Starting phenix.real_space_refine
on Sat Aug 23 22:49:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gel_29974/08_2025/8gel_29974.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gel_29974/08_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_29974/08_2025/8gel_29974.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gel_29974/08_2025/8gel_29974.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gel_29974/08_2025/8gel_29974.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gel_29974/08_2025/8gel_29974.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C, D
  Time building chain proxies: 3.49, per 1000 atoms: 0.22
  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: 1.45
  Conformation dependent library (CDL) restraints added in 611.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.41
  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: 2.74

  Time building geometry restraints manager: 1.90 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.140
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.980
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG D 330 
 TYR   0.001   0.001   TYR D 416 
 PHE   0.009   0.002   PHE A 106 
 HIS   0.008   0.002   HIS D 383 

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

*********************** 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  : 0.738 
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: 0.1266
  time to fit residues: 49.9468
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  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A  51 ASN
A 240 ASN
** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 GLN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 GLN
C  51 ASN
C 240 ASN
** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 GLN
D  51 ASN
** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.161590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.139284 restraints weight = 14058.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.142848 restraints weight = 8092.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.145304 restraints weight = 5758.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.146866 restraints weight = 4627.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.147866 restraints weight = 3996.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.1538

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= 0.146
  Angle     :  0.566   8.903  20904  Z= 0.274
  Chirality :  0.031   0.136   2588
  Planarity :  0.002   0.023   2668
  Dihedral  :  3.826  23.109   2112
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.01 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.77 (0.17), residues: 1976
  helix:  2.67 (0.11), residues: 1892
  sheet:  None (None), residues: 0
  loop : -2.64 (0.56), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 463 
 TYR   0.001   0.000   TYR A 416 
 PHE   0.007   0.001   PHE B 106 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (15600)
  covalent geometry    : angle       0.56626 (20904)
  hydrogen bonds       : bond        0.03417 ( 1677)
  hydrogen bonds       : angle       3.22799 ( 5031)

*********************** 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
  201 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 GLU cc_start: 0.8310 (tp30) cc_final: 0.8055 (tp30)
REVERT: A   81 ARG cc_start: 0.7408 (tpt170) cc_final: 0.7202 (tpp-160)
REVERT: A  198 MET cc_start: 0.7191 (mtm) cc_final: 0.6945 (mtt)
REVERT: A  227 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6341 (tm-30)
REVERT: B   10 GLU cc_start: 0.8337 (tp30) cc_final: 0.8070 (tp30)
REVERT: B   81 ARG cc_start: 0.7422 (tpt170) cc_final: 0.7103 (tpp-160)
REVERT: C   81 ARG cc_start: 0.7429 (tpt170) cc_final: 0.7214 (tpp-160)
REVERT: C  195 MET cc_start: 0.8096 (tpt) cc_final: 0.7724 (tpp)
REVERT: D   10 GLU cc_start: 0.8336 (tp30) cc_final: 0.8088 (tp30)
  outliers start: 36
  outliers final: 32
  residues processed: 197
  average time/residue: 0.1244
  time to fit residues: 36.9859
Evaluate side-chains
  168 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
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   67 LEU
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   25 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  251 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   25 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  251 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   25 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  251 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 183 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 145 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   chunk 194 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 189 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9980
   chunk 146 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.160012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.137684 restraints weight = 14320.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.141290 restraints weight = 8123.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.143728 restraints weight = 5774.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.145270 restraints weight = 4640.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.146365 restraints weight = 4011.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15600  Z= 0.171
  Angle     :  0.584   7.352  20904  Z= 0.280
  Chirality :  0.032   0.150   2588
  Planarity :  0.002   0.022   2668
  Dihedral  :  3.765  22.690   2112
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.12 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.30 (0.17), residues: 1976
  helix:  3.00 (0.11), residues: 1908
  sheet:  None (None), residues: 0
  loop : -3.62 (0.47), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 463 
 TYR   0.001   0.000   TYR B 416 
 PHE   0.008   0.001   PHE D 106 
 HIS   0.004   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (15600)
  covalent geometry    : angle       0.58387 (20904)
  hydrogen bonds       : bond        0.03357 ( 1677)
  hydrogen bonds       : angle       3.20701 ( 5031)

*********************** 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
  194 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 143
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A   47 GLU cc_start: 0.5587 (mm-30) cc_final: 0.4606 (tm-30)
REVERT: A  198 MET cc_start: 0.7141 (mtm) cc_final: 0.6848 (mtt)
REVERT: B   47 GLU cc_start: 0.5698 (mm-30) cc_final: 0.4702 (tm-30)
REVERT: C   47 GLU cc_start: 0.5631 (mm-30) cc_final: 0.4625 (tm-30)
REVERT: D   47 GLU cc_start: 0.5671 (mm-30) cc_final: 0.4680 (tm-30)
  outliers start: 51
  outliers final: 44
  residues processed: 186
  average time/residue: 0.1256
  time to fit residues: 35.5319
Evaluate side-chains
  180 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 136
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
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   67 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  142 SER
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  214 ASP
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  350 ILE
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   67 LEU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  214 ASP
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  350 ILE
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 54 optimal weight:   10.0000
   chunk 138 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 158 optimal weight:    9.9990
   chunk 179 optimal weight:    1.9990
   chunk 178 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 114 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.4559 r_free = 0.4559 target = 0.164455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.141688 restraints weight = 14178.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.145390 restraints weight = 8134.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.147878 restraints weight = 5829.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.149532 restraints weight = 4678.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.150520 restraints weight = 4053.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.4477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15600  Z= 0.130
  Angle     :  0.497   6.984  20904  Z= 0.244
  Chirality :  0.030   0.129   2588
  Planarity :  0.002   0.014   2668
  Dihedral  :  3.628  23.101   2112
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.04 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.01 (0.17), residues: 1976
  helix:  3.45 (0.11), residues: 1908
  sheet:  None (None), residues: 0
  loop : -3.60 (0.45), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 463 
 TYR   0.001   0.000   TYR A 416 
 PHE   0.008   0.001   PHE B 106 
 HIS   0.002   0.001   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (15600)
  covalent geometry    : angle       0.49704 (20904)
  hydrogen bonds       : bond        0.03004 ( 1677)
  hydrogen bonds       : angle       3.01514 ( 5031)

*********************** 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
  200 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 147
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A   47 GLU cc_start: 0.5773 (mm-30) cc_final: 0.4749 (tm-30)
REVERT: C   47 GLU cc_start: 0.5858 (mm-30) cc_final: 0.4825 (tm-30)
  outliers start: 53
  outliers final: 35
  residues processed: 190
  average time/residue: 0.1241
  time to fit residues: 36.4722
Evaluate side-chains
  173 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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  142 SER
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  323 LEU
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  212 LEU
Chi-restraints excluded: chain B residue  214 ASP
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   25 ILE
Chi-restraints excluded: chain C residue  142 SER
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  347 ILE
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  142 SER
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  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 146 optimal weight:    2.9990
   chunk 170 optimal weight:    0.9990
   chunk 142 optimal weight:    4.9990
   chunk 153 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 131 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 240 ASN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.262231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 222)---------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.227084 restraints weight = 17200.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.226045 restraints weight = 23628.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.226030 restraints weight = 25448.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.226050 restraints weight = 24254.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4889 r_free = 0.4889 target = 0.226053 restraints weight = 24312.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.4811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15600  Z= 0.141
  Angle     :  0.544   9.234  20904  Z= 0.263
  Chirality :  0.030   0.130   2588
  Planarity :  0.002   0.016   2668
  Dihedral  :  3.610  23.253   2112
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.98 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.08 (0.17), residues: 1976
  helix:  3.49 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.75 (0.51), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  81 
 TYR   0.001   0.000   TYR B 416 
 PHE   0.008   0.001   PHE B 106 
 HIS   0.003   0.001   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (15600)
  covalent geometry    : angle       0.54398 (20904)
  hydrogen bonds       : bond        0.03089 ( 1677)
  hydrogen bonds       : angle       3.03498 ( 5031)

*********************** 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
  197 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 138
  time to evaluate  : 0.610 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6223 (tm-30)
REVERT: C  317 MET cc_start: 0.7336 (ttm) cc_final: 0.7097 (ttp)
REVERT: D  198 MET cc_start: 0.6434 (mtt) cc_final: 0.6217 (tmm)
  outliers start: 59
  outliers final: 51
  residues processed: 184
  average time/residue: 0.1146
  time to fit residues: 33.4545
Evaluate side-chains
  186 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 135
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
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  142 SER
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  357 LEU
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   25 ILE
Chi-restraints excluded: chain B residue   69 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  357 LEU
Chi-restraints excluded: chain B residue  483 ASP
Chi-restraints excluded: chain B residue  488 LEU
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  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  347 ILE
Chi-restraints excluded: chain C residue  357 LEU
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   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  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  483 ASP
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 170 optimal weight:    6.9990
   chunk 179 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 144 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 132 optimal weight:    7.9990
   chunk 163 optimal weight:    2.9990
   chunk 128 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.262471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 165)---------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.227134 restraints weight = 17190.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.226981 restraints weight = 18774.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.226849 restraints weight = 18427.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.226790 restraints weight = 19895.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.226781 restraints weight = 20066.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  15600  Z= 0.138
  Angle     :  0.527   7.618  20904  Z= 0.257
  Chirality :  0.029   0.125   2588
  Planarity :  0.002   0.018   2668
  Dihedral  :  3.579  23.068   2112
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 17.60 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.13 (0.17), residues: 1976
  helix:  3.52 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.76 (0.52), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  81 
 TYR   0.001   0.000   TYR B 416 
 PHE   0.008   0.001   PHE B 106 
 HIS   0.003   0.001   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (15600)
  covalent geometry    : angle       0.52707 (20904)
  hydrogen bonds       : bond        0.03077 ( 1677)
  hydrogen bonds       : angle       3.02094 ( 5031)

*********************** 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
  209 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 145
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6188 (tm-30)
REVERT: A  317 MET cc_start: 0.7350 (ttm) cc_final: 0.7127 (ttp)
REVERT: C  317 MET cc_start: 0.7306 (ttm) cc_final: 0.7097 (ttp)
REVERT: D  198 MET cc_start: 0.6558 (mtt) cc_final: 0.6065 (ttm)
  outliers start: 64
  outliers final: 55
  residues processed: 199
  average time/residue: 0.1147
  time to fit residues: 35.7439
Evaluate side-chains
  193 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 138
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
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  212 LEU
Chi-restraints excluded: chain A residue  214 ASP
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  323 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  405 VAL
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   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  347 ILE
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  488 LEU
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  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  357 LEU
Chi-restraints excluded: chain C residue  405 VAL
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   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  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
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 109 optimal weight:    1.9990
   chunk 180 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 154 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 179 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 152 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 177 optimal weight:    1.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.264325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 206)---------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.229564 restraints weight = 16966.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.228933 restraints weight = 21394.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.228893 restraints weight = 23183.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.228869 restraints weight = 22063.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.228861 restraints weight = 21497.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.4825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2819

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     :  0.512   7.399  20904  Z= 0.253
  Chirality :  0.029   0.121   2588
  Planarity :  0.002   0.017   2668
  Dihedral  :  3.511  22.728   2112
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 17.54 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.38 (0.17), residues: 1976
  helix:  3.68 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.84 (0.50), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.001   0.000   TYR D 416 
 PHE   0.007   0.001   PHE C 106 
 HIS   0.002   0.001   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (15600)
  covalent geometry    : angle       0.51188 (20904)
  hydrogen bonds       : bond        0.02927 ( 1677)
  hydrogen bonds       : angle       2.94715 ( 5031)

*********************** 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
  223 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 150
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  227 GLU cc_start: 0.6450 (tm-30) cc_final: 0.6064 (tm-30)
REVERT: B  227 GLU cc_start: 0.6554 (tm-30) cc_final: 0.6216 (tm-30)
REVERT: C  227 GLU cc_start: 0.6491 (tm-30) cc_final: 0.6189 (tm-30)
REVERT: D  198 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6008 (ttm)
REVERT: D  227 GLU cc_start: 0.6546 (tm-30) cc_final: 0.6233 (tm-30)
  outliers start: 73
  outliers final: 59
  residues processed: 208
  average time/residue: 0.1025
  time to fit residues: 34.6568
Evaluate side-chains
  199 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 139
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
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  212 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  323 LEU
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  488 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  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  292 VAL
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  488 LEU
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  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  292 VAL
Chi-restraints excluded: chain C residue  323 LEU
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    7 ILE
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  198 MET
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  292 VAL
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  405 VAL
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 72 optimal weight:    0.9980
   chunk 192 optimal weight:    8.9990
   chunk 111 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 193 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 175 optimal weight:    2.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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 = 0.4882 r_free = 0.4882 target = 0.261752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 167)---------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.228047 restraints weight = 17255.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.227398 restraints weight = 28287.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4845 r_free = 0.4845 target = 0.227781 restraints weight = 25660.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.227330 restraints weight = 22913.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.227508 restraints weight = 22542.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.4651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15600  Z= 0.149
  Angle     :  0.559   8.166  20904  Z= 0.270
  Chirality :  0.030   0.128   2588
  Planarity :  0.002   0.026   2668
  Dihedral  :  3.578  22.641   2112
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.66 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.24 (0.17), residues: 1976
  helix:  3.59 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.83 (0.54), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.000   0.000   TYR D 416 
 PHE   0.008   0.001   PHE C 106 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (15600)
  covalent geometry    : angle       0.55857 (20904)
  hydrogen bonds       : bond        0.03064 ( 1677)
  hydrogen bonds       : angle       3.01470 ( 5031)

*********************** 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
  211 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 146
  time to evaluate  : 0.569 
Fit side-chains
REVERT: C  195 MET cc_start: 0.7990 (tpt) cc_final: 0.7664 (tpp)
REVERT: D  198 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6155 (ttm)
  outliers start: 65
  outliers final: 64
  residues processed: 201
  average time/residue: 0.1158
  time to fit residues: 36.5975
Evaluate side-chains
  208 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 143
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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  212 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  323 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  357 LEU
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   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  292 VAL
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  488 LEU
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  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  292 VAL
Chi-restraints excluded: chain C residue  323 LEU
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain C residue  405 VAL
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   69 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  198 MET
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  292 VAL
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  405 VAL
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 65 optimal weight:    0.8980
   chunk 158 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 133 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 155 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.4881 r_free = 0.4881 target = 0.261885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 199)---------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.226383 restraints weight = 17268.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.226005 restraints weight = 20487.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.225879 restraints weight = 24252.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.225913 restraints weight = 22994.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.225898 restraints weight = 22019.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.4670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15600  Z= 0.150
  Angle     :  0.569  10.386  20904  Z= 0.274
  Chirality :  0.030   0.128   2588
  Planarity :  0.002   0.025   2668
  Dihedral  :  3.586  22.824   2112
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.09 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.21 (0.17), residues: 1976
  helix:  3.57 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.73 (0.60), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.001   0.000   TYR B 416 
 PHE   0.008   0.001   PHE C 106 
 HIS   0.003   0.001   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (15600)
  covalent geometry    : angle       0.56947 (20904)
  hydrogen bonds       : bond        0.03079 ( 1677)
  hydrogen bonds       : angle       3.03036 ( 5031)

*********************** 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
  213 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 147
  time to evaluate  : 0.659 
Fit side-chains
REVERT: D  172 GLU cc_start: 0.5540 (tm-30) cc_final: 0.5277 (tm-30)
REVERT: D  198 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6182 (ttm)
  outliers start: 66
  outliers final: 61
  residues processed: 203
  average time/residue: 0.1081
  time to fit residues: 35.5191
Evaluate side-chains
  204 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 142
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
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  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  357 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  405 VAL
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   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  292 VAL
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  488 LEU
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  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  292 VAL
Chi-restraints excluded: chain C residue  323 LEU
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  357 LEU
Chi-restraints excluded: chain C residue  405 VAL
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   69 ILE
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  198 MET
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  292 VAL
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  405 VAL
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 140 optimal weight:    7.9990
   chunk 165 optimal weight:    0.8980
   chunk 172 optimal weight:    9.9990
   chunk 145 optimal weight:    1.9990
   chunk 150 optimal weight:    2.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.4862 r_free = 0.4862 target = 0.259633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 237)---------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.224286 restraints weight = 17302.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.223446 restraints weight = 24595.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.223435 restraints weight = 25345.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4858 r_free = 0.4858 target = 0.223447 restraints weight = 23761.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4858 r_free = 0.4858 target = 0.223426 restraints weight = 24032.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.4651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2749

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= 0.176
  Angle     :  0.631  12.931  20904  Z= 0.303
  Chirality :  0.031   0.135   2588
  Planarity :  0.003   0.030   2668
  Dihedral  :  3.673  22.945   2112
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.66 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.96 (0.17), residues: 1976
  helix:  3.41 (0.10), residues: 1912
  sheet:  None (None), residues: 0
  loop : -3.63 (0.63), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  81 
 TYR   0.000   0.000   TYR D 416 
 PHE   0.009   0.001   PHE D 401 
 HIS   0.003   0.001   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (15600)
  covalent geometry    : angle       0.63128 (20904)
  hydrogen bonds       : bond        0.03307 ( 1677)
  hydrogen bonds       : angle       3.14468 ( 5031)

********************** 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
  225 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 150
  time to evaluate  : 0.617 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.5714 (tm-30) cc_final: 0.5469 (tm-30)
REVERT: A  346 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8047 (tp)
REVERT: D  198 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6084 (ttm)
  outliers start: 75
  outliers final: 57
  residues processed: 212
  average time/residue: 0.1049
  time to fit residues: 36.0620
Evaluate side-chains
  202 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 143
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
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  214 ASP
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  346 ILE
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  405 VAL
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  292 VAL
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  488 LEU
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  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  292 VAL
Chi-restraints excluded: chain C residue  323 LEU
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  192 VAL
Chi-restraints excluded: chain D residue  198 MET
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  292 VAL
Chi-restraints excluded: chain D residue  323 LEU
Chi-restraints excluded: chain D residue  347 ILE
Chi-restraints excluded: chain D residue  357 LEU
Chi-restraints excluded: chain D residue  405 VAL
Chi-restraints excluded: chain D residue  488 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 177 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 145 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 118 optimal weight:    0.0870
   chunk 155 optimal weight:    0.0020
   chunk 160 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 195 optimal weight:    0.0770
   overall best weight:    0.3924

-------------------------------------------------------------------------------
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 = 0.4947 r_free = 0.4947 target = 0.267715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.237158 restraints weight = 16927.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.236623 restraints weight = 27340.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4915 r_free = 0.4915 target = 0.237033 restraints weight = 23439.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.237013 restraints weight = 21040.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.237151 restraints weight = 19725.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15600  Z= 0.115
  Angle     :  0.550  10.953  20904  Z= 0.272
  Chirality :  0.029   0.111   2588
  Planarity :  0.002   0.018   2668
  Dihedral  :  3.490  22.879   2112
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.08 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.70 (0.17), residues: 1976
  helix:  3.86 (0.10), residues: 1916
  sheet:  None (None), residues: 0
  loop : -3.63 (0.64), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 193 
 TYR   0.002   0.001   TYR D 416 
 PHE   0.008   0.001   PHE D 401 
 HIS   0.001   0.000   HIS D 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (15600)
  covalent geometry    : angle       0.55008 (20904)
  hydrogen bonds       : bond        0.02823 ( 1677)
  hydrogen bonds       : angle       2.93744 ( 5031)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2211.79 seconds
wall clock time: 39 minutes 12.21 seconds (2352.21 seconds total)