Starting phenix.real_space_refine
on Tue Mar  3 15:57:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ss5_25404/03_2026/7ss5_25404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ss5_25404/03_2026/7ss5_25404.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ss5_25404/03_2026/7ss5_25404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ss5_25404/03_2026/7ss5_25404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ss5_25404/03_2026/7ss5_25404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ss5_25404/03_2026/7ss5_25404.cif"
  }
  resolution = 2.7
  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=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     P      48      5.49       5
     S      18      5.16       5
     C    3844      2.51       5
     N    1140      2.21       5
     O    1871      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6927
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2672
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 19, 'TRANS': 318}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 492
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 254
          Classifications: {'water': 254}
          Link IDs: {None: 253}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 43
          Classifications: {'water': 43}
          Link IDs: {None: 42}
    Chain: "B"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 253
          Classifications: {'water': 253}
          Link IDs: {None: 252}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 43
          Classifications: {'water': 43}
          Link IDs: {None: 42}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 2.03, per 1000 atoms: 0.29
  Number of scatterers: 6927
  At special positions: 0
  Unit cell: (83, 86.32, 106.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      18     16.00
     P      48     15.00
     O    1871      8.00
     N    1140      7.00
     C    3844      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 179.7 milliseconds
  

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1264

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 4 sheets defined
      51.8% alpha, 8.3% beta
      18 base pairs and 42 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 13
    Processing helix  chain 'A' and resid 14 through 18
      removed outlier: 3.653A  pdb=" N   ARG A  18 " --> pdb=" O   THR A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 48
    Processing helix  chain 'A' and resid 56 through 62
    Processing helix  chain 'A' and resid 63 through 68
    Processing helix  chain 'A' and resid 69 through 83
    Processing helix  chain 'A' and resid 90 through 123
    Processing helix  chain 'A' and resid 161 through 178
      removed outlier: 4.050A  pdb=" N   VAL A 167 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASP A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 199
    Processing helix  chain 'A' and resid 201 through 205
      removed outlier: 3.983A  pdb=" N   TRP A 204 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 221
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 4.029A  pdb=" N   ARG A 225 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 221 through 226'
    Processing helix  chain 'A' and resid 231 through 233
      No H-bonds generated for 'chain 'A' and resid 231 through 233'
    Processing helix  chain 'A' and resid 250 through 265
      removed outlier: 4.015A  pdb=" N   LEU A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN A 261 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 291
    Processing helix  chain 'A' and resid 318 through 334
    Processing helix  chain 'A' and resid 335 through 337
      No H-bonds generated for 'chain 'A' and resid 335 through 337'
    Processing helix  chain 'B' and resid 6 through 13
    Processing helix  chain 'B' and resid 14 through 18
      removed outlier: 3.653A  pdb=" N   ARG B  18 " --> pdb=" O   THR B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 48
    Processing helix  chain 'B' and resid 56 through 62
    Processing helix  chain 'B' and resid 63 through 68
    Processing helix  chain 'B' and resid 69 through 83
    Processing helix  chain 'B' and resid 90 through 123
    Processing helix  chain 'B' and resid 161 through 178
      removed outlier: 4.049A  pdb=" N   VAL B 167 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP B 178 " --> pdb=" O   GLY B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 199
    Processing helix  chain 'B' and resid 201 through 205
      removed outlier: 3.983A  pdb=" N   TRP B 204 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 221
    Processing helix  chain 'B' and resid 221 through 226
      removed outlier: 4.028A  pdb=" N   ARG B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU B 226 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 221 through 226'
    Processing helix  chain 'B' and resid 231 through 233
      No H-bonds generated for 'chain 'B' and resid 231 through 233'
    Processing helix  chain 'B' and resid 250 through 265
      removed outlier: 4.015A  pdb=" N   LEU B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN B 261 " --> pdb=" O   ALA B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 291
    Processing helix  chain 'B' and resid 318 through 334
    Processing helix  chain 'B' and resid 335 through 337
      No H-bonds generated for 'chain 'B' and resid 335 through 337'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149
      removed outlier: 6.822A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE A 235 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   GLU A 276 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ALA A 238 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   HIS A 278 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ALA A 240 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 9.867A  pdb=" N   LYS A 242 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 8.870A  pdb=" N   TYR A 314 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL A 277 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22
    Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 149
      removed outlier: 6.822A  pdb=" N   VAL B 193 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE B 235 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   GLU B 276 " --> pdb=" O   SER B 236 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ALA B 238 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   HIS B 278 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ALA B 240 " --> pdb=" O   HIS B 278 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   LEU B 280 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 9.866A  pdb=" N   LYS B 242 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 8.870A  pdb=" N   TYR B 314 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL B 277 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)

    226 hydrogen bonds defined for protein.
    648 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      76 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      42 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1665
        1.33 -     1.45: 1397
        1.45 -     1.57: 3376
        1.57 -     1.69: 94
        1.69 -     1.81: 32
  Bond restraints: 6564
  Sorted by residual:
  bond pdb=" CA  LEU A 296 "
       pdb=" C   LEU A 296 "
    ideal  model  delta    sigma   weight residual
    1.530  1.513  0.017 1.10e-02 8.26e+03 2.44e+00
  bond pdb=" CD  ARG A 303 "
       pdb=" NE  ARG A 303 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.40e-02 5.10e+03 2.40e+00
  bond pdb=" CA  LEU B 296 "
       pdb=" C   LEU B 296 "
    ideal  model  delta    sigma   weight residual
    1.530  1.513  0.017 1.10e-02 8.26e+03 2.39e+00
  bond pdb=" CD  ARG B 303 "
       pdb=" NE  ARG B 303 "
    ideal  model  delta    sigma   weight residual
    1.458  1.479 -0.021 1.40e-02 5.10e+03 2.33e+00
  bond pdb=" CA  TYR B 297 "
       pdb=" C   TYR B 297 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.016 1.10e-02 8.26e+03 2.08e+00
  ... (remaining 6559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 8853
        1.56 -     3.11: 197
        3.11 -     4.67: 40
        4.67 -     6.22: 16
        6.22 -     7.78: 4
  Bond angle restraints: 9110
  Sorted by residual:
  angle pdb=" N   GLU A 292 "
        pdb=" CA  GLU A 292 "
        pdb=" C   GLU A 292 "
      ideal   model   delta    sigma   weight residual
     110.68  102.90    7.78 1.39e+00 5.18e-01 3.13e+01
  angle pdb=" N   GLU B 292 "
        pdb=" CA  GLU B 292 "
        pdb=" C   GLU B 292 "
      ideal   model   delta    sigma   weight residual
     110.68  102.94    7.74 1.39e+00 5.18e-01 3.10e+01
  angle pdb=" N   ARG A 311 "
        pdb=" CA  ARG A 311 "
        pdb=" C   ARG A 311 "
      ideal   model   delta    sigma   weight residual
     111.28  117.33   -6.05 1.09e+00 8.42e-01 3.08e+01
  angle pdb=" N   ARG B 311 "
        pdb=" CA  ARG B 311 "
        pdb=" C   ARG B 311 "
      ideal   model   delta    sigma   weight residual
     111.28  117.31   -6.03 1.09e+00 8.42e-01 3.06e+01
  angle pdb=" N   GLY B  58 "
        pdb=" CA  GLY B  58 "
        pdb=" C   GLY B  58 "
      ideal   model   delta    sigma   weight residual
     112.73  107.77    4.96 1.20e+00 6.94e-01 1.71e+01
  ... (remaining 9105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.80: 3547
       34.80 -    69.60: 261
       69.60 -   104.40: 6
      104.40 -   139.20: 0
      139.20 -   174.00: 2
  Dihedral angle restraints: 3816
    sinusoidal: 1858
      harmonic: 1958
  Sorted by residual:
  dihedral pdb=" C   ALA B  55 "
           pdb=" N   ALA B  55 "
           pdb=" CA  ALA B  55 "
           pdb=" CB  ALA B  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.34  -11.26     0      2.50e+00 1.60e-01 2.03e+01
  dihedral pdb=" C   ALA A  55 "
           pdb=" N   ALA A  55 "
           pdb=" CA  ALA A  55 "
           pdb=" CB  ALA A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.36  -11.24     0      2.50e+00 1.60e-01 2.02e+01
  dihedral pdb=" CA  GLN B 129 "
           pdb=" C   GLN B 129 "
           pdb=" N   PRO B 130 "
           pdb=" CA  PRO B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.48   21.52     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 3813 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 913
       0.077 -    0.155: 83
       0.155 -    0.232: 4
       0.232 -    0.309: 0
       0.309 -    0.386: 2
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" CA  ALA B  55 "
            pdb=" N   ALA B  55 "
            pdb=" C   ALA B  55 "
            pdb=" CB  ALA B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.87   -0.39 2.00e-01 2.50e+01 3.73e+00
  chirality pdb=" CA  ALA A  55 "
            pdb=" N   ALA A  55 "
            pdb=" C   ALA A  55 "
            pdb=" CB  ALA A  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.87   -0.38 2.00e-01 2.50e+01 3.70e+00
  chirality pdb=" CA  GLU B 292 "
            pdb=" N   GLU B 292 "
            pdb=" C   GLU B 292 "
            pdb=" CB  GLU B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.12e-01
  ... (remaining 999 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  55 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.46e+00
        pdb=" C   ALA B  55 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ALA B  55 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER B  56 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  55 "   -0.011 2.00e-02 2.50e+03   2.33e-02 5.44e+00
        pdb=" C   ALA A  55 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ALA A  55 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER A  56 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 155 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.05e+00
        pdb=" C   ASP A 155 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ASP A 155 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   TRP A 156 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 441
        2.72 -     3.27: 6424
        3.27 -     3.81: 12394
        3.81 -     4.36: 16446
        4.36 -     4.90: 24478
  Nonbonded interactions: 60183
  Sorted by model distance:
  nonbonded pdb=" CG  GLU A 301 "
            pdb=" CG  GLU B 301 "
     model   vdw
     2.179 3.840
  nonbonded pdb=" CA  GLY B 266 "
            pdb=" OH  TYR B 297 "
     model   vdw
     2.241 3.440
  nonbonded pdb=" CA  GLY A 266 "
            pdb=" OH  TYR A 297 "
     model   vdw
     2.242 3.440
  nonbonded pdb=" O   HOH B 553 "
            pdb=" O   HOH B 666 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OD1 ASN B  92 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.287 3.040
  ... (remaining 60178 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 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.230
  Find NCS groups from input model:        0.040
  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:8.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
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      :  0.003   0.035   6564  Z= 0.167
  Angle     :  0.633   7.778   9110  Z= 0.381
  Chirality :  0.046   0.386   1002
  Planarity :  0.004   0.033   1032
  Dihedral  : 19.806 173.997   2552
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.32 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.34), residues: 672
  helix:  1.32 (0.34), residues: 280
  sheet: -0.62 (0.74), residues: 50
  loop :  0.09 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 127 
 TYR   0.014   0.001   TYR A  64 
 PHE   0.021   0.001   PHE A 171 
 TRP   0.022   0.002   TRP B 156 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6564)
  covalent geometry    : angle       0.63314 ( 9110)
  hydrogen bonds       : bond        0.17770 (  268)
  hydrogen bonds       : angle       5.94029 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.270 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.8018
  time to fit residues: 127.9378
Evaluate side-chains
  88 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A 129 GLN
A 307 HIS
B 112 ASN
B 227 GLN
B 307 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.107828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.083260 restraints weight = 12372.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.50
r_work: 0.2894 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6564  Z= 0.226
  Angle     :  0.657   7.070   9110  Z= 0.348
  Chirality :  0.043   0.130   1002
  Planarity :  0.005   0.043   1032
  Dihedral  : 22.426 170.602   1270
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.77 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.34), residues: 672
  helix:  1.84 (0.33), residues: 292
  sheet: -0.40 (0.73), residues: 50
  loop :  0.15 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 333 
 TYR   0.013   0.002   TYR A   5 
 PHE   0.013   0.001   PHE A  54 
 TRP   0.021   0.002   TRP A 156 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 6564)
  covalent geometry    : angle       0.65651 ( 9110)
  hydrogen bonds       : bond        0.06350 (  268)
  hydrogen bonds       : angle       4.22934 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.254 
Fit side-chains
REVERT: B  129 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8894 (tp40)
  outliers start: 11
  outliers final: 3
  residues processed: 95
  average time/residue: 0.7345
  time to fit residues: 72.6230
Evaluate side-chains
  83 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  220 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0470
   chunk 23 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.3482

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

Flipped N/Q/H residues before XYZ refinement:
** A  39 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 = 0.3526 r_free = 0.3526 target = 0.111868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.087056 restraints weight = 11935.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.54
r_work: 0.2955 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6564  Z= 0.132
  Angle     :  0.562   7.819   9110  Z= 0.293
  Chirality :  0.040   0.127   1002
  Planarity :  0.004   0.025   1032
  Dihedral  : 22.109 168.855   1270
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.60 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.34), residues: 672
  helix:  2.09 (0.32), residues: 292
  sheet: -0.35 (0.71), residues: 50
  loop :  0.35 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  84 
 TYR   0.013   0.001   TYR B 297 
 PHE   0.011   0.001   PHE B 171 
 TRP   0.025   0.001   TRP A 156 
 HIS   0.001   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6564)
  covalent geometry    : angle       0.56201 ( 9110)
  hydrogen bonds       : bond        0.05446 (  268)
  hydrogen bonds       : angle       3.88472 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  202 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7360 (mm-30)
REVERT: A  205 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8473 (mtt180)
REVERT: A  224 GLN cc_start: 0.9337 (mt0) cc_final: 0.9090 (mp10)
REVERT: B  260 MET cc_start: 0.9180 (mtp) cc_final: 0.8839 (mmt)
REVERT: B  314 TYR cc_start: 0.9004 (t80) cc_final: 0.8764 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 90
  average time/residue: 0.7426
  time to fit residues: 69.6485
Evaluate side-chains
  81 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 47 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    1.9544

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.111717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.087402 restraints weight = 12138.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.51
r_work: 0.2942 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.145
  Angle     :  0.563   7.977   9110  Z= 0.293
  Chirality :  0.040   0.126   1002
  Planarity :  0.004   0.039   1032
  Dihedral  : 22.253 168.964   1270
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.84 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.35), residues: 672
  helix:  2.26 (0.32), residues: 292
  sheet:  0.10 (0.74), residues: 48
  loop :  0.39 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 311 
 TYR   0.015   0.001   TYR B   5 
 PHE   0.007   0.001   PHE B  54 
 TRP   0.025   0.002   TRP A 156 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6564)
  covalent geometry    : angle       0.56294 ( 9110)
  hydrogen bonds       : bond        0.05408 (  268)
  hydrogen bonds       : angle       3.83768 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  202 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7838 (mm-30)
REVERT: A  205 ARG cc_start: 0.8890 (mtp180) cc_final: 0.8500 (mtt180)
REVERT: A  224 GLN cc_start: 0.9365 (mt0) cc_final: 0.9131 (mp10)
REVERT: A  321 ASP cc_start: 0.9261 (t0) cc_final: 0.8874 (t0)
REVERT: B   36 GLN cc_start: 0.8963 (tt0) cc_final: 0.8497 (tt0)
REVERT: B  314 TYR cc_start: 0.9081 (t80) cc_final: 0.8809 (t80)
  outliers start: 10
  outliers final: 3
  residues processed: 94
  average time/residue: 0.7547
  time to fit residues: 73.7967
Evaluate side-chains
  77 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0870
   chunk 64 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   overall best weight:    3.7964

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

Flipped N/Q/H residues before XYZ refinement:
B 252 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.110057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.085324 restraints weight = 12161.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.52
r_work: 0.2898 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6564  Z= 0.211
  Angle     :  0.586   5.722   9110  Z= 0.311
  Chirality :  0.042   0.129   1002
  Planarity :  0.004   0.038   1032
  Dihedral  : 22.469 169.959   1270
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.91 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.61 (0.35), residues: 672
  helix:  2.17 (0.32), residues: 294
  sheet: -0.07 (0.69), residues: 52
  loop :  0.33 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 311 
 TYR   0.020   0.002   TYR B   5 
 PHE   0.008   0.001   PHE B  54 
 TRP   0.025   0.002   TRP A 156 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 6564)
  covalent geometry    : angle       0.58580 ( 9110)
  hydrogen bonds       : bond        0.06015 (  268)
  hydrogen bonds       : angle       4.00266 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  321 ASP cc_start: 0.9311 (t0) cc_final: 0.8808 (t0)
REVERT: A  335 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8956 (pp20)
REVERT: B  129 GLN cc_start: 0.9051 (tp40) cc_final: 0.8793 (tp40)
REVERT: B  311 ARG cc_start: 0.9314 (ttt90) cc_final: 0.9091 (ttp80)
  outliers start: 9
  outliers final: 4
  residues processed: 88
  average time/residue: 0.6984
  time to fit residues: 64.0928
Evaluate side-chains
  77 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  335 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   overall best weight:    3.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.111296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.085787 restraints weight = 12250.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.57
r_work: 0.2977 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6564  Z= 0.190
  Angle     :  0.593   9.347   9110  Z= 0.308
  Chirality :  0.042   0.126   1002
  Planarity :  0.004   0.031   1032
  Dihedral  : 22.428 169.666   1270
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.38 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.64 (0.35), residues: 672
  helix:  2.23 (0.32), residues: 294
  sheet: -0.22 (0.65), residues: 52
  loop :  0.33 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  65 
 TYR   0.018   0.002   TYR B   5 
 PHE   0.008   0.001   PHE B  54 
 TRP   0.027   0.002   TRP A 156 
 HIS   0.002   0.001   HIS A 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6564)
  covalent geometry    : angle       0.59251 ( 9110)
  hydrogen bonds       : bond        0.05652 (  268)
  hydrogen bonds       : angle       3.94050 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8500 (tpp-160)
REVERT: A  224 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9031 (mp10)
REVERT: B  129 GLN cc_start: 0.9111 (tp40) cc_final: 0.8834 (tp40)
REVERT: B  314 TYR cc_start: 0.9052 (t80) cc_final: 0.8753 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 89
  average time/residue: 0.7783
  time to fit residues: 72.1438
Evaluate side-chains
  78 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  176 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 63 optimal weight:    0.6980
   chunk 2 optimal weight:   20.0000
   chunk 23 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    8.9990
   overall best weight:    1.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.113157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.088370 restraints weight = 12164.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.54
r_work: 0.2982 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.140
  Angle     :  0.553   7.271   9110  Z= 0.290
  Chirality :  0.040   0.127   1002
  Planarity :  0.004   0.032   1032
  Dihedral  : 22.367 171.385   1270
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 18.62 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.35), residues: 672
  helix:  2.32 (0.32), residues: 294
  sheet: -0.05 (0.68), residues: 48
  loop :  0.44 (0.38), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  65 
 TYR   0.013   0.001   TYR B   5 
 PHE   0.007   0.001   PHE B  54 
 TRP   0.028   0.002   TRP A 156 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6564)
  covalent geometry    : angle       0.55328 ( 9110)
  hydrogen bonds       : bond        0.05242 (  268)
  hydrogen bonds       : angle       3.80228 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8677 (mm-30)
REVERT: A  176 ARG cc_start: 0.8777 (tpp-160) cc_final: 0.8513 (tpp-160)
REVERT: A  224 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8971 (mp10)
REVERT: B  129 GLN cc_start: 0.9104 (tp40) cc_final: 0.8802 (tp40)
REVERT: B  176 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7773 (tpm170)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.7982
  time to fit residues: 66.2913
Evaluate side-chains
  73 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  176 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    0.1980
   chunk 38 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.114839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.089807 restraints weight = 12226.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.56
r_work: 0.3026 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6564  Z= 0.120
  Angle     :  0.559   9.008   9110  Z= 0.288
  Chirality :  0.040   0.127   1002
  Planarity :  0.003   0.034   1032
  Dihedral  : 22.229 169.498   1270
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 18.44 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.35), residues: 672
  helix:  2.49 (0.32), residues: 294
  sheet: -0.04 (0.67), residues: 48
  loop :  0.53 (0.38), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  65 
 TYR   0.011   0.001   TYR B 297 
 PHE   0.006   0.001   PHE B  54 
 TRP   0.029   0.002   TRP A 156 
 HIS   0.001   0.000   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6564)
  covalent geometry    : angle       0.55922 ( 9110)
  hydrogen bonds       : bond        0.04902 (  268)
  hydrogen bonds       : angle       3.68719 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   63 ASP cc_start: 0.8632 (t0) cc_final: 0.8088 (t0)
REVERT: A   64 TYR cc_start: 0.9417 (OUTLIER) cc_final: 0.8924 (t80)
REVERT: A  166 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8682 (mm-30)
REVERT: A  176 ARG cc_start: 0.8793 (tpp-160) cc_final: 0.8514 (tpp-160)
REVERT: A  201 ASP cc_start: 0.9000 (m-30) cc_final: 0.8783 (m-30)
REVERT: A  224 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8990 (mp10)
REVERT: A  321 ASP cc_start: 0.9213 (t0) cc_final: 0.8867 (t0)
REVERT: B  129 GLN cc_start: 0.9104 (tp40) cc_final: 0.8783 (tp40)
REVERT: B  335 GLU cc_start: 0.9422 (tt0) cc_final: 0.8958 (tp30)
  outliers start: 7
  outliers final: 6
  residues processed: 98
  average time/residue: 0.6581
  time to fit residues: 67.3914
Evaluate side-chains
  88 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    2.3188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.114036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.088759 restraints weight = 12203.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.56
r_work: 0.2976 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6564  Z= 0.157
  Angle     :  0.583   7.318   9110  Z= 0.305
  Chirality :  0.041   0.126   1002
  Planarity :  0.004   0.039   1032
  Dihedral  : 22.390 173.421   1270
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.62 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.35), residues: 672
  helix:  2.49 (0.32), residues: 292
  sheet:  0.13 (0.68), residues: 48
  loop :  0.55 (0.38), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  65 
 TYR   0.016   0.002   TYR B   5 
 PHE   0.006   0.001   PHE B  54 
 TRP   0.025   0.002   TRP A 156 
 HIS   0.002   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6564)
  covalent geometry    : angle       0.58290 ( 9110)
  hydrogen bonds       : bond        0.05338 (  268)
  hydrogen bonds       : angle       3.77535 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   63 ASP cc_start: 0.8716 (t0) cc_final: 0.8171 (t0)
REVERT: A  166 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8678 (mm-30)
REVERT: A  176 ARG cc_start: 0.8786 (tpp-160) cc_final: 0.8512 (tpp-160)
REVERT: A  201 ASP cc_start: 0.8944 (m-30) cc_final: 0.8721 (m-30)
REVERT: A  203 MET cc_start: 0.9392 (ppp) cc_final: 0.9130 (ppp)
REVERT: A  224 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8977 (mp10)
REVERT: A  321 ASP cc_start: 0.9258 (t0) cc_final: 0.8902 (t0)
REVERT: B  129 GLN cc_start: 0.9120 (tp40) cc_final: 0.8770 (tp40)
REVERT: B  176 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7747 (tpm170)
REVERT: B  335 GLU cc_start: 0.9430 (tt0) cc_final: 0.8944 (tp30)
  outliers start: 11
  outliers final: 4
  residues processed: 94
  average time/residue: 0.6643
  time to fit residues: 65.4131
Evaluate side-chains
  81 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  176 ARG
Chi-restraints excluded: chain B residue  220 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.116192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.090943 restraints weight = 12180.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.54
r_work: 0.3009 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.141
  Angle     :  0.574   7.316   9110  Z= 0.300
  Chirality :  0.040   0.126   1002
  Planarity :  0.004   0.041   1032
  Dihedral  : 22.295 170.811   1270
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 19.33 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.35), residues: 672
  helix:  2.48 (0.32), residues: 292
  sheet:  0.08 (0.69), residues: 48
  loop :  0.55 (0.38), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  65 
 TYR   0.012   0.001   TYR B   5 
 PHE   0.007   0.001   PHE B  54 
 TRP   0.029   0.002   TRP A 156 
 HIS   0.004   0.001   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6564)
  covalent geometry    : angle       0.57430 ( 9110)
  hydrogen bonds       : bond        0.05121 (  268)
  hydrogen bonds       : angle       3.72273 (  724)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  166 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8719 (mm-30)
REVERT: A  176 ARG cc_start: 0.8773 (tpp-160) cc_final: 0.8496 (tpp-160)
REVERT: A  203 MET cc_start: 0.9411 (ppp) cc_final: 0.9107 (ppp)
REVERT: A  224 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8977 (mp10)
REVERT: B  129 GLN cc_start: 0.9110 (tp40) cc_final: 0.8764 (tp40)
REVERT: B  335 GLU cc_start: 0.9447 (tt0) cc_final: 0.8976 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 84
  average time/residue: 0.6893
  time to fit residues: 60.5617
Evaluate side-chains
  80 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0980
   chunk 17 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 30 optimal weight:   20.0000
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 14 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 252 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.119271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.093959 restraints weight = 12230.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.58
r_work: 0.3073 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.4357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6564  Z= 0.122
  Angle     :  0.566   7.616   9110  Z= 0.296
  Chirality :  0.040   0.126   1002
  Planarity :  0.004   0.042   1032
  Dihedral  : 22.163 169.427   1270
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 19.33 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.35), residues: 672
  helix:  2.55 (0.32), residues: 292
  sheet:  0.07 (0.71), residues: 48
  loop :  0.56 (0.38), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  65 
 TYR   0.011   0.001   TYR B 297 
 PHE   0.005   0.001   PHE B 171 
 TRP   0.027   0.002   TRP A 156 
 HIS   0.001   0.000   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6564)
  covalent geometry    : angle       0.56593 ( 9110)
  hydrogen bonds       : bond        0.04741 (  268)
  hydrogen bonds       : angle       3.59633 (  724)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2561.70 seconds
wall clock time: 44 minutes 11.12 seconds (2651.12 seconds total)