Starting phenix.real_space_refine
on Thu Oct 22 21:54:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21am_67514/10_2026/21am_67514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21am_67514/10_2026/21am_67514.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/21am_67514/10_2026/21am_67514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21am_67514/10_2026/21am_67514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/21am_67514/10_2026/21am_67514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21am_67514/10_2026/21am_67514.cif"
  }
  resolution = 3.59
  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=   0.008
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      46      5.16       5
     C    3812      2.51       5
     N    1042      2.21       5
     O    1148      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6048
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1794
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219}
    Chain: "B"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1794
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219}
    Chain: "D"
      Number of atoms: 1230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1230
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 6, 'TRANS': 150}
    Chain: "E"
      Number of atoms: 1230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1230
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 6, 'TRANS': 150}
  Time building chain proxies: 1.54, per 1000 atoms: 0.25
  Number of scatterers: 6048
  At special positions: 0
  Unit cell: (91.02, 102.5, 81.18, 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      46     16.00
     O    1148      8.00
     N    1042      7.00
     C    3812      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 105 " - pdb=" SG  CYS B 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 148 " - pdb=" SG  CYS A 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 234 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 148 " - pdb=" SG  CYS B 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 234 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 226.8 milliseconds
  

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1448

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      37.5% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 247 through 258
    Processing helix  chain 'B' and resid 175 through 180
    Processing helix  chain 'B' and resid 247 through 258
    Processing helix  chain 'D' and resid 255 through 267
      removed outlier: 3.508A  pdb=" N   ASP D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 282
      removed outlier: 3.691A  pdb=" N   LYS D 282 " --> pdb=" O   ASN D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 304
    Processing helix  chain 'D' and resid 312 through 320
      removed outlier: 3.986A  pdb=" N   PHE D 320 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 343
      removed outlier: 3.577A  pdb=" N   GLU D 343 " --> pdb=" O   ASP D 339 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 346 through 358
      removed outlier: 3.994A  pdb=" N   PHE D 350 " --> pdb=" O   GLU D 346 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 359 through 378
    Processing helix  chain 'D' and resid 388 through 410
    Processing helix  chain 'E' and resid 255 through 267
      removed outlier: 3.580A  pdb=" N   ASP E 267 " --> pdb=" O   SER E 263 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 282
      removed outlier: 3.707A  pdb=" N   LYS E 282 " --> pdb=" O   ASN E 278 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 286 through 304
    Processing helix  chain 'E' and resid 312 through 320
      removed outlier: 4.003A  pdb=" N   PHE E 320 " --> pdb=" O   LEU E 316 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 327 through 344
      removed outlier: 3.652A  pdb=" N   LEU E 344 " --> pdb=" O   ALA E 340 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 346 through 357
      removed outlier: 4.265A  pdb=" N   PHE E 350 " --> pdb=" O   GLU E 346 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 359 through 378
    Processing helix  chain 'E' and resid 388 through 410
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
      removed outlier: 3.507A  pdb=" N   THR A 172 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   CYS A 197 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   ILE A 244 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   THR A 226 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   PHE A 222 " --> pdb=" O   CYS A 218 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   CYS A 218 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   ALA A 151 " --> pdb=" O   PRO A 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 95
      removed outlier: 6.321A  pdb=" N   TRP A  63 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 100 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLU A 100 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLN A 119 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 34
      removed outlier: 4.256A  pdb=" N   CYS B 197 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   ILE B 244 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   THR B 226 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LEU B 216 " --> pdb=" O   ARG B 223 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   ALA B 151 " --> pdb=" O   PRO B 215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 95
      removed outlier: 6.362A  pdb=" N   TRP B  63 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   LEU B 117 " --> pdb=" O   GLU B 100 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   GLU B 100 " --> pdb=" O   LEU B 117 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   GLN B 119 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    798 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.69

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2024
        1.34 -     1.46: 1168
        1.46 -     1.58: 2884
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 6146
  Sorted by residual:
  bond pdb=" CA  GLY B 199 "
       pdb=" C   GLY B 199 "
    ideal  model  delta    sigma   weight residual
    1.524  1.512  0.012 1.20e-02 6.94e+03 1.05e+00
  bond pdb=" CA  HIS A 184 "
       pdb=" CB  HIS A 184 "
    ideal  model  delta    sigma   weight residual
    1.539  1.527  0.012 1.36e-02 5.41e+03 7.41e-01
  bond pdb=" N   PRO D 314 "
       pdb=" CA  PRO D 314 "
    ideal  model  delta    sigma   weight residual
    1.469  1.479 -0.010 1.28e-02 6.10e+03 6.07e-01
  bond pdb=" CA  LEU B 246 "
       pdb=" C   LEU B 246 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.008 1.10e-02 8.26e+03 5.49e-01
  bond pdb=" CA  ASP A 114 "
       pdb=" C   ASP A 114 "
    ideal  model  delta    sigma   weight residual
    1.531  1.523  0.008 1.12e-02 7.97e+03 4.95e-01
  ... (remaining 6141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 7901
        1.01 -     2.02: 321
        2.02 -     3.03: 56
        3.03 -     4.04: 16
        4.04 -     5.05: 6
  Bond angle restraints: 8300
  Sorted by residual:
  angle pdb=" N   SER E 345 "
        pdb=" CA  SER E 345 "
        pdb=" C   SER E 345 "
      ideal   model   delta    sigma   weight residual
     112.93  107.88    5.05 1.33e+00 5.65e-01 1.44e+01
  angle pdb=" N   SER D 345 "
        pdb=" CA  SER D 345 "
        pdb=" C   SER D 345 "
      ideal   model   delta    sigma   weight residual
     112.13  108.18    3.95 1.37e+00 5.33e-01 8.30e+00
  angle pdb=" CA  GLY B 229 "
        pdb=" C   GLY B 229 "
        pdb=" N   LEU B 230 "
      ideal   model   delta    sigma   weight residual
     114.82  117.83   -3.01 1.35e+00 5.49e-01 4.98e+00
  angle pdb=" C   SER E 345 "
        pdb=" CA  SER E 345 "
        pdb=" CB  SER E 345 "
      ideal   model   delta    sigma   weight residual
     110.08  113.42   -3.34 1.57e+00 4.06e-01 4.52e+00
  angle pdb=" CA  ASP B 114 "
        pdb=" C   ASP B 114 "
        pdb=" N   LEU B 115 "
      ideal   model   delta    sigma   weight residual
     114.76  117.04   -2.28 1.14e+00 7.69e-01 4.01e+00
  ... (remaining 8295 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.26: 3464
       11.26 -    22.51: 286
       22.51 -    33.77: 63
       33.77 -    45.02: 12
       45.02 -    56.28: 4
  Dihedral angle restraints: 3829
    sinusoidal: 1591
      harmonic: 2238
  Sorted by residual:
  dihedral pdb=" CA  GLU A 168 "
           pdb=" CB  GLU A 168 "
           pdb=" CG  GLU A 168 "
           pdb=" CD  GLU A 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -123.72  -56.28     3      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" CA  ASP B 206 "
           pdb=" C   ASP B 206 "
           pdb=" N   SER B 207 "
           pdb=" CA  SER B 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.98   15.02     0      5.00e+00 4.00e-02 9.02e+00
  dihedral pdb=" CA  ASP A 206 "
           pdb=" C   ASP A 206 "
           pdb=" N   SER A 207 "
           pdb=" CA  SER A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.40   14.60     0      5.00e+00 4.00e-02 8.53e+00
  ... (remaining 3826 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 539
       0.025 -    0.049: 257
       0.049 -    0.074: 70
       0.074 -    0.098: 54
       0.098 -    0.123: 32
  Chirality restraints: 952
  Sorted by residual:
  chirality pdb=" CA  VAL A  78 "
            pdb=" N   VAL A  78 "
            pdb=" C   VAL A  78 "
            pdb=" CB  VAL A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  chirality pdb=" CA  VAL A 225 "
            pdb=" N   VAL A 225 "
            pdb=" C   VAL A 225 "
            pdb=" CB  VAL A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.63e-01
  chirality pdb=" CA  VAL B 130 "
            pdb=" N   VAL B 130 "
            pdb=" C   VAL B 130 "
            pdb=" CB  VAL B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.57e-01
  ... (remaining 949 not shown)

  Planarity restraints: 1068
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 239 "    0.031 5.00e-02 4.00e+02   4.61e-02 3.41e+00
        pdb=" N   PRO B 240 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 240 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 240 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 239 "    0.028 5.00e-02 4.00e+02   4.18e-02 2.80e+00
        pdb=" N   PRO A 240 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 240 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 240 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 382 "    0.015 5.00e-02 4.00e+02   2.29e-02 8.35e-01
        pdb=" N   PRO E 383 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO E 383 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO E 383 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1065 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.08: 4351
        3.08 -     3.54: 6482
        3.54 -     3.99: 9857
        3.99 -     4.45: 12026
        4.45 -     4.90: 17762
  Nonbonded interactions: 50478
  Sorted by model distance:
  nonbonded pdb=" N   ALA B  60 "
            pdb=" O   ALA B  60 "
     model   vdw
     2.625 2.496
  nonbonded pdb=" N   ALA A  60 "
            pdb=" O   ALA A  60 "
     model   vdw
     2.627 2.496
  nonbonded pdb=" N   ASN A 127 "
            pdb=" O   ASN A 127 "
     model   vdw
     2.628 2.496
  nonbonded pdb=" N   ASN B 127 "
            pdb=" O   ASN B 127 "
     model   vdw
     2.633 2.496
  nonbonded pdb=" N   THR A  66 "
            pdb=" O   THR A  66 "
     model   vdw
     2.642 2.496
  ... (remaining 50473 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.050
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
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      :  0.002   0.023   6155  Z= 0.127
  Angle     :  0.503   5.046   8318  Z= 0.291
  Chirality :  0.039   0.123    952
  Planarity :  0.003   0.046   1068
  Dihedral  :  8.772  56.276   2354
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.26 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.99 (0.32), residues: 770
  helix:  2.76 (0.31), residues: 270
  sheet: -0.54 (0.78), residues: 50
  loop :  0.77 (0.32), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  75 
 TYR   0.008   0.001   TYR A 185 
 PHE   0.004   0.001   PHE A 101 
 TRP   0.007   0.001   TRP B 162 
 HIS   0.002   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.13 ( 6146)
  covalent geometry    : angle       0.50158 /  0.29 ( 8300)
  SS BOND              : bond        0.00289 /  0.20 (    9)
  SS BOND              : angle       1.05068 /  0.59 (   18)
  hydrogen bonds       : bond        0.12318 /  7.85 (  280)
  hydrogen bonds       : angle       7.45015 /  5.04 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8603 (p0)
REVERT: B  193 MET cc_start: 0.7983 (mmm) cc_final: 0.7745 (mmt)
REVERT: D  275 ASP cc_start: 0.6463 (m-30) cc_final: 0.6001 (m-30)
REVERT: D  337 PHE cc_start: 0.8200 (t80) cc_final: 0.7961 (t80)
REVERT: E  330 ARG cc_start: 0.7314 (mtt180) cc_final: 0.6986 (mtt-85)
  outliers start: 1
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1107
  time to fit residues: 31.7495
Evaluate side-chains
  135 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  38 HIS
B  38 HIS
B 149 GLN
E 349 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.074477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.061692 restraints weight = 29383.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.063516 restraints weight = 17650.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.064856 restraints weight = 12003.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.065837 restraints weight = 8810.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.066518 restraints weight = 6908.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6155  Z= 0.160
  Angle     :  0.658   7.120   8318  Z= 0.334
  Chirality :  0.043   0.170    952
  Planarity :  0.004   0.049   1068
  Dihedral  :  4.079  23.965    828
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 11.42 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.23 (0.31), residues: 770
  helix:  1.72 (0.30), residues: 288
  sheet: -1.19 (0.70), residues: 54
  loop :  0.60 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  87 
 TYR   0.010   0.001   TYR B 243 
 PHE   0.015   0.002   PHE D 320 
 TRP   0.006   0.001   TRP B  63 
 HIS   0.004   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 ( 6146)
  covalent geometry    : angle       0.65556 /  0.33 ( 8300)
  SS BOND              : bond        0.00265 /  0.19 (    9)
  SS BOND              : angle       1.33444 /  0.68 (   18)
  hydrogen bonds       : bond        0.03956 /  2.70 (  280)
  hydrogen bonds       : angle       5.88836 /  4.02 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8549 (mmm) cc_final: 0.8236 (mmm)
REVERT: A  166 LEU cc_start: 0.8998 (tp) cc_final: 0.8651 (tp)
REVERT: A  168 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7277 (tm-30)
REVERT: A  243 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.6819 (m-80)
REVERT: A  248 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9144 (ttmt)
REVERT: B   44 VAL cc_start: 0.7617 (t) cc_final: 0.7327 (p)
REVERT: B  182 ARG cc_start: 0.8623 (mmt-90) cc_final: 0.8382 (mmm-85)
REVERT: B  193 MET cc_start: 0.9007 (mmm) cc_final: 0.8739 (mmt)
REVERT: B  248 LYS cc_start: 0.9392 (ttmt) cc_final: 0.9065 (ttmt)
REVERT: D  291 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9099 (pm20)
REVERT: D  326 LEU cc_start: 0.9096 (tp) cc_final: 0.8588 (tp)
REVERT: D  349 GLN cc_start: 0.9166 (mp10) cc_final: 0.8933 (mp10)
REVERT: D  350 PHE cc_start: 0.9434 (m-80) cc_final: 0.9194 (m-80)
REVERT: D  368 LYS cc_start: 0.9432 (tttt) cc_final: 0.9089 (tppt)
  outliers start: 22
  outliers final: 12
  residues processed: 157
  average time/residue: 0.0760
  time to fit residues: 15.4728
Evaluate side-chains
  135 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  325 VAL
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  316 LEU
Chi-restraints excluded: chain E residue  325 VAL
Chi-restraints excluded: chain E residue  359 THR
Chi-restraints excluded: chain E residue  407 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [44, 26, 73, 75, 20, 7, 13, 16, 32, 36, 23]
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 149 GLN
D 278 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.074103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.062413 restraints weight = 29585.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.064146 restraints weight = 17817.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.065452 restraints weight = 12122.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.066378 restraints weight = 8896.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.067071 restraints weight = 6946.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6155  Z= 0.151
  Angle     :  0.641   7.163   8318  Z= 0.320
  Chirality :  0.042   0.134    952
  Planarity :  0.004   0.047   1068
  Dihedral  :  3.944  14.577    826
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.24 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.05 (0.31), residues: 770
  helix:  1.61 (0.30), residues: 286
  sheet: -1.43 (0.66), residues: 54
  loop :  0.49 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  50 
 TYR   0.012   0.001   TYR D 398 
 PHE   0.016   0.002   PHE B 222 
 TRP   0.014   0.001   TRP A 253 
 HIS   0.004   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.15 ( 6146)
  covalent geometry    : angle       0.63771 /  0.32 ( 8300)
  SS BOND              : bond        0.00488 /  0.26 (    9)
  SS BOND              : angle       1.48520 /  0.72 (   18)
  hydrogen bonds       : bond        0.03551 /  2.41 (  280)
  hydrogen bonds       : angle       5.59071 /  3.85 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8538 (mmm) cc_final: 0.8228 (mmm)
REVERT: A  105 CYS cc_start: 0.7261 (t) cc_final: 0.6742 (t)
REVERT: A  166 LEU cc_start: 0.9044 (tp) cc_final: 0.8751 (tp)
REVERT: A  168 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7168 (tm-30)
REVERT: A  243 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.6894 (m-80)
REVERT: A  253 TRP cc_start: 0.9186 (t-100) cc_final: 0.8933 (t-100)
REVERT: B   44 VAL cc_start: 0.7635 (t) cc_final: 0.7407 (p)
REVERT: B  193 MET cc_start: 0.9016 (mmm) cc_final: 0.8595 (mmm)
REVERT: B  248 LYS cc_start: 0.9403 (ttmt) cc_final: 0.8995 (ttmt)
REVERT: D  328 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8233 (tm-30)
REVERT: D  332 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8732 (mmmm)
REVERT: D  336 ASP cc_start: 0.9091 (m-30) cc_final: 0.8821 (p0)
REVERT: D  350 PHE cc_start: 0.9404 (m-80) cc_final: 0.9169 (m-80)
REVERT: D  368 LYS cc_start: 0.9419 (tttt) cc_final: 0.9089 (tppt)
REVERT: E  274 LYS cc_start: 0.9379 (mtpp) cc_final: 0.8914 (mtmm)
REVERT: E  332 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8691 (mtmm)
  outliers start: 18
  outliers final: 13
  residues processed: 141
  average time/residue: 0.0914
  time to fit residues: 16.4229
Evaluate side-chains
  136 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  359 THR
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain D residue  387 TYR
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  316 LEU
Chi-restraints excluded: chain E residue  359 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [12, 22, 56, 30, 24, 57, 21, 0, 23, 45, 7]
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 149 GLN
E 307 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.075751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.063163 restraints weight = 28622.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.064991 restraints weight = 17292.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.066271 restraints weight = 11715.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.067201 restraints weight = 8640.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.067887 restraints weight = 6796.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6155  Z= 0.129
  Angle     :  0.626   7.842   8318  Z= 0.307
  Chirality :  0.042   0.206    952
  Planarity :  0.004   0.049   1068
  Dihedral  :  3.821  13.728    826
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.39 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.99 (0.30), residues: 770
  helix:  1.62 (0.30), residues: 286
  sheet: -1.49 (0.64), residues: 54
  loop :  0.42 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 296 
 TYR   0.010   0.001   TYR D 398 
 PHE   0.013   0.002   PHE B 222 
 TRP   0.011   0.001   TRP A 253 
 HIS   0.003   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 6146)
  covalent geometry    : angle       0.62434 /  0.31 ( 8300)
  SS BOND              : bond        0.00352 /  0.20 (    9)
  SS BOND              : angle       1.20057 /  0.58 (   18)
  hydrogen bonds       : bond        0.03219 /  2.19 (  280)
  hydrogen bonds       : angle       5.31950 /  3.67 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8607 (mmm) cc_final: 0.8329 (mmm)
REVERT: A  105 CYS cc_start: 0.7049 (t) cc_final: 0.6629 (t)
REVERT: A  166 LEU cc_start: 0.9058 (tp) cc_final: 0.8785 (tp)
REVERT: A  168 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7258 (tm-30)
REVERT: B  168 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: B  193 MET cc_start: 0.9021 (mmm) cc_final: 0.8741 (mmp)
REVERT: B  227 SER cc_start: 0.7372 (t) cc_final: 0.6891 (p)
REVERT: B  248 LYS cc_start: 0.9407 (ttmt) cc_final: 0.8940 (ttpp)
REVERT: D  296 ARG cc_start: 0.9379 (mmm160) cc_final: 0.8807 (mmm160)
REVERT: D  332 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8694 (mmtp)
REVERT: D  350 PHE cc_start: 0.9426 (m-80) cc_final: 0.9171 (m-80)
REVERT: D  368 LYS cc_start: 0.9416 (tttt) cc_final: 0.9077 (tppt)
REVERT: E  274 LYS cc_start: 0.9365 (mtpp) cc_final: 0.8917 (mtmt)
REVERT: E  282 LYS cc_start: 0.8954 (mttt) cc_final: 0.8750 (ptpp)
REVERT: E  395 CYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6226 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 150
  average time/residue: 0.1012
  time to fit residues: 18.9716
Evaluate side-chains
  140 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  105 CYS
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 TRP
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  325 VAL
Chi-restraints excluded: chain D residue  359 THR
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  316 LEU
Chi-restraints excluded: chain E residue  325 VAL
Chi-restraints excluded: chain E residue  359 THR
Chi-restraints excluded: chain E residue  395 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [6, 69, 60, 72, 51, 18, 68, 54, 15, 1, 9]
   chunk 6 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.2782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.074288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.061486 restraints weight = 29890.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.063275 restraints weight = 17988.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.064614 restraints weight = 12306.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.065536 restraints weight = 9082.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.066243 restraints weight = 7137.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6155  Z= 0.155
  Angle     :  0.630   7.654   8318  Z= 0.313
  Chirality :  0.041   0.133    952
  Planarity :  0.004   0.048   1068
  Dihedral  :  3.889  14.240    826
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 19.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.47 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.81 (0.30), residues: 770
  helix:  1.51 (0.30), residues: 286
  sheet: -1.58 (0.63), residues: 54
  loop :  0.27 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 111 
 TYR   0.015   0.001   TYR D 398 
 PHE   0.013   0.002   PHE B 222 
 TRP   0.017   0.001   TRP A 253 
 HIS   0.003   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 6146)
  covalent geometry    : angle       0.62880 /  0.31 ( 8300)
  SS BOND              : bond        0.00282 /  0.18 (    9)
  SS BOND              : angle       1.11864 /  0.57 (   18)
  hydrogen bonds       : bond        0.03326 /  2.27 (  280)
  hydrogen bonds       : angle       5.31471 /  3.65 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8642 (mmm) cc_final: 0.8096 (mmm)
REVERT: A  105 CYS cc_start: 0.7144 (t) cc_final: 0.6751 (t)
REVERT: A  166 LEU cc_start: 0.9135 (tp) cc_final: 0.8902 (tp)
REVERT: A  243 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.7169 (m-80)
REVERT: A  253 TRP cc_start: 0.9253 (t-100) cc_final: 0.8973 (t-100)
REVERT: B  193 MET cc_start: 0.9027 (mmm) cc_final: 0.8742 (mmp)
REVERT: B  209 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7620 (p0)
REVERT: B  248 LYS cc_start: 0.9390 (ttmt) cc_final: 0.8975 (ttmt)
REVERT: D  296 ARG cc_start: 0.9449 (mmm160) cc_final: 0.8864 (mmm160)
REVERT: D  350 PHE cc_start: 0.9442 (m-80) cc_final: 0.9179 (m-80)
REVERT: D  368 LYS cc_start: 0.9428 (tttt) cc_final: 0.9103 (tppt)
REVERT: E  274 LYS cc_start: 0.9358 (mtpp) cc_final: 0.8889 (mmtt)
REVERT: E  332 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8621 (mtmm)
REVERT: E  395 CYS cc_start: 0.6462 (OUTLIER) cc_final: 0.5993 (p)
  outliers start: 28
  outliers final: 19
  residues processed: 141
  average time/residue: 0.0846
  time to fit residues: 15.3139
Evaluate side-chains
  133 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  105 CYS
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 TRP
Chi-restraints excluded: chain B residue  209 ASN
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  325 VAL
Chi-restraints excluded: chain D residue  359 THR
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain D residue  387 TYR
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  359 THR
Chi-restraints excluded: chain E residue  395 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [52, 19, 34, 2, 3, 71, 27, 22, 70, 35, 40]
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.7984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.076074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.064095 restraints weight = 29408.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.065935 restraints weight = 17809.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.067228 restraints weight = 12083.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.068098 restraints weight = 8851.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.068889 restraints weight = 6968.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.4964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6155  Z= 0.124
  Angle     :  0.626   8.017   8318  Z= 0.305
  Chirality :  0.041   0.131    952
  Planarity :  0.004   0.049   1068
  Dihedral  :  3.830  15.039    826
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 16.47 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.73 (0.30), residues: 770
  helix:  1.51 (0.30), residues: 288
  sheet: -1.84 (0.54), residues: 64
  loop :  0.26 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  40 
 TYR   0.014   0.001   TYR D 398 
 PHE   0.013   0.001   PHE B 222 
 TRP   0.015   0.001   TRP A 253 
 HIS   0.003   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 6146)
  covalent geometry    : angle       0.62474 /  0.30 ( 8300)
  SS BOND              : bond        0.00244 /  0.15 (    9)
  SS BOND              : angle       1.01330 /  0.51 (   18)
  hydrogen bonds       : bond        0.03167 /  2.15 (  280)
  hydrogen bonds       : angle       5.19814 /  3.58 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8539 (mmm) cc_final: 0.8255 (mmm)
REVERT: A  105 CYS cc_start: 0.7163 (t) cc_final: 0.6735 (t)
REVERT: A  166 LEU cc_start: 0.9042 (tp) cc_final: 0.8818 (tp)
REVERT: A  168 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7084 (tm-30)
REVERT: A  243 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7459 (m-80)
REVERT: B   44 VAL cc_start: 0.7736 (t) cc_final: 0.7533 (p)
REVERT: B  227 SER cc_start: 0.7339 (t) cc_final: 0.6813 (p)
REVERT: B  248 LYS cc_start: 0.9374 (ttmt) cc_final: 0.8872 (ttpp)
REVERT: D  296 ARG cc_start: 0.9450 (mmm160) cc_final: 0.8879 (mmm160)
REVERT: D  350 PHE cc_start: 0.9407 (m-80) cc_final: 0.9148 (m-80)
REVERT: D  368 LYS cc_start: 0.9398 (tttt) cc_final: 0.9083 (tppt)
REVERT: D  373 GLN cc_start: 0.7848 (pt0) cc_final: 0.7634 (mm-40)
REVERT: E  395 CYS cc_start: 0.6530 (OUTLIER) cc_final: 0.5988 (p)
  outliers start: 28
  outliers final: 20
  residues processed: 145
  average time/residue: 0.0827
  time to fit residues: 15.7351
Evaluate side-chains
  138 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  105 CYS
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 TRP
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  308 MET
Chi-restraints excluded: chain D residue  325 VAL
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  325 VAL
Chi-restraints excluded: chain E residue  359 THR
Chi-restraints excluded: chain E residue  395 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [24, 38, 55, 59, 32, 58, 19, 36, 74, 48, 5]
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0060
   chunk 55 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0050
   chunk 48 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0070
   overall best weight:    0.2828

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.077915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.065899 restraints weight = 29048.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.067790 restraints weight = 17297.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.069065 restraints weight = 11626.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.070151 restraints weight = 8613.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.070885 restraints weight = 6584.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6155  Z= 0.109
  Angle     :  0.644   8.139   8318  Z= 0.307
  Chirality :  0.043   0.270    952
  Planarity :  0.004   0.048   1068
  Dihedral  :  3.615  17.940    826
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.10 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.03 (0.30), residues: 770
  helix:  1.69 (0.30), residues: 286
  sheet: -1.52 (0.53), residues: 64
  loop :  0.48 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  40 
 TYR   0.013   0.001   TYR D 398 
 PHE   0.012   0.001   PHE B 222 
 TRP   0.021   0.001   TRP A 253 
 HIS   0.002   0.000   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 ( 6146)
  covalent geometry    : angle       0.64373 /  0.31 ( 8300)
  SS BOND              : bond        0.00189 /  0.12 (    9)
  SS BOND              : angle       0.79410 /  0.40 (   18)
  hydrogen bonds       : bond        0.03110 /  2.13 (  280)
  hydrogen bonds       : angle       5.06248 /  3.52 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8594 (mmm) cc_final: 0.8255 (mmm)
REVERT: A  101 PHE cc_start: 0.9263 (m-80) cc_final: 0.9062 (m-10)
REVERT: A  105 CYS cc_start: 0.7244 (t) cc_final: 0.6824 (t)
REVERT: A  166 LEU cc_start: 0.9045 (tp) cc_final: 0.8810 (tp)
REVERT: A  243 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7851 (m-80)
REVERT: A  248 LYS cc_start: 0.9426 (ttmt) cc_final: 0.9018 (ttmt)
REVERT: A  253 TRP cc_start: 0.9210 (t-100) cc_final: 0.8610 (t60)
REVERT: B  119 GLN cc_start: 0.8238 (tt0) cc_final: 0.7976 (tp40)
REVERT: B  193 MET cc_start: 0.8904 (mmm) cc_final: 0.8668 (mmm)
REVERT: B  219 GLU cc_start: 0.8689 (mp0) cc_final: 0.8394 (mp0)
REVERT: B  227 SER cc_start: 0.7256 (t) cc_final: 0.6860 (p)
REVERT: B  248 LYS cc_start: 0.9359 (ttmt) cc_final: 0.9132 (ttmm)
REVERT: D  296 ARG cc_start: 0.9454 (mmm160) cc_final: 0.8961 (mmm160)
REVERT: D  336 ASP cc_start: 0.9207 (m-30) cc_final: 0.8873 (p0)
REVERT: D  350 PHE cc_start: 0.9399 (m-80) cc_final: 0.9143 (m-80)
REVERT: D  368 LYS cc_start: 0.9413 (tttt) cc_final: 0.9046 (tppt)
  outliers start: 23
  outliers final: 17
  residues processed: 147
  average time/residue: 0.0886
  time to fit residues: 16.7867
Evaluate side-chains
  140 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  105 CYS
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 TRP
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain D residue  387 TYR
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  325 VAL
Chi-restraints excluded: chain E residue  359 THR
Chi-restraints excluded: chain E residue  407 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [31, 55, 43, 27, 32, 75, 58, 25, 21, 65, 24]
   chunk 31 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.076036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.064142 restraints weight = 29703.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.065974 restraints weight = 17860.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.067279 restraints weight = 12043.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.068230 restraints weight = 8798.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.068988 restraints weight = 6838.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.5411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6155  Z= 0.137
  Angle     :  0.689   9.842   8318  Z= 0.330
  Chirality :  0.042   0.177    952
  Planarity :  0.004   0.049   1068
  Dihedral  :  3.702  14.739    826
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.73 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.87 (0.30), residues: 770
  helix:  1.62 (0.30), residues: 286
  sheet: -1.26 (0.48), residues: 90
  loop :  0.40 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 182 
 TYR   0.015   0.001   TYR D 398 
 PHE   0.011   0.001   PHE B 222 
 TRP   0.018   0.001   TRP A 253 
 HIS   0.003   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 6146)
  covalent geometry    : angle       0.68827 /  0.33 ( 8300)
  SS BOND              : bond        0.00246 /  0.14 (    9)
  SS BOND              : angle       0.91642 /  0.47 (   18)
  hydrogen bonds       : bond        0.03229 /  2.21 (  280)
  hydrogen bonds       : angle       5.14027 /  3.55 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8518 (mmm) cc_final: 0.8169 (mmm)
REVERT: A  105 CYS cc_start: 0.7119 (t) cc_final: 0.6690 (t)
REVERT: A  166 LEU cc_start: 0.9053 (tp) cc_final: 0.8839 (tp)
REVERT: A  243 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7718 (m-80)
REVERT: A  248 LYS cc_start: 0.9384 (ttmt) cc_final: 0.8996 (ttmt)
REVERT: B  119 GLN cc_start: 0.8364 (tt0) cc_final: 0.8008 (tp40)
REVERT: B  193 MET cc_start: 0.8891 (mmm) cc_final: 0.8613 (mmm)
REVERT: B  219 GLU cc_start: 0.8669 (mp0) cc_final: 0.8365 (mp0)
REVERT: B  227 SER cc_start: 0.7274 (t) cc_final: 0.6830 (p)
REVERT: B  248 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9027 (mtpt)
REVERT: D  296 ARG cc_start: 0.9437 (mmm160) cc_final: 0.8901 (mmm160)
REVERT: D  336 ASP cc_start: 0.9188 (m-30) cc_final: 0.8918 (p0)
REVERT: D  350 PHE cc_start: 0.9380 (m-80) cc_final: 0.9112 (m-80)
REVERT: D  368 LYS cc_start: 0.9381 (tttt) cc_final: 0.9102 (tppt)
REVERT: E  328 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8344 (mp0)
  outliers start: 20
  outliers final: 17
  residues processed: 139
  average time/residue: 0.0820
  time to fit residues: 14.8253
Evaluate side-chains
  138 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  105 CYS
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 TRP
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  359 THR
Chi-restraints excluded: chain E residue  407 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [56, 53, 57, 1, 30, 35, 36, 65, 41, 39, 54]
   chunk 56 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.8582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.076442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.064448 restraints weight = 29912.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.066306 restraints weight = 17980.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.067603 restraints weight = 12107.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.068616 restraints weight = 8869.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.069373 restraints weight = 6837.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.5569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6155  Z= 0.134
  Angle     :  0.702  10.325   8318  Z= 0.336
  Chirality :  0.044   0.283    952
  Planarity :  0.004   0.048   1068
  Dihedral  :  3.733  14.422    826
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.73 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.82 (0.30), residues: 770
  helix:  1.57 (0.30), residues: 286
  sheet: -1.48 (0.49), residues: 86
  loop :  0.40 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 182 
 TYR   0.017   0.001   TYR D 398 
 PHE   0.011   0.001   PHE B 222 
 TRP   0.024   0.001   TRP A 253 
 HIS   0.003   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 ( 6146)
  covalent geometry    : angle       0.70119 /  0.34 ( 8300)
  SS BOND              : bond        0.00233 /  0.14 (    9)
  SS BOND              : angle       0.92889 /  0.48 (   18)
  hydrogen bonds       : bond        0.03335 /  2.26 (  280)
  hydrogen bonds       : angle       5.15094 /  3.55 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8549 (mmm) cc_final: 0.8262 (mmm)
REVERT: A  105 CYS cc_start: 0.7005 (t) cc_final: 0.6533 (t)
REVERT: A  166 LEU cc_start: 0.9057 (tp) cc_final: 0.8844 (tp)
REVERT: A  243 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7628 (m-80)
REVERT: A  253 TRP cc_start: 0.9298 (t-100) cc_final: 0.9022 (t-100)
REVERT: B  119 GLN cc_start: 0.8428 (tt0) cc_final: 0.8071 (tp40)
REVERT: B  193 MET cc_start: 0.8887 (mmm) cc_final: 0.8617 (mmm)
REVERT: B  209 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7603 (p0)
REVERT: B  219 GLU cc_start: 0.8633 (mp0) cc_final: 0.8350 (mp0)
REVERT: B  227 SER cc_start: 0.7291 (t) cc_final: 0.6846 (p)
REVERT: B  248 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9030 (mtpt)
REVERT: D  278 ASN cc_start: 0.9219 (m110) cc_final: 0.8798 (p0)
REVERT: D  292 ASP cc_start: 0.9413 (m-30) cc_final: 0.9210 (m-30)
REVERT: D  296 ARG cc_start: 0.9420 (mmm160) cc_final: 0.8946 (mmm160)
REVERT: D  336 ASP cc_start: 0.9203 (m-30) cc_final: 0.9000 (p0)
REVERT: D  350 PHE cc_start: 0.9382 (m-80) cc_final: 0.9121 (m-80)
REVERT: D  368 LYS cc_start: 0.9359 (tttt) cc_final: 0.9070 (tppt)
REVERT: E  328 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8328 (mp0)
  outliers start: 22
  outliers final: 18
  residues processed: 139
  average time/residue: 0.0800
  time to fit residues: 14.6953
Evaluate side-chains
  137 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 TRP
Chi-restraints excluded: chain B residue  209 ASN
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain D residue  365 ASP
Chi-restraints excluded: chain D residue  387 TYR
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  359 THR
Chi-restraints excluded: chain E residue  407 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [4, 19, 31, 15, 56, 36, 11, 29, 60, 73, 28]
   chunk 4 optimal weight:    0.4980
   chunk 19 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 15 optimal weight:    0.1980
   chunk 56 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0010
   chunk 11 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 73 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.3586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.078698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.066676 restraints weight = 28800.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.068631 restraints weight = 17275.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.069852 restraints weight = 11505.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.070881 restraints weight = 8615.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.071643 restraints weight = 6642.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.5774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6155  Z= 0.119
  Angle     :  0.719  10.898   8318  Z= 0.337
  Chirality :  0.043   0.154    952
  Planarity :  0.004   0.048   1068
  Dihedral  :  3.624  14.087    826
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.92 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.89 (0.30), residues: 770
  helix:  1.55 (0.30), residues: 286
  sheet: -1.48 (0.55), residues: 76
  loop :  0.45 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 182 
 TYR   0.021   0.001   TYR D 398 
 PHE   0.015   0.002   PHE A 101 
 TRP   0.022   0.001   TRP A 253 
 HIS   0.002   0.000   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 ( 6146)
  covalent geometry    : angle       0.71833 /  0.34 ( 8300)
  SS BOND              : bond        0.00182 /  0.10 (    9)
  SS BOND              : angle       0.83519 /  0.43 (   18)
  hydrogen bonds       : bond        0.03144 /  2.13 (  280)
  hydrogen bonds       : angle       5.09017 /  3.51 (  798)

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8515 (mmm) cc_final: 0.8285 (mmm)
REVERT: A  101 PHE cc_start: 0.9164 (m-10) cc_final: 0.8961 (m-10)
REVERT: A  105 CYS cc_start: 0.7052 (t) cc_final: 0.6530 (t)
REVERT: A  243 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7430 (m-80)
REVERT: A  248 LYS cc_start: 0.9369 (ttmt) cc_final: 0.8932 (ttmt)
REVERT: A  253 TRP cc_start: 0.9253 (t-100) cc_final: 0.8976 (t-100)
REVERT: B  119 GLN cc_start: 0.8400 (tt0) cc_final: 0.8137 (tp40)
REVERT: B  219 GLU cc_start: 0.8699 (mp0) cc_final: 0.8331 (mp0)
REVERT: B  227 SER cc_start: 0.7220 (t) cc_final: 0.6866 (p)
REVERT: B  248 LYS cc_start: 0.9341 (ttmt) cc_final: 0.9036 (mtpt)
REVERT: D  278 ASN cc_start: 0.9250 (m110) cc_final: 0.8835 (p0)
REVERT: D  296 ARG cc_start: 0.9384 (mmm160) cc_final: 0.8942 (mmm160)
REVERT: D  336 ASP cc_start: 0.9165 (m-30) cc_final: 0.8886 (p0)
REVERT: D  350 PHE cc_start: 0.9376 (m-80) cc_final: 0.9148 (m-80)
REVERT: D  368 LYS cc_start: 0.9342 (tttt) cc_final: 0.9035 (tppt)
REVERT: D  371 MET cc_start: 0.8055 (tmm) cc_final: 0.7492 (tmm)
REVERT: E  254 MET cc_start: 0.5974 (mmp) cc_final: 0.5714 (mmp)
REVERT: E  328 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8374 (mp0)
  outliers start: 16
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0835
  time to fit residues: 13.9870
Evaluate side-chains
  131 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  243 TYR
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   72 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  138 LYS
Chi-restraints excluded: chain B residue  162 TRP
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  291 GLN
Chi-restraints excluded: chain E residue  265 LEU
Chi-restraints excluded: chain E residue  359 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [64, 5, 50, 10, 68, 26, 39, 41, 23, 42, 7]
   chunk 64 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 119 GLN ** 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 = 0.3887 r_free = 0.3887 target = 0.075854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.063852 restraints weight = 29239.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.065724 restraints weight = 17278.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.067056 restraints weight = 11646.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.067946 restraints weight = 8466.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.068722 restraints weight = 6640.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.5752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6155  Z= 0.155
  Angle     :  0.724  11.115   8318  Z= 0.345
  Chirality :  0.043   0.147    952
  Planarity :  0.004   0.049   1068
  Dihedral  :  3.813  14.155    826
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 20.77 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.89 (0.30), residues: 770
  helix:  1.45 (0.30), residues: 284
  sheet: -1.47 (0.61), residues: 54
  loop :  0.41 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 176 
 TYR   0.018   0.001   TYR D 398 
 PHE   0.010   0.002   PHE A 101 
 TRP   0.021   0.002   TRP A 253 
 HIS   0.004   0.001   HIS B  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 6146)
  covalent geometry    : angle       0.72280 /  0.34 ( 8300)
  SS BOND              : bond        0.00295 /  0.17 (    9)
  SS BOND              : angle       1.09216 /  0.56 (   18)
  hydrogen bonds       : bond        0.03413 /  2.32 (  280)
  hydrogen bonds       : angle       5.24155 /  3.62 (  798)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1219.09 seconds
wall clock time: 21 minutes 40.77 seconds (1300.77 seconds total)