Starting phenix.real_space_refine
on Fri Aug 22 22:32:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8grx_34216/08_2025/8grx_34216.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8grx_34216/08_2025/8grx_34216.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8grx_34216/08_2025/8grx_34216.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8grx_34216/08_2025/8grx_34216.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8grx_34216/08_2025/8grx_34216.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8grx_34216/08_2025/8grx_34216.cif"
  }
  resolution = 3.0
  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=   0.002 sd=   0.116
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      42      5.16       5
     C    5256      2.51       5
     N    1474      2.21       5
     O    1556      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8328
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1140
          Classifications: {'peptide': 138}
          Link IDs: {'TRANS': 137}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3024
          Classifications: {'peptide': 390}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 352}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 2.10, per 1000 atoms: 0.25
  Number of scatterers: 8328
  At special positions: 0
  Unit cell: (124.063, 150.412, 77.9509, 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      42     16.00
     O    1556      8.00
     N    1474      7.00
     C    5256      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  49 " - pdb=" SG  CYS B  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 196 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 245 " - pdb=" SG  CYS B 296 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 345 " - pdb=" SG  CYS B 396 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  49 " - pdb=" SG  CYS D  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 144 " - pdb=" SG  CYS D 196 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 245 " - pdb=" SG  CYS D 296 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 345 " - pdb=" SG  CYS D 396 " distance=2.04

  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 335.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 22 sheets defined
      27.2% alpha, 30.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 43
      removed outlier: 3.953A  pdb=" N   LEU A  43 " --> pdb=" O   TRP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 51
    Processing helix  chain 'A' and resid 54 through 82
    Processing helix  chain 'A' and resid 87 through 125
    Processing helix  chain 'A' and resid 130 through 162
      removed outlier: 3.543A  pdb=" N   ARG A 147 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 171
    Processing helix  chain 'B' and resid 287 through 291
    Processing helix  chain 'B' and resid 387 through 391
      removed outlier: 3.619A  pdb=" N   ALA B 391 " --> pdb=" O   SER B 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 43
      removed outlier: 3.953A  pdb=" N   LEU C  43 " --> pdb=" O   TRP C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 51
    Processing helix  chain 'C' and resid 54 through 82
    Processing helix  chain 'C' and resid 87 through 125
    Processing helix  chain 'C' and resid 130 through 162
      removed outlier: 3.543A  pdb=" N   ARG C 147 " --> pdb=" O   LYS C 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 171
    Processing helix  chain 'D' and resid 287 through 291
    Processing helix  chain 'D' and resid 387 through 391
      removed outlier: 3.619A  pdb=" N   ALA D 391 " --> pdb=" O   SER D 388 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34
    Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39
      removed outlier: 6.525A  pdb=" N   MET B 117 " --> pdb=" O   TRP B 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 62
      removed outlier: 3.613A  pdb=" N   GLU B  57 " --> pdb=" O   TYR B 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 62
      removed outlier: 3.613A  pdb=" N   GLU B  57 " --> pdb=" O   TYR B 101 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 129
    Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 135
      removed outlier: 4.213A  pdb=" N   TRP B 192 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   ARG B 193 " --> pdb=" O   GLU B 158 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 226 through 229
      removed outlier: 5.807A  pdb=" N   LEU B 241 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 235
      removed outlier: 6.664A  pdb=" N   LEU B 235 " --> pdb=" O   ALA B 318 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   GLN B 320 " --> pdb=" O   LEU B 235 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   MET B 317 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 268
    Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 330
      removed outlier: 4.059A  pdb=" N   VAL B 341 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336
    Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 34
    Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 39
      removed outlier: 6.525A  pdb=" N   MET D 117 " --> pdb=" O   TRP D 207 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 62
      removed outlier: 3.613A  pdb=" N   GLU D  57 " --> pdb=" O   TYR D 101 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 62
      removed outlier: 3.613A  pdb=" N   GLU D  57 " --> pdb=" O   TYR D 101 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 129
    Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 135
      removed outlier: 4.213A  pdb=" N   TRP D 192 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   ARG D 193 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 226 through 229
      removed outlier: 5.807A  pdb=" N   LEU D 241 " --> pdb=" O   LEU D 283 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 235
      removed outlier: 6.664A  pdb=" N   LEU D 235 " --> pdb=" O   ALA D 318 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   GLN D 320 " --> pdb=" O   LEU D 235 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   MET D 317 " --> pdb=" O   LEU D 407 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 268
    Processing sheet with id=AC3, first strand: chain 'D' and resid 326 through 330
      removed outlier: 4.059A  pdb=" N   VAL D 341 " --> pdb=" O   MET D 383 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 334 through 336

    439 hydrogen bonds defined for protein.
    1167 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1926
        1.33 -     1.45: 1864
        1.45 -     1.57: 4692
        1.57 -     1.69: 0
        1.69 -     1.81: 68
  Bond restraints: 8550
  Sorted by residual:
  bond pdb=" C   HIS D 363 "
       pdb=" N   PRO D 364 "
    ideal  model  delta    sigma   weight residual
    1.331  1.368 -0.037 8.70e-03 1.32e+04 1.81e+01
  bond pdb=" C   HIS B 363 "
       pdb=" N   PRO B 364 "
    ideal  model  delta    sigma   weight residual
    1.331  1.368 -0.037 8.70e-03 1.32e+04 1.81e+01
  bond pdb=" C   GLY D 284 "
       pdb=" N   PRO D 285 "
    ideal  model  delta    sigma   weight residual
    1.331  1.371 -0.040 1.27e-02 6.20e+03 9.90e+00
  bond pdb=" C   GLY B 284 "
       pdb=" N   PRO B 285 "
    ideal  model  delta    sigma   weight residual
    1.331  1.371 -0.040 1.27e-02 6.20e+03 9.90e+00
  bond pdb=" C   PHE B 181 "
       pdb=" N   PRO B 182 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 8.70e-03 1.32e+04 8.46e+00
  ... (remaining 8545 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 10724
        2.13 -     4.25: 712
        4.25 -     6.38: 112
        6.38 -     8.50: 32
        8.50 -    10.63: 18
  Bond angle restraints: 11598
  Sorted by residual:
  angle pdb=" C   GLU B  67 "
        pdb=" N   PRO B  68 "
        pdb=" CA  PRO B  68 "
      ideal   model   delta    sigma   weight residual
     119.76  113.46    6.30 1.00e+00 1.00e+00 3.97e+01
  angle pdb=" C   GLU D  67 "
        pdb=" N   PRO D  68 "
        pdb=" CA  PRO D  68 "
      ideal   model   delta    sigma   weight residual
     119.76  113.46    6.30 1.00e+00 1.00e+00 3.97e+01
  angle pdb=" C   ARG D 267 "
        pdb=" N   PRO D 268 "
        pdb=" CA  PRO D 268 "
      ideal   model   delta    sigma   weight residual
     120.03  114.22    5.81 9.90e-01 1.02e+00 3.45e+01
  angle pdb=" C   ARG B 267 "
        pdb=" N   PRO B 268 "
        pdb=" CA  PRO B 268 "
      ideal   model   delta    sigma   weight residual
     120.03  114.22    5.81 9.90e-01 1.02e+00 3.45e+01
  angle pdb=" C   GLY D 184 "
        pdb=" N   PRO D 185 "
        pdb=" CA  PRO D 185 "
      ideal   model   delta    sigma   weight residual
     119.84  126.74   -6.90 1.25e+00 6.40e-01 3.05e+01
  ... (remaining 11593 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.18: 4966
       25.18 -    50.36: 152
       50.36 -    75.54: 18
       75.54 -   100.72: 2
      100.72 -   125.90: 4
  Dihedral angle restraints: 5142
    sinusoidal: 2098
      harmonic: 3044
  Sorted by residual:
  dihedral pdb=" CA  GLN B 330 "
           pdb=" C   GLN B 330 "
           pdb=" N   PRO B 331 "
           pdb=" CA  PRO B 331 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   54.10  125.90     0      5.00e+00 4.00e-02 6.34e+02
  dihedral pdb=" CA  GLN D 330 "
           pdb=" C   GLN D 330 "
           pdb=" N   PRO D 331 "
           pdb=" CA  PRO D 331 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   54.10  125.90     0      5.00e+00 4.00e-02 6.34e+02
  dihedral pdb=" CA  GLY B 184 "
           pdb=" C   GLY B 184 "
           pdb=" N   PRO B 185 "
           pdb=" CA  PRO B 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -67.33 -112.67     0      5.00e+00 4.00e-02 5.08e+02
  ... (remaining 5139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 758
       0.040 -    0.080: 302
       0.080 -    0.120: 116
       0.120 -    0.159: 38
       0.159 -    0.199: 2
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" CA  SER A  54 "
            pdb=" N   SER A  54 "
            pdb=" C   SER A  54 "
            pdb=" CB  SER A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CA  SER C  54 "
            pdb=" N   SER C  54 "
            pdb=" C   SER C  54 "
            pdb=" CB  SER C  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CG  LEU D 235 "
            pdb=" CB  LEU D 235 "
            pdb=" CD1 LEU D 235 "
            pdb=" CD2 LEU D 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.81e-01
  ... (remaining 1213 not shown)

  Planarity restraints: 1514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 131 "    0.037 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO D 132 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO D 132 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D 132 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 131 "   -0.037 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO B 132 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  86 "   -0.007 2.00e-02 2.50e+03   1.47e-02 2.17e+00
        pdb=" C   ALA A  86 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ALA A  86 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLU A  87 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1511 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 2944
        2.88 -     3.38: 7335
        3.38 -     3.89: 14411
        3.89 -     4.39: 16410
        4.39 -     4.90: 26746
  Nonbonded interactions: 67846
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 102 "
            pdb=" O   GLY D 105 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" OG  SER B 102 "
            pdb=" O   GLY B 105 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" NE  ARG B 253 "
            pdb=" O   HIS B 300 "
     model   vdw
     2.522 3.120
  nonbonded pdb=" NE  ARG D 253 "
            pdb=" O   HIS D 300 "
     model   vdw
     2.522 3.120
  nonbonded pdb=" O   ARG B 223 "
            pdb=" OH  TYR B 251 "
     model   vdw
     2.551 3.040
  ... (remaining 67841 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 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.850
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   8558  Z= 0.480
  Angle     :  1.263  10.628  11614  Z= 0.794
  Chirality :  0.051   0.199   1216
  Planarity :  0.005   0.057   1514
  Dihedral  : 12.300 125.903   3170
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  3.27 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.83 %
    Favored  : 93.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 8.11 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.25), residues: 1040
  helix:  1.26 (0.28), residues: 256
  sheet: -0.08 (0.28), residues: 310
  loop : -1.28 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 253 
 TYR   0.020   0.002   TYR B 197 
 PHE   0.010   0.002   PHE B 177 
 TRP   0.012   0.002   TRP A  26 
 HIS   0.003   0.001   HIS D 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 ( 8550)
  covalent geometry    : angle       1.26351 (11598)
  SS BOND              : bond        0.00819 (    8)
  SS BOND              : angle       1.03658 (   16)
  hydrogen bonds       : bond        0.15753 (  429)
  hydrogen bonds       : angle       7.61385 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 154
  average time/residue: 0.5898
  time to fit residues: 95.5899
Evaluate side-chains
  98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0570
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
A  58 GLN
A  81 GLN
A 117 GLN
A 128 GLN
A 140 HIS
A 156 GLN
B  92 HIS
B 190 HIS
B 205 GLN
B 266 GLN
B 280 ASN
B 290 HIS
B 301 ASN
B 346 GLN
C  46 GLN
C  58 GLN
C  81 GLN
C 117 GLN
C 128 GLN
C 140 HIS
C 156 GLN
D  92 HIS
D 190 HIS
D 205 GLN
D 266 GLN
D 290 HIS
D 301 ASN
D 346 GLN

Total number of N/Q/H flips: 29

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.199902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151914 restraints weight = 9098.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 3.27
r_work: 0.3327 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8558  Z= 0.144
  Angle     :  0.561   7.048  11614  Z= 0.294
  Chirality :  0.039   0.145   1216
  Planarity :  0.006   0.091   1514
  Dihedral  :  5.673  90.799   1164
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  0.77 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.54 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.41 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.26), residues: 1040
  helix:  3.54 (0.28), residues: 254
  sheet:  0.35 (0.28), residues: 316
  loop : -0.23 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.015   0.001   TYR B 372 
 PHE   0.009   0.001   PHE B 351 
 TRP   0.014   0.001   TRP D  32 
 HIS   0.004   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8550)
  covalent geometry    : angle       0.56084 (11598)
  SS BOND              : bond        0.00452 (    8)
  SS BOND              : angle       0.62570 (   16)
  hydrogen bonds       : bond        0.05219 (  429)
  hydrogen bonds       : angle       5.27148 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7707 (ptm)
REVERT: A  125 MET cc_start: 0.8394 (mmm) cc_final: 0.8149 (mmt)
REVERT: A  151 ASP cc_start: 0.8623 (m-30) cc_final: 0.8258 (m-30)
REVERT: B   32 TRP cc_start: 0.7338 (p90) cc_final: 0.6742 (p90)
REVERT: B  223 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8413 (ttp80)
REVERT: B  248 ASP cc_start: 0.7747 (p0) cc_final: 0.7534 (p0)
REVERT: B  339 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7445 (mt-10)
REVERT: C   64 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7712 (ptm)
REVERT: C  125 MET cc_start: 0.8420 (mmm) cc_final: 0.8177 (mmt)
REVERT: C  151 ASP cc_start: 0.8630 (m-30) cc_final: 0.8264 (m-30)
REVERT: D   32 TRP cc_start: 0.7329 (p90) cc_final: 0.6733 (p90)
REVERT: D  223 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8413 (ttp80)
REVERT: D  248 ASP cc_start: 0.7751 (p0) cc_final: 0.7544 (p0)
REVERT: D  339 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7447 (mt-10)
  outliers start: 14
  outliers final: 2
  residues processed: 108
  average time/residue: 0.5263
  time to fit residues: 60.2779
Evaluate side-chains
  100 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
B 266 GLN
B 405 HIS
C  46 GLN
D 266 GLN
D 280 ASN
D 405 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.194154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.149590 restraints weight = 8938.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.93
r_work: 0.3372 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8558  Z= 0.143
  Angle     :  0.537   6.886  11614  Z= 0.280
  Chirality :  0.038   0.135   1216
  Planarity :  0.006   0.098   1514
  Dihedral  :  5.092  81.487   1164
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.50 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.88 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.27), residues: 1040
  helix:  3.93 (0.29), residues: 254
  sheet:  0.69 (0.29), residues: 318
  loop : -0.05 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 253 
 TYR   0.012   0.001   TYR B 197 
 PHE   0.007   0.001   PHE B 351 
 TRP   0.009   0.001   TRP A  26 
 HIS   0.004   0.001   HIS D 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8550)
  covalent geometry    : angle       0.53663 (11598)
  SS BOND              : bond        0.00564 (    8)
  SS BOND              : angle       0.76578 (   16)
  hydrogen bonds       : bond        0.04761 (  429)
  hydrogen bonds       : angle       4.80423 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.8485 (m-30) cc_final: 0.8065 (m-30)
REVERT: B   32 TRP cc_start: 0.7577 (p90) cc_final: 0.7020 (p90)
REVERT: B  114 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7418 (mt-10)
REVERT: B  223 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8508 (ttp80)
REVERT: B  224 LYS cc_start: 0.8878 (pttm) cc_final: 0.8664 (pttt)
REVERT: B  339 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7593 (mt-10)
REVERT: C  151 ASP cc_start: 0.8486 (m-30) cc_final: 0.8066 (m-30)
REVERT: D   32 TRP cc_start: 0.7579 (p90) cc_final: 0.7022 (p90)
REVERT: D  114 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7408 (mt-10)
REVERT: D  223 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8506 (ttp80)
REVERT: D  224 LYS cc_start: 0.8876 (pttm) cc_final: 0.8663 (pttt)
REVERT: D  339 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7595 (mt-10)
  outliers start: 16
  outliers final: 8
  residues processed: 110
  average time/residue: 0.6415
  time to fit residues: 74.7172
Evaluate side-chains
  106 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:    0.3980
   chunk 79 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.192894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.144290 restraints weight = 9140.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.17
r_work: 0.3317 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8558  Z= 0.163
  Angle     :  0.533   6.811  11614  Z= 0.276
  Chirality :  0.038   0.139   1216
  Planarity :  0.006   0.098   1514
  Dihedral  :  5.063  77.442   1164
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  1.54 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 11.10 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.27), residues: 1040
  helix:  3.68 (0.29), residues: 254
  sheet:  0.59 (0.28), residues: 332
  loop :  0.02 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  61 
 TYR   0.012   0.002   TYR B 198 
 PHE   0.007   0.001   PHE D 351 
 TRP   0.009   0.001   TRP A  26 
 HIS   0.004   0.001   HIS D 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8550)
  covalent geometry    : angle       0.53273 (11598)
  SS BOND              : bond        0.00630 (    8)
  SS BOND              : angle       0.81514 (   16)
  hydrogen bonds       : bond        0.04676 (  429)
  hydrogen bonds       : angle       4.62299 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7746 (tp30)
REVERT: A  151 ASP cc_start: 0.8635 (m-30) cc_final: 0.8219 (m-30)
REVERT: B   32 TRP cc_start: 0.7447 (p90) cc_final: 0.7116 (p90)
REVERT: B  223 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8597 (ttp80)
REVERT: B  224 LYS cc_start: 0.8880 (pttm) cc_final: 0.8635 (pttt)
REVERT: B  339 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7694 (mp0)
REVERT: C  132 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7742 (tp30)
REVERT: C  151 ASP cc_start: 0.8642 (m-30) cc_final: 0.8231 (m-30)
REVERT: D   32 TRP cc_start: 0.7433 (p90) cc_final: 0.7104 (p90)
REVERT: D  223 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8587 (ttp80)
REVERT: D  224 LYS cc_start: 0.8878 (pttm) cc_final: 0.8631 (pttt)
REVERT: D  339 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7691 (mp0)
  outliers start: 25
  outliers final: 12
  residues processed: 121
  average time/residue: 0.6704
  time to fit residues: 85.8570
Evaluate side-chains
  108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain D residue  174 SER
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  248 ASP
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 103 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    8.9990
   chunk 58 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.191289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146031 restraints weight = 9004.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.04
r_work: 0.3311 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8558  Z= 0.130
  Angle     :  0.501   6.432  11614  Z= 0.258
  Chirality :  0.037   0.136   1216
  Planarity :  0.006   0.107   1514
  Dihedral  :  4.926  75.433   1164
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.69 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.78 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.27), residues: 1040
  helix:  3.79 (0.28), residues: 254
  sheet:  0.63 (0.28), residues: 332
  loop :  0.17 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  61 
 TYR   0.011   0.001   TYR B 197 
 PHE   0.004   0.001   PHE D 351 
 TRP   0.010   0.001   TRP A  26 
 HIS   0.005   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8550)
  covalent geometry    : angle       0.50104 (11598)
  SS BOND              : bond        0.00453 (    8)
  SS BOND              : angle       0.76061 (   16)
  hydrogen bonds       : bond        0.04432 (  429)
  hydrogen bonds       : angle       4.49609 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.8553 (m-30) cc_final: 0.8216 (m-30)
REVERT: B   32 TRP cc_start: 0.7504 (p90) cc_final: 0.7170 (p90)
REVERT: B  223 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8551 (ttp80)
REVERT: B  224 LYS cc_start: 0.8861 (pttm) cc_final: 0.8617 (pttt)
REVERT: C  151 ASP cc_start: 0.8551 (m-30) cc_final: 0.8211 (m-30)
REVERT: D   32 TRP cc_start: 0.7505 (p90) cc_final: 0.7178 (p90)
REVERT: D  223 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8545 (ttp80)
REVERT: D  224 LYS cc_start: 0.8864 (pttm) cc_final: 0.8619 (pttt)
  outliers start: 14
  outliers final: 8
  residues processed: 102
  average time/residue: 0.6173
  time to fit residues: 67.1534
Evaluate side-chains
  98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0270
   chunk 17 optimal weight:   30.0000
   chunk 94 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.191205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.146262 restraints weight = 8919.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.00
r_work: 0.3371 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8558  Z= 0.127
  Angle     :  0.498   6.253  11614  Z= 0.256
  Chirality :  0.037   0.135   1216
  Planarity :  0.006   0.114   1514
  Dihedral  :  4.837  72.456   1164
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.22 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.27), residues: 1040
  helix:  3.81 (0.28), residues: 254
  sheet:  0.67 (0.28), residues: 336
  loop :  0.27 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  61 
 TYR   0.011   0.001   TYR B 198 
 PHE   0.004   0.001   PHE B 351 
 TRP   0.010   0.001   TRP A  26 
 HIS   0.005   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8550)
  covalent geometry    : angle       0.49808 (11598)
  SS BOND              : bond        0.00465 (    8)
  SS BOND              : angle       0.69381 (   16)
  hydrogen bonds       : bond        0.04291 (  429)
  hydrogen bonds       : angle       4.38245 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7905 (ptm)
REVERT: A  132 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7748 (tp30)
REVERT: A  151 ASP cc_start: 0.8609 (m-30) cc_final: 0.8281 (m-30)
REVERT: B   32 TRP cc_start: 0.7457 (p90) cc_final: 0.7124 (p90)
REVERT: B  223 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8611 (ttp80)
REVERT: B  224 LYS cc_start: 0.8874 (pttm) cc_final: 0.8572 (pttt)
REVERT: B  383 MET cc_start: 0.8422 (mtm) cc_final: 0.8182 (mtt)
REVERT: C  132 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7748 (tp30)
REVERT: C  151 ASP cc_start: 0.8608 (m-30) cc_final: 0.8279 (m-30)
REVERT: D   32 TRP cc_start: 0.7453 (p90) cc_final: 0.7120 (p90)
REVERT: D  223 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8609 (ttp80)
REVERT: D  224 LYS cc_start: 0.8880 (pttm) cc_final: 0.8576 (pttt)
REVERT: D  383 MET cc_start: 0.8437 (mtm) cc_final: 0.8194 (mtt)
  outliers start: 23
  outliers final: 13
  residues processed: 110
  average time/residue: 0.6601
  time to fit residues: 77.0495
Evaluate side-chains
  102 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain D residue  174 SER
Chi-restraints excluded: chain D residue  221 VAL
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 89 optimal weight:    0.0000
   chunk 36 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0270
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 46 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0050
   chunk 49 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.2256

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.193432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.149915 restraints weight = 9026.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 1.87
r_work: 0.3426 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8558  Z= 0.091
  Angle     :  0.464   5.690  11614  Z= 0.241
  Chirality :  0.035   0.135   1216
  Planarity :  0.005   0.111   1514
  Dihedral  :  4.651  69.477   1164
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.22 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.27), residues: 1040
  helix:  4.05 (0.28), residues: 254
  sheet:  0.71 (0.28), residues: 338
  loop :  0.41 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 147 
 TYR   0.011   0.001   TYR B 377 
 PHE   0.004   0.001   PHE B 354 
 TRP   0.010   0.001   TRP A  26 
 HIS   0.005   0.001   HIS D 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 8550)
  covalent geometry    : angle       0.46411 (11598)
  SS BOND              : bond        0.00265 (    8)
  SS BOND              : angle       0.55236 (   16)
  hydrogen bonds       : bond        0.03778 (  429)
  hydrogen bonds       : angle       4.23872 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7051 (mt-10)
REVERT: A  132 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7612 (tp30)
REVERT: A  151 ASP cc_start: 0.8561 (m-30) cc_final: 0.8234 (m-30)
REVERT: B   32 TRP cc_start: 0.7494 (p90) cc_final: 0.7161 (p90)
REVERT: B  223 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8576 (ttp80)
REVERT: B  224 LYS cc_start: 0.8842 (pttm) cc_final: 0.8580 (pttt)
REVERT: C   49 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7047 (mt-10)
REVERT: C  132 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7605 (tp30)
REVERT: C  151 ASP cc_start: 0.8573 (m-30) cc_final: 0.8245 (m-30)
REVERT: D   32 TRP cc_start: 0.7496 (p90) cc_final: 0.7167 (p90)
REVERT: D  223 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8577 (ttp80)
REVERT: D  224 LYS cc_start: 0.8844 (pttm) cc_final: 0.8581 (pttt)
  outliers start: 22
  outliers final: 14
  residues processed: 105
  average time/residue: 0.6251
  time to fit residues: 69.8191
Evaluate side-chains
  102 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain D residue  174 SER
Chi-restraints excluded: chain D residue  221 VAL
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 74 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.192792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145009 restraints weight = 9039.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.14
r_work: 0.3265 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8558  Z= 0.140
  Angle     :  0.499   5.859  11614  Z= 0.256
  Chirality :  0.037   0.130   1216
  Planarity :  0.006   0.106   1514
  Dihedral  :  4.744  68.539   1164
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.89 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 1040
  helix:  3.85 (0.28), residues: 254
  sheet:  0.72 (0.28), residues: 334
  loop :  0.38 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  61 
 TYR   0.013   0.001   TYR B 377 
 PHE   0.005   0.001   PHE D 381 
 TRP   0.008   0.001   TRP B 306 
 HIS   0.005   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8550)
  covalent geometry    : angle       0.49788 (11598)
  SS BOND              : bond        0.00565 (    8)
  SS BOND              : angle       0.83960 (   16)
  hydrogen bonds       : bond        0.04256 (  429)
  hydrogen bonds       : angle       4.29349 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6999 (mt-10)
REVERT: A  108 MET cc_start: 0.8675 (mtt) cc_final: 0.8341 (mtp)
REVERT: A  112 ARG cc_start: 0.7358 (mtm110) cc_final: 0.7023 (mtp-110)
REVERT: A  132 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7723 (tp30)
REVERT: A  151 ASP cc_start: 0.8548 (m-30) cc_final: 0.8213 (m-30)
REVERT: B   32 TRP cc_start: 0.7535 (p90) cc_final: 0.7235 (p90)
REVERT: B  223 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8550 (ttp80)
REVERT: B  224 LYS cc_start: 0.8875 (pttm) cc_final: 0.8601 (pttt)
REVERT: C   49 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7008 (mt-10)
REVERT: C  108 MET cc_start: 0.8668 (mtt) cc_final: 0.8332 (mtp)
REVERT: C  112 ARG cc_start: 0.7357 (mtm110) cc_final: 0.7017 (mtp-110)
REVERT: C  132 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7720 (tp30)
REVERT: C  151 ASP cc_start: 0.8549 (m-30) cc_final: 0.8214 (m-30)
REVERT: D   32 TRP cc_start: 0.7538 (p90) cc_final: 0.7242 (p90)
REVERT: D  223 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8548 (ttp80)
REVERT: D  224 LYS cc_start: 0.8878 (pttm) cc_final: 0.8602 (pttt)
  outliers start: 22
  outliers final: 14
  residues processed: 106
  average time/residue: 0.6239
  time to fit residues: 70.3026
Evaluate side-chains
  105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain D residue  174 SER
Chi-restraints excluded: chain D residue  221 VAL
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  287 SER
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 75 optimal weight:    0.2980
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0010
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    0.4980
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.4186

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.194602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.145505 restraints weight = 9115.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.31
r_work: 0.3315 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8558  Z= 0.098
  Angle     :  0.461   5.467  11614  Z= 0.238
  Chirality :  0.036   0.139   1216
  Planarity :  0.005   0.104   1514
  Dihedral  :  4.637  67.577   1164
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.56 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.27), residues: 1040
  helix:  4.07 (0.28), residues: 254
  sheet:  0.86 (0.29), residues: 334
  loop :  0.53 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 147 
 TYR   0.013   0.001   TYR B 377 
 PHE   0.004   0.001   PHE D 281 
 TRP   0.010   0.001   TRP A  26 
 HIS   0.005   0.001   HIS D 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8550)
  covalent geometry    : angle       0.46071 (11598)
  SS BOND              : bond        0.00350 (    8)
  SS BOND              : angle       0.61276 (   16)
  hydrogen bonds       : bond        0.03804 (  429)
  hydrogen bonds       : angle       4.20101 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6971 (mt-10)
REVERT: A   64 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7796 (ptm)
REVERT: A  132 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7695 (tp30)
REVERT: A  151 ASP cc_start: 0.8528 (m-30) cc_final: 0.8206 (m-30)
REVERT: B   32 TRP cc_start: 0.7538 (p90) cc_final: 0.7251 (p90)
REVERT: B  223 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8499 (ttp80)
REVERT: B  224 LYS cc_start: 0.8834 (pttm) cc_final: 0.8532 (pttt)
REVERT: C   49 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6958 (mt-10)
REVERT: C   64 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7808 (ptm)
REVERT: C  132 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7687 (tp30)
REVERT: C  151 ASP cc_start: 0.8534 (m-30) cc_final: 0.8216 (m-30)
REVERT: D   32 TRP cc_start: 0.7540 (p90) cc_final: 0.7254 (p90)
REVERT: D  223 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8504 (ttp80)
REVERT: D  224 LYS cc_start: 0.8836 (pttm) cc_final: 0.8535 (pttt)
  outliers start: 22
  outliers final: 12
  residues processed: 99
  average time/residue: 0.6060
  time to fit residues: 64.1478
Evaluate side-chains
  101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  202 ASN
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain D residue  174 SER
Chi-restraints excluded: chain D residue  202 ASN
Chi-restraints excluded: chain D residue  221 VAL
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 68 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0170
   chunk 78 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.193747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146344 restraints weight = 9070.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.11
r_work: 0.3314 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8558  Z= 0.131
  Angle     :  0.486   5.555  11614  Z= 0.249
  Chirality :  0.037   0.138   1216
  Planarity :  0.005   0.102   1514
  Dihedral  :  4.692  66.908   1164
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.68 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.27), residues: 1040
  helix:  3.89 (0.28), residues: 254
  sheet:  0.85 (0.29), residues: 330
  loop :  0.48 (0.32), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 112 
 TYR   0.013   0.001   TYR B 377 
 PHE   0.006   0.001   PHE D 381 
 TRP   0.009   0.001   TRP D 306 
 HIS   0.005   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8550)
  covalent geometry    : angle       0.48508 (11598)
  SS BOND              : bond        0.00506 (    8)
  SS BOND              : angle       0.79749 (   16)
  hydrogen bonds       : bond        0.04085 (  429)
  hydrogen bonds       : angle       4.25870 ( 1167)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7020 (mt-10)
REVERT: A  132 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7729 (tp30)
REVERT: A  151 ASP cc_start: 0.8549 (m-30) cc_final: 0.8220 (m-30)
REVERT: B   32 TRP cc_start: 0.7553 (p90) cc_final: 0.7283 (p90)
REVERT: B  223 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8512 (ttp80)
REVERT: B  224 LYS cc_start: 0.8852 (pttm) cc_final: 0.8542 (pttt)
REVERT: C   49 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7023 (mt-10)
REVERT: C  132 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7729 (tp30)
REVERT: C  151 ASP cc_start: 0.8555 (m-30) cc_final: 0.8226 (m-30)
REVERT: D   32 TRP cc_start: 0.7561 (p90) cc_final: 0.7298 (p90)
REVERT: D  223 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8525 (ttp80)
REVERT: D  224 LYS cc_start: 0.8854 (pttm) cc_final: 0.8542 (pttt)
  outliers start: 18
  outliers final: 12
  residues processed: 104
  average time/residue: 0.6517
  time to fit residues: 71.9070
Evaluate side-chains
  106 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 MET
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  223 ARG
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain C residue   64 MET
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain D residue  174 SER
Chi-restraints excluded: chain D residue  221 VAL
Chi-restraints excluded: chain D residue  223 ARG
Chi-restraints excluded: chain D residue  249 VAL
Chi-restraints excluded: chain D residue  326 SER
Chi-restraints excluded: chain D residue  368 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0170
   chunk 82 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
D 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.194398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.147133 restraints weight = 9084.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.12
r_work: 0.3332 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8558  Z= 0.113
  Angle     :  0.468   5.392  11614  Z= 0.241
  Chirality :  0.036   0.127   1216
  Planarity :  0.005   0.102   1514
  Dihedral  :  4.635  66.344   1164
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.57 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 1040
  helix:  3.98 (0.28), residues: 254
  sheet:  0.91 (0.29), residues: 334
  loop :  0.58 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 112 
 TYR   0.012   0.001   TYR D 377 
 PHE   0.004   0.001   PHE D 281 
 TRP   0.009   0.001   TRP A  26 
 HIS   0.005   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8550)
  covalent geometry    : angle       0.46718 (11598)
  SS BOND              : bond        0.00399 (    8)
  SS BOND              : angle       0.69226 (   16)
  hydrogen bonds       : bond        0.03857 (  429)
  hydrogen bonds       : angle       4.20924 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2831.60 seconds
wall clock time: 49 minutes 6.71 seconds (2946.71 seconds total)