " --> pdb=" O   ASP B  92 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU B 131 " --> pdb=" O   GLU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 170
    Processing helix  chain 'B' and resid 173 through 210
      removed outlier: 3.815A  pdb=" N   ARG B 179 " --> pdb=" O   LYS B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 213
      No H-bonds generated for 'chain 'B' and resid 211 through 213'
    Processing helix  chain 'B' and resid 214 through 253
    Processing helix  chain 'B' and resid 256 through 294
      removed outlier: 4.510A  pdb=" N   GLU B 294 " --> pdb=" O   ILE B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 335
    Processing helix  chain 'B' and resid 338 through 375
    Processing helix  chain 'B' and resid 378 through 422
      removed outlier: 3.601A  pdb=" N   VAL B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 464
    Processing helix  chain 'B' and resid 466 through 500
    Processing helix  chain 'C' and resid 2 through 43
      removed outlier: 3.847A  pdb=" N   GLU C  42 " --> pdb=" O   GLU C  38 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP C  43 " --> pdb=" O   LYS C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 89
      removed outlier: 4.183A  pdb=" N   ASN C  55 " --> pdb=" O   ASN C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 131
      removed outlier: 3.727A  pdb=" N   ILE C  96 " --> pdb=" O   ASP C  92 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU C 131 " --> pdb=" O   GLU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 170
    Processing helix  chain 'C' and resid 173 through 210
      removed outlier: 3.815A  pdb=" N   ARG C 179 " --> pdb=" O   LYS C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 213
      No H-bonds generated for 'chain 'C' and resid 211 through 213'
    Processing helix  chain 'C' and resid 214 through 253
    Processing helix  chain 'C' and resid 256 through 294
      removed outlier: 4.510A  pdb=" N   GLU C 294 " --> pdb=" O   ILE C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 335
    Processing helix  chain 'C' and resid 338 through 375
    Processing helix  chain 'C' and resid 378 through 422
      removed outlier: 3.602A  pdb=" N   VAL C 382 " --> pdb=" O   ASP C 378 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 425 through 464
    Processing helix  chain 'C' and resid 466 through 500
    Processing helix  chain 'D' and resid 2 through 43
      removed outlier: 3.848A  pdb=" N   GLU D  42 " --> pdb=" O   GLU D  38 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP D  43 " --> pdb=" O   LYS D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 89
      removed outlier: 4.182A  pdb=" N   ASN D  55 " --> pdb=" O   ASN D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 131
      removed outlier: 3.726A  pdb=" N   ILE D  96 " --> pdb=" O   ASP D  92 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU D 131 " --> pdb=" O   GLU D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 170
    Processing helix  chain 'D' and resid 173 through 210
      removed outlier: 3.815A  pdb=" N   ARG D 179 " --> pdb=" O   LYS D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 213
      No H-bonds generated for 'chain 'D' and resid 211 through 213'
    Processing helix  chain 'D' and resid 214 through 253
    Processing helix  chain 'D' and resid 256 through 294
      removed outlier: 4.510A  pdb=" N   GLU D 294 " --> pdb=" O   ILE D 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 335
    Processing helix  chain 'D' and resid 338 through 375
    Processing helix  chain 'D' and resid 378 through 422
      removed outlier: 3.601A  pdb=" N   VAL D 382 " --> pdb=" O   ASP D 378 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 425 through 464
    Processing helix  chain 'D' and resid 466 through 500

    1677 hydrogen bonds defined for protein.
    5031 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: 5.00

  Time building geometry restraints manager: 4.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5396
        1.34 -     1.46: 713
        1.46 -     1.57: 9387
        1.57 -     1.69: 0
        1.69 -     1.80: 104
  Bond restraints: 15600
  Sorted by residual:
  bond pdb=" CG1 ILE D  18 "
       pdb=" CD1 ILE D  18 "
    ideal  model  delta    sigma   weight residual
    1.513  1.444  0.069 3.90e-02 6.57e+02 3.14e+00
  bond pdb=" CG1 ILE B  18 "
       pdb=" CD1 ILE B  18 "
    ideal  model  delta    sigma   weight residual
    1.513  1.444  0.069 3.90e-02 6.57e+02 3.11e+00
  bond pdb=" CG1 ILE A  18 "
       pdb=" CD1 ILE A  18 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.08e+00
  bond pdb=" CG1 ILE C  18 "
       pdb=" CD1 ILE C  18 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.07e+00
  bond pdb=" CG1 ILE C   7 "
       pdb=" CD1 ILE C   7 "
    ideal  model  delta    sigma   weight residual
    1.513  1.446  0.067 3.90e-02 6.57e+02 2.98e+00
  ... (remaining 15595 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 20396
        2.19 -     4.37: 356
        4.37 -     6.56: 104
        6.56 -     8.75: 36
        8.75 -    10.93: 12
  Bond angle restraints: 20904
  Sorted by residual:
  angle pdb=" N   GLU A 130 "
        pdb=" CA  GLU A 130 "
        pdb=" C   GLU A 130 "
      ideal   model   delta    sigma   weight residual
     111.82  106.40    5.42 1.16e+00 7.43e-01 2.18e+01
  angle pdb=" N   GLU B 130 "
        pdb=" CA  GLU B 130 "
        pdb=" C   GLU B 130 "
      ideal   model   delta    sigma   weight residual
     111.82  106.43    5.39 1.16e+00 7.43e-01 2.16e+01
  angle pdb=" N   GLU C 130 "
        pdb=" CA  GLU C 130 "
        pdb=" C   GLU C 130 "
      ideal   model   delta    sigma   weight residual
     111.82  106.45    5.37 1.16e+00 7.43e-01 2.14e+01
  angle pdb=" N   GLU D 130 "
        pdb=" CA  GLU D 130 "
        pdb=" C   GLU D 130 "
      ideal   model   delta    sigma   weight residual
     111.82  106.45    5.37 1.16e+00 7.43e-01 2.14e+01
  angle pdb=" N   ASP A 173 "
        pdb=" CA  ASP A 173 "
        pdb=" C   ASP A 173 "
      ideal   model   delta    sigma   weight residual
     109.52  115.76   -6.24 1.55e+00 4.16e-01 1.62e+01
  ... (remaining 20899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 8969
       17.58 -    35.17: 899
       35.17 -    52.75: 168
       52.75 -    70.33: 24
       70.33 -    87.91: 20
  Dihedral angle restraints: 10080
    sinusoidal: 4172
      harmonic: 5908
  Sorted by residual:
  dihedral pdb=" CA  LEU A 334 "
           pdb=" C   LEU A 334 "
           pdb=" N   ALA A 335 "
           pdb=" CA  ALA A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.67  -24.33     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  LEU B 334 "
           pdb=" C   LEU B 334 "
           pdb=" N   ALA B 335 "
           pdb=" CA  ALA B 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.68  -24.32     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  LEU D 334 "
           pdb=" C   LEU D 334 "
           pdb=" N   ALA D 335 "
           pdb=" CA  ALA D 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.69  -24.31     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 10077 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 2416
       0.075 -    0.150: 156
       0.150 -    0.225: 12
       0.225 -    0.300: 0
       0.300 -    0.375: 4
  Chirality restraints: 2588
  Sorted by residual:
  chirality pdb=" CB  ILE C 307 "
            pdb=" CA  ILE C 307 "
            pdb=" CG1 ILE C 307 "
            pdb=" CG2 ILE C 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" CB  ILE D 307 "
            pdb=" CA  ILE D 307 "
            pdb=" CG1 ILE D 307 "
            pdb=" CG2 ILE D 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.49e+00
  chirality pdb=" CB  ILE A 307 "
            pdb=" CA  ILE A 307 "
            pdb=" CG1 ILE A 307 "
            pdb=" CG2 ILE A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.47e+00
  ... (remaining 2585 not shown)

  Planarity restraints: 2668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 210 "    0.011 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   ILE A 210 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A 210 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS A 211 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 210 "   -0.011 2.00e-02 2.50e+03   2.32e-02 5.39e+00
        pdb=" C   ILE C 210 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ILE C 210 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LYS C 211 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 210 "    0.011 2.00e-02 2.50e+03   2.31e-02 5.33e+00
        pdb=" C   ILE D 210 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE D 210 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS D 211 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2665 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 161
        2.66 -     3.22: 15492
        3.22 -     3.78: 26605
        3.78 -     4.34: 31000
        4.34 -     4.90: 50887
  Nonbonded interactions: 124145
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 144 "
            pdb=" NH2 ARG B 147 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" OE1 GLU A 144 "
            pdb=" NH2 ARG A 147 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" OE1 GLU C 144 "
            pdb=" NH2 ARG C 147 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" OE1 GLU D 144 "
            pdb=" NH2 ARG D 147 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" OE2 GLU C 144 "
            pdb=" NH2 ARG C 147 "
     model   vdw
     2.106 3.120
  ... (remaining 124140 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     31.650
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
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      :  0.007   0.069  15600  Z= 0.319
  Angle     :  0.871  10.932  20904  Z= 0.467
  Chirality :  0.044   0.375   2588
  Planarity :  0.003   0.023   2668
  Dihedral  : 14.516  87.915   6160
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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:  1.36 (0.16), residues: 1976
  helix:  1.15 (0.10), residues: 1892
  sheet:  None (None), residues: 0
  loop : -3.42 (0.40), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS D 383 
 PHE   0.009   0.002   PHE A 106 
 TYR   0.001   0.001   TYR D 416 
 ARG   0.003   0.000   ARG D 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06981 ( 1677)
  hydrogen bonds       : angle       4.05209 ( 5031)
  covalent geometry    : bond        0.00730 (15600)
  covalent geometry    : angle       0.87096 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.833 
Fit side-chains
REVERT: A  195 MET cc_start: 0.8114 (tpt) cc_final: 0.7733 (tpt)
REVERT: B   10 GLU cc_start: 0.8331 (tp30) cc_final: 0.8055 (tp30)
REVERT: B  195 MET cc_start: 0.8077 (tpt) cc_final: 0.7751 (tpt)
REVERT: C  195 MET cc_start: 0.8076 (tpt) cc_final: 0.7772 (tpt)
REVERT: D   10 GLU cc_start: 0.8326 (tp30) cc_final: 0.8085 (tp30)
REVERT: D  195 MET cc_start: 0.8156 (tpt) cc_final: 0.7784 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.2542
  time to fit residues: 98.8482
Evaluate side-chains
  141 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    6.9990
   chunk 148 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 153 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 177 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 448 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 = 0.4560 r_free = 0.4560 target = 0.165037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.142944 restraints weight = 13924.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.146627 restraints weight = 7833.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.149013 restraints weight = 5546.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15600  Z= 0.123
  Angle     :  0.528   9.246  20904  Z= 0.258
  Chirality :  0.030   0.133   2588
  Planarity :  0.002   0.018   2668
  Dihedral  :  3.773  23.392   2112
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.32 %
    Favored  : 88.25 %
  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:  4.03 (0.17), residues: 1976
  helix:  2.84 (0.11), residues: 1892
  sheet:  None (None), residues: 0
  loop : -2.67 (0.53), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS C 383 
 PHE   0.007   0.001   PHE B 106 
 TYR   0.002   0.000   TYR A 416 
 ARG   0.003   0.000   ARG B 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 ( 1677)
  hydrogen bonds       : angle       3.15745 ( 5031)
  covalent geometry    : bond        0.00281 (15600)
  covalent geometry    : angle       0.52765 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 1.876 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.8272 (tp30) cc_final: 0.8005 (tp30)
REVERT: A   81 ARG cc_start: 0.7386 (tpt170) cc_final: 0.7071 (tpp-160)
REVERT: A  227 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6252 (tm-30)
REVERT: A  277 ILE cc_start: 0.8722 (tp) cc_final: 0.8521 (mm)
REVERT: B   18 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8045 (mt)
REVERT: B   81 ARG cc_start: 0.7433 (tpt170) cc_final: 0.7105 (tpp-160)
REVERT: C   18 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8031 (mt)
REVERT: C   81 ARG cc_start: 0.7436 (tpt170) cc_final: 0.7085 (tpp-160)
REVERT: C  216 GLU cc_start: 0.7008 (tp30) cc_final: 0.6426 (tm-30)
REVERT: C  227 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6301 (tm-30)
REVERT: D   81 ARG cc_start: 0.7434 (tpt170) cc_final: 0.7120 (tpp-160)
  outliers start: 23
  outliers final: 21
  residues processed: 182
  average time/residue: 0.2728
  time to fit residues: 74.4586
Evaluate side-chains
  157 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 1.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  483 ASP
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  483 ASP
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  483 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 170 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 84 optimal weight:    0.9990
   chunk 69 optimal weight:    0.2980
   chunk 54 optimal weight:    6.9990
   chunk 135 optimal weight:    0.0270
   chunk 161 optimal weight:    2.9990
   chunk 171 optimal weight:    4.9990
   chunk 191 optimal weight:    0.9990
   overall best weight:    0.5240

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 ASN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN
** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 118 ASN
** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.269323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.239966 restraints weight = 16833.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.239606 restraints weight = 24221.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.240200 restraints weight = 21455.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.4865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  15600  Z= 0.108
  Angle     :  0.484   7.905  20904  Z= 0.242
  Chirality :  0.029   0.124   2588
  Planarity :  0.002   0.014   2668
  Dihedral  :  3.591  22.678   2112
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.13 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.02 (0.17), residues: 1976
  helix:  3.46 (0.10), residues: 1908
  sheet:  None (None), residues: 0
  loop : -3.67 (0.40), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 383 
 PHE   0.006   0.001   PHE B 106 
 TYR   0.001   0.000   TYR D 416 
 ARG   0.002   0.000   ARG C 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02904 ( 1677)
  hydrogen bonds       : angle       3.01024 ( 5031)
  covalent geometry    : bond        0.00236 (15600)
  covalent geometry    : angle       0.48393 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 1.732 
Fit side-chains
REVERT: A   47 GLU cc_start: 0.5556 (mm-30) cc_final: 0.4916 (tm-30)
REVERT: A  227 GLU cc_start: 0.6629 (tm-30) cc_final: 0.6262 (tm-30)
REVERT: A  229 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7997 (mt)
REVERT: A  277 ILE cc_start: 0.8764 (tp) cc_final: 0.8542 (mm)
REVERT: A  441 MET cc_start: 0.7633 (mmm) cc_final: 0.7038 (mmt)
REVERT: B   47 GLU cc_start: 0.5673 (mm-30) cc_final: 0.5071 (tm-30)
REVERT: C   47 GLU cc_start: 0.5659 (mm-30) cc_final: 0.5056 (tm-30)
REVERT: C  216 GLU cc_start: 0.6826 (tp30) cc_final: 0.6365 (tm-30)
REVERT: D   47 GLU cc_start: 0.5659 (mm-30) cc_final: 0.5051 (tm-30)
REVERT: D  227 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6190 (tm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 182
  average time/residue: 0.2740
  time to fit residues: 74.5633
Evaluate side-chains
  164 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 1.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  483 ASP
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  483 ASP
Chi-restraints excluded: chain C residue  488 LEU
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  483 ASP
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 170 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 175 optimal weight:    0.8980
   chunk 132 optimal weight:    7.9990
   chunk 185 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 163 optimal weight:    3.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 448 ASN
D 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.266389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 120)---------------|
| r_work = 0.4958 r_free = 0.4958 target = 0.231236 restraints weight = 16809.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.231137 restraints weight = 20661.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4979 r_free = 0.4979 target = 0.231228 restraints weight = 20060.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15600  Z= 0.112
  Angle     :  0.489  12.203  20904  Z= 0.240
  Chirality :  0.029   0.130   2588
  Planarity :  0.002   0.010   2668
  Dihedral  :  3.504  22.600   2112
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.43 %
    Favored  : 83.89 %
  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:  5.38 (0.17), residues: 1976
  helix:  3.69 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.91 (0.37), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 383 
 PHE   0.007   0.001   PHE C 106 
 TYR   0.001   0.000   TYR B 416 
 ARG   0.001   0.000   ARG D 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02816 ( 1677)
  hydrogen bonds       : angle       2.93084 ( 5031)
  covalent geometry    : bond        0.00261 (15600)
  covalent geometry    : angle       0.48949 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 163
  time to evaluate  : 1.711 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6230 (tm-30)
REVERT: A  277 ILE cc_start: 0.8750 (tp) cc_final: 0.8491 (mm)
REVERT: A  441 MET cc_start: 0.7416 (mmm) cc_final: 0.6956 (mmt)
REVERT: C  216 GLU cc_start: 0.6606 (tp30) cc_final: 0.6278 (tm-30)
REVERT: C  227 GLU cc_start: 0.6479 (tm-30) cc_final: 0.6242 (tm-30)
REVERT: D   47 GLU cc_start: 0.5618 (mm-30) cc_final: 0.4914 (tm-30)
  outliers start: 43
  outliers final: 26
  residues processed: 191
  average time/residue: 0.2489
  time to fit residues: 72.8744
Evaluate side-chains
  169 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  488 LEU
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 191 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 150 optimal weight:    9.9990
   chunk 175 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 157 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 GLN
B 118 ASN
B 448 ASN
C  22 GLN
C 118 ASN
D 118 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.264762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 198)---------------|
| r_work = 0.4940 r_free = 0.4940 target = 0.229649 restraints weight = 17109.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 117)---------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.229061 restraints weight = 21687.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.229075 restraints weight = 20596.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.4855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15600  Z= 0.125
  Angle     :  0.506  14.841  20904  Z= 0.247
  Chirality :  0.029   0.137   2588
  Planarity :  0.002   0.012   2668
  Dihedral  :  3.498  22.629   2112
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.60 %
    Favored  : 81.09 %
  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:  5.42 (0.17), residues: 1976
  helix:  3.71 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.99 (0.35), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 383 
 PHE   0.010   0.001   PHE A 401 
 TYR   0.001   0.000   TYR D 416 
 ARG   0.002   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02839 ( 1677)
  hydrogen bonds       : angle       2.92074 ( 5031)
  covalent geometry    : bond        0.00301 (15600)
  covalent geometry    : angle       0.50645 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 1.579 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6273 (tm-30)
REVERT: A  277 ILE cc_start: 0.8705 (tp) cc_final: 0.8443 (mm)
REVERT: A  441 MET cc_start: 0.7429 (mmm) cc_final: 0.6961 (mmt)
REVERT: B   47 GLU cc_start: 0.5459 (mm-30) cc_final: 0.4626 (tm-30)
REVERT: B  227 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6257 (tm-30)
REVERT: B  280 GLU cc_start: 0.7722 (tp30) cc_final: 0.7448 (mm-30)
REVERT: C   47 GLU cc_start: 0.5426 (mm-30) cc_final: 0.4658 (tm-30)
REVERT: C  227 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6280 (tm-30)
REVERT: C  280 GLU cc_start: 0.7712 (tp30) cc_final: 0.7460 (mm-30)
REVERT: D   47 GLU cc_start: 0.5470 (mm-30) cc_final: 0.4652 (tm-30)
REVERT: D  280 GLU cc_start: 0.7680 (tp30) cc_final: 0.7437 (mm-30)
  outliers start: 37
  outliers final: 27
  residues processed: 177
  average time/residue: 0.2396
  time to fit residues: 65.9534
Evaluate side-chains
  167 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 1.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  488 LEU
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 134 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 155 optimal weight:    1.9990
   chunk 141 optimal weight:    0.8980
   chunk 189 optimal weight:   10.0000
   chunk 176 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 131 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 ASN
C 118 ASN
D 118 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.263786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.233134 restraints weight = 17122.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 136)---------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.228340 restraints weight = 19326.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 71)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.227831 restraints weight = 25409.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15600  Z= 0.133
  Angle     :  0.543  15.243  20904  Z= 0.261
  Chirality :  0.029   0.131   2588
  Planarity :  0.002   0.023   2668
  Dihedral  :  3.490  22.532   2112
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.41 %
    Favored  : 80.29 %
  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:  5.40 (0.17), residues: 1976
  helix:  3.70 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -4.04 (0.36), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 383 
 PHE   0.009   0.001   PHE D 401 
 TYR   0.000   0.000   TYR D 416 
 ARG   0.002   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02912 ( 1677)
  hydrogen bonds       : angle       2.93813 ( 5031)
  covalent geometry    : bond        0.00320 (15600)
  covalent geometry    : angle       0.54282 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 148
  time to evaluate  : 1.795 
Fit side-chains
REVERT: A   47 GLU cc_start: 0.5597 (mm-30) cc_final: 0.4661 (tm-30)
REVERT: A  227 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6258 (tm-30)
REVERT: A  277 ILE cc_start: 0.8749 (tp) cc_final: 0.8452 (mm)
REVERT: A  441 MET cc_start: 0.7349 (mmm) cc_final: 0.6864 (mmt)
REVERT: B   47 GLU cc_start: 0.5595 (mm-30) cc_final: 0.4688 (tm-30)
REVERT: B  227 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6236 (tm-30)
REVERT: B  280 GLU cc_start: 0.7659 (tp30) cc_final: 0.7400 (mm-30)
REVERT: C   47 GLU cc_start: 0.5582 (mm-30) cc_final: 0.4684 (tm-30)
REVERT: C  227 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6251 (tm-30)
REVERT: C  280 GLU cc_start: 0.7660 (tp30) cc_final: 0.7411 (mm-30)
REVERT: D   47 GLU cc_start: 0.5600 (mm-30) cc_final: 0.4700 (tm-30)
REVERT: D  280 GLU cc_start: 0.7631 (tp30) cc_final: 0.7401 (mm-30)
  outliers start: 37
  outliers final: 36
  residues processed: 180
  average time/residue: 0.2477
  time to fit residues: 71.5259
Evaluate side-chains
  178 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 1.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  488 LEU
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 165 optimal weight:    1.9990
   chunk 181 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 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 = 0.4922 r_free = 0.4922 target = 0.265016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 232)---------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.229629 restraints weight = 17172.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.229321 restraints weight = 26870.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.229214 restraints weight = 25203.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.4864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15600  Z= 0.119
  Angle     :  0.508  14.262  20904  Z= 0.249
  Chirality :  0.028   0.124   2588
  Planarity :  0.002   0.018   2668
  Dihedral  :  3.450  22.433   2112
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.48 %
    Favored  : 80.47 %
  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:  5.54 (0.17), residues: 1976
  helix:  3.78 (0.10), residues: 1916
  sheet:  None (None), residues: 0
  loop : -3.99 (0.38), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 383 
 PHE   0.008   0.001   PHE A 401 
 TYR   0.001   0.000   TYR D 416 
 ARG   0.002   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02853 ( 1677)
  hydrogen bonds       : angle       2.89732 ( 5031)
  covalent geometry    : bond        0.00283 (15600)
  covalent geometry    : angle       0.50761 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 160
  time to evaluate  : 1.706 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6499 (tm-30) cc_final: 0.6202 (tm-30)
REVERT: A  277 ILE cc_start: 0.8710 (tp) cc_final: 0.8392 (mm)
REVERT: A  441 MET cc_start: 0.7363 (mmm) cc_final: 0.7055 (mmt)
REVERT: B   18 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8166 (mt)
REVERT: B  202 ASN cc_start: 0.7910 (t0) cc_final: 0.7687 (t0)
REVERT: B  227 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6132 (tm-30)
REVERT: C   47 GLU cc_start: 0.5527 (mm-30) cc_final: 0.4594 (tm-30)
REVERT: C  202 ASN cc_start: 0.7929 (t0) cc_final: 0.7713 (t0)
REVERT: C  227 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6154 (tm-30)
REVERT: D   47 GLU cc_start: 0.5607 (mm-30) cc_final: 0.4566 (tm-30)
  outliers start: 49
  outliers final: 38
  residues processed: 201
  average time/residue: 0.2466
  time to fit residues: 75.7572
Evaluate side-chains
  191 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 152
  time to evaluate  : 1.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  488 LEU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 80 optimal weight:    3.9990
   chunk 187 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9980
   chunk 145 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 180 optimal weight:    0.8980
   chunk 177 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 99 optimal weight:    0.7980
   chunk 102 optimal weight:    6.9990
   overall best weight:    2.5384

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.259976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 142)---------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.223965 restraints weight = 17189.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 79)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.223720 restraints weight = 20560.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.223666 restraints weight = 21080.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15600  Z= 0.170
  Angle     :  0.593   9.163  20904  Z= 0.288
  Chirality :  0.031   0.139   2588
  Planarity :  0.002   0.021   2668
  Dihedral  :  3.577  22.502   2112
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.67 %
    Favored  : 79.91 %
  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:  5.11 (0.17), residues: 1976
  helix:  3.51 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -4.11 (0.37), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 383 
 PHE   0.009   0.001   PHE B 106 
 TYR   0.001   0.000   TYR C 416 
 ARG   0.002   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03182 ( 1677)
  hydrogen bonds       : angle       3.06445 ( 5031)
  covalent geometry    : bond        0.00412 (15600)
  covalent geometry    : angle       0.59336 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 162
  time to evaluate  : 1.998 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6275 (tm-30)
REVERT: A  277 ILE cc_start: 0.8717 (tp) cc_final: 0.8422 (mm)
REVERT: A  441 MET cc_start: 0.7390 (mmm) cc_final: 0.7033 (mmt)
REVERT: B  227 GLU cc_start: 0.6473 (tm-30) cc_final: 0.6193 (tm-30)
REVERT: B  484 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7763 (tmm)
REVERT: C  227 GLU cc_start: 0.6439 (tm-30) cc_final: 0.6193 (tm-30)
  outliers start: 55
  outliers final: 50
  residues processed: 212
  average time/residue: 0.2371
  time to fit residues: 79.0707
Evaluate side-chains
  203 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 152
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  484 MET
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  214 ASP
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  488 LEU
Chi-restraints excluded: chain D residue    7 ILE
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 167 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 166 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 135 optimal weight:    9.9990
   chunk 180 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 173 optimal weight:    7.9990
   chunk 125 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 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 = 0.4833 r_free = 0.4833 target = 0.256621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 183)---------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.221950 restraints weight = 17304.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.221294 restraints weight = 26759.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.221358 restraints weight = 24899.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.4546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  15600  Z= 0.229
  Angle     :  0.726  16.392  20904  Z= 0.348
  Chirality :  0.034   0.146   2588
  Planarity :  0.003   0.038   2668
  Dihedral  :  3.819  22.986   2112
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.11 %
    Favored  : 79.85 %
  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:  4.47 (0.17), residues: 1976
  helix:  3.12 (0.10), residues: 1908
  sheet:  None (None), residues: 0
  loop : -3.86 (0.43), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 383 
 PHE   0.012   0.002   PHE D 401 
 TYR   0.001   0.001   TYR A 416 
 ARG   0.005   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 ( 1677)
  hydrogen bonds       : angle       3.31344 ( 5031)
  covalent geometry    : bond        0.00552 (15600)
  covalent geometry    : angle       0.72559 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 160
  time to evaluate  : 1.645 
Fit side-chains
REVERT: A  277 ILE cc_start: 0.8733 (tp) cc_final: 0.8436 (mm)
REVERT: A  346 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8333 (tt)
REVERT: A  482 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6887 (tm-30)
REVERT: B  227 GLU cc_start: 0.6691 (tm-30) cc_final: 0.6463 (tm-30)
REVERT: B  346 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8363 (tt)
REVERT: B  484 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7714 (tmm)
REVERT: C  227 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6451 (tm-30)
REVERT: C  346 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8358 (tt)
REVERT: D  346 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8349 (tt)
  outliers start: 65
  outliers final: 51
  residues processed: 219
  average time/residue: 0.2261
  time to fit residues: 79.0639
Evaluate side-chains
  206 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 150
  time to evaluate  : 1.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  484 MET
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   69 ILE
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  214 ASP
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  346 ILE
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  346 ILE
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9990
   chunk 173 optimal weight:    3.9990
   chunk 134 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 120 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 119 optimal weight:    8.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 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 = 0.4901 r_free = 0.4901 target = 0.263291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 164)---------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.229862 restraints weight = 17139.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.228861 restraints weight = 21711.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 81)----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.228831 restraints weight = 20646.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15600  Z= 0.140
  Angle     :  0.567  11.994  20904  Z= 0.280
  Chirality :  0.030   0.148   2588
  Planarity :  0.002   0.023   2668
  Dihedral  :  3.610  23.553   2112
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.79 %
    Favored  : 79.04 %
  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:  5.06 (0.17), residues: 1976
  helix:  3.47 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.68 (0.48), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 383 
 PHE   0.007   0.001   PHE A 401 
 TYR   0.001   0.000   TYR D 416 
 ARG   0.002   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03141 ( 1677)
  hydrogen bonds       : angle       3.08808 ( 5031)
  covalent geometry    : bond        0.00338 (15600)
  covalent geometry    : angle       0.56718 (20904)

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

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

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3952 Ramachandran restraints generated.
    1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 170
  time to evaluate  : 1.680 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6618 (tm-30) cc_final: 0.6238 (tm-30)
REVERT: A  277 ILE cc_start: 0.8665 (tp) cc_final: 0.8318 (mm)
REVERT: B  227 GLU cc_start: 0.6531 (tm-30) cc_final: 0.6177 (tm-30)
REVERT: B  484 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7502 (tmm)
REVERT: C  227 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6180 (tm-30)
REVERT: C  441 MET cc_start: 0.7751 (tpp) cc_final: 0.7464 (mmt)
REVERT: D  227 GLU cc_start: 0.6436 (tm-30) cc_final: 0.6101 (tm-30)
  outliers start: 51
  outliers final: 46
  residues processed: 215
  average time/residue: 0.2307
  time to fit residues: 78.4992
Evaluate side-chains
  202 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 155
  time to evaluate  : 1.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  484 MET
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   69 ILE
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  274 VAL
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain C residue  488 LEU
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue   25 ILE
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  212 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  257 VAL
Chi-restraints excluded: chain D residue  274 VAL
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 191 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 133 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 448 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 = 0.4939 r_free = 0.4939 target = 0.265354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.236230 restraints weight = 16957.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.231683 restraints weight = 18684.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 102)---------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.230866 restraints weight = 24410.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.4861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15600  Z= 0.122
  Angle     :  0.583  15.474  20904  Z= 0.279
  Chirality :  0.029   0.138   2588
  Planarity :  0.002   0.024   2668
  Dihedral  :  3.509  22.905   2112
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.28 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.50 (0.17), residues: 1976
  helix:  3.75 (0.10), residues: 1916
  sheet:  None (None), residues: 0
  loop : -4.00 (0.45), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 265 
 PHE   0.009   0.001   PHE D 401 
 TYR   0.001   0.000   TYR D 416 
 ARG   0.002   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02914 ( 1677)
  hydrogen bonds       : angle       2.96457 ( 5031)
  covalent geometry    : bond        0.00288 (15600)
  covalent geometry    : angle       0.58273 (20904)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4172.36 seconds
wall clock time: 74 minutes 11.18 seconds (4451.18 seconds total)