Starting phenix.real_space_refine
on Tue Mar 11 15:13:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyi_42807/03_2025/8uyi_42807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyi_42807/03_2025/8uyi_42807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uyi_42807/03_2025/8uyi_42807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyi_42807/03_2025/8uyi_42807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyi_42807/03_2025/8uyi_42807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyi_42807/03_2025/8uyi_42807.cif"
  }
  resolution = 3.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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
     P       8      5.49       5
     Mg      4      5.21       5
     S      40      5.16       5
     C    3804      2.51       5
     N    1003      2.21       5
     O    1121      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5980
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2966
          Classifications: {'peptide': 369}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 351}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 2956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2956
          Classifications: {'peptide': 369}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 17, 'TRANS': 351}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.14, per 1000 atoms: 0.69
  Number of scatterers: 5980
  At special positions: 0
  Unit cell: (116.352, 74.336, 72.72, 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)
     S      40     16.00
     P       8     15.00
     Mg      4     11.99
     O    1121      8.00
     N    1003      7.00
     C    3804      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 779.5 milliseconds
  

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      45.0% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 136
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 155 through 159
    Processing helix  chain 'A' and resid 203 through 215
      removed outlier: 3.602A  pdb=" N   THR A 215 " --> pdb=" O   MET A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 307 through 328
      removed outlier: 3.769A  pdb=" N   HIS A 328 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 406 through 420
      removed outlier: 4.042A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
      removed outlier: 3.578A  pdb=" N   SER A 459 " --> pdb=" O   ARG A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 484
    Processing helix  chain 'A' and resid 486 through 490
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 542 through 554
    Processing helix  chain 'A' and resid 557 through 572
      removed outlier: 3.501A  pdb=" N   HIS A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 138
      removed outlier: 3.541A  pdb=" N   CYS B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 157
      No H-bonds generated for 'chain 'B' and resid 155 through 157'
    Processing helix  chain 'B' and resid 203 through 215
      removed outlier: 3.546A  pdb=" N   THR B 215 " --> pdb=" O   MET B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.564A  pdb=" N   ARG B 302 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.868A  pdb=" N   HIS B 328 " --> pdb=" O   HIS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
      removed outlier: 4.539A  pdb=" N   CYS B 360 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 406 through 420
      removed outlier: 3.743A  pdb=" N   TRP B 410 " --> pdb=" O   LYS B 406 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 411 " --> pdb=" O   SER B 407 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 462
      removed outlier: 3.556A  pdb=" N   SER B 459 " --> pdb=" O   ARG B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 485
    Processing helix  chain 'B' and resid 498 through 515
      removed outlier: 3.624A  pdb=" N   LYS B 512 " --> pdb=" O   CYS B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 555
      removed outlier: 3.897A  pdb=" N   ARG B 555 " --> pdb=" O   SER B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 574
    Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 167
      removed outlier: 6.739A  pdb=" N   VAL A 173 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LYS A 167 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ALA A 171 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER A 251 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   LYS A 291 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   MET A 249 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296
    Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 167
      removed outlier: 5.522A  pdb=" N   LEU B 161 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LYS B 177 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLU B 163 " --> pdb=" O   SER B 175 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   LYS B 167 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ALA B 171 " --> pdb=" O   LYS B 167 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER B 251 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   LYS B 291 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   MET B 249 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   TYR B 250 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.521A  pdb=" N   CYS B 295 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 372

    266 hydrogen bonds defined for protein.
    765 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: 1.62

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1895
        1.34 -     1.46: 1213
        1.46 -     1.58: 2905
        1.58 -     1.69: 20
        1.69 -     1.81: 62
  Bond restraints: 6095
  Sorted by residual:
  bond pdb=" OG1 TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.611  0.106 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" OG1 TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.611  0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" O2P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" O3P TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" O3P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  ... (remaining 6090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 8170
        2.40 -     4.79: 69
        4.79 -     7.19: 20
        7.19 -     9.59: 2
        9.59 -    11.99: 4
  Bond angle restraints: 8265
  Sorted by residual:
  angle pdb=" CB  TPO A 305 "
        pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.32   11.99 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" C   THR B 215 "
        pdb=" N   VAL B 216 "
        pdb=" CA  VAL B 216 "
      ideal   model   delta    sigma   weight residual
     120.33  123.43   -3.10 8.00e-01 1.56e+00 1.50e+01
  angle pdb=" CB  TPO B 305 "
        pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
      ideal   model   delta    sigma   weight residual
     119.31  108.58   10.73 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
        pdb=" O1P TPO B 305 "
      ideal   model   delta    sigma   weight residual
     100.43  111.06  -10.63 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
        pdb=" O1P TPO A 305 "
      ideal   model   delta    sigma   weight residual
     100.43  110.11   -9.68 3.00e+00 1.11e-01 1.04e+01
  ... (remaining 8260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.23: 3638
       33.23 -    66.46: 60
       66.46 -    99.69: 2
       99.69 -   132.91: 0
      132.91 -   166.14: 2
  Dihedral angle restraints: 3702
    sinusoidal: 1516
      harmonic: 2186
  Sorted by residual:
  dihedral pdb=" C5' ADP A 601 "
           pdb=" O5' ADP A 601 "
           pdb=" PA  ADP A 601 "
           pdb=" O2A ADP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  133.86  166.14     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" O1B ADP A 601 "
           pdb=" O3A ADP A 601 "
           pdb=" PB  ADP A 601 "
           pdb=" PA  ADP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   89.85 -149.86     1      2.00e+01 2.50e-03 4.48e+01
  dihedral pdb=" O2A ADP B 601 "
           pdb=" O3A ADP B 601 "
           pdb=" PA  ADP B 601 "
           pdb=" PB  ADP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   24.11  -84.11     1      2.00e+01 2.50e-03 2.15e+01
  ... (remaining 3699 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 597
       0.031 -    0.062: 220
       0.062 -    0.093: 69
       0.093 -    0.124: 38
       0.124 -    0.155: 8
  Chirality restraints: 932
  Sorted by residual:
  chirality pdb=" CA  ILE A 450 "
            pdb=" N   ILE A 450 "
            pdb=" C   ILE A 450 "
            pdb=" CB  ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CA  ILE A 246 "
            pdb=" N   ILE A 246 "
            pdb=" C   ILE A 246 "
            pdb=" CB  ILE A 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  ILE B 246 "
            pdb=" N   ILE B 246 "
            pdb=" C   ILE B 246 "
            pdb=" CB  ILE B 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  ... (remaining 929 not shown)

  Planarity restraints: 1029
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 243 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.91e+00
        pdb=" N   PRO A 244 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 244 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 244 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 243 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO B 244 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 244 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 244 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 450 "   -0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO B 451 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1026 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 67
        2.63 -     3.19: 4804
        3.19 -     3.76: 8944
        3.76 -     4.33: 12969
        4.33 -     4.90: 21241
  Nonbonded interactions: 48025
  Sorted by model distance:
  nonbonded pdb=" O2A ADP B 601 "
            pdb="MG    MG B 603 "
     model   vdw
     2.057 2.170
  nonbonded pdb=" OD1 ASP B 357 "
            pdb="MG    MG B 602 "
     model   vdw
     2.073 2.170
  nonbonded pdb=" OD1 ASN A 339 "
            pdb="MG    MG A 603 "
     model   vdw
     2.105 2.170
  nonbonded pdb=" OD1 ASN B 339 "
            pdb="MG    MG B 603 "
     model   vdw
     2.205 2.170
  nonbonded pdb=" OD2 ASP A 357 "
            pdb="MG    MG A 603 "
     model   vdw
     2.240 2.170
  ... (remaining 48020 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 122 through 223 or resid 237 through 572 or resid 601 thro \ 
ugh 603))
  selection = (chain 'B' and (resid 122 through 136 or resid 148 through 572 or resid 601 thro \ 
ugh 603))
}

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:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.810
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
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      :  0.004   0.106   6095  Z= 0.237
  Angle     :  0.673  11.987   8265  Z= 0.341
  Chirality :  0.041   0.155    932
  Planarity :  0.005   0.043   1029
  Dihedral  : 12.678 166.142   2272
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  4.92 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.29), residues: 698
  helix: -0.70 (0.24), residues: 299
  sheet: -0.09 (0.56), residues: 92
  loop : -0.35 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 489 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.007   0.001   TYR B 438 
 ARG   0.003   0.001   ARG B 469 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 193
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7676 (mt) cc_final: 0.7309 (mm)
REVERT: A  194 MET cc_start: 0.8047 (ttt) cc_final: 0.7398 (tmm)
REVERT: A  197 ASN cc_start: 0.8029 (t0) cc_final: 0.7664 (t0)
REVERT: A  219 MET cc_start: 0.8061 (mtt) cc_final: 0.7833 (mtt)
REVERT: A  236 PHE cc_start: 0.5701 (m-80) cc_final: 0.5054 (m-80)
REVERT: A  318 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7616 (tt)
REVERT: A  334 ASP cc_start: 0.7492 (t70) cc_final: 0.7116 (t0)
REVERT: A  433 LEU cc_start: 0.8041 (mt) cc_final: 0.7794 (mp)
REVERT: A  436 LYS cc_start: 0.7240 (tttt) cc_final: 0.6742 (ttpt)
REVERT: A  452 PHE cc_start: 0.7155 (t80) cc_final: 0.6787 (t80)
REVERT: A  456 ASN cc_start: 0.8273 (m-40) cc_final: 0.7861 (m-40)
REVERT: A  558 LEU cc_start: 0.7429 (tp) cc_final: 0.7100 (tp)
REVERT: B  129 TRP cc_start: 0.7335 (t60) cc_final: 0.6833 (t60)
REVERT: B  298 LYS cc_start: 0.7700 (tttt) cc_final: 0.7418 (ttpt)
REVERT: B  377 ASP cc_start: 0.5506 (t70) cc_final: 0.5239 (t0)
REVERT: B  393 ASN cc_start: 0.7864 (m-40) cc_final: 0.7141 (m110)
REVERT: B  401 TRP cc_start: 0.7061 (m100) cc_final: 0.6809 (m-90)
REVERT: B  403 ASN cc_start: 0.8165 (t0) cc_final: 0.7454 (p0)
REVERT: B  418 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7227 (tt0)
REVERT: B  436 LYS cc_start: 0.6073 (tttt) cc_final: 0.4809 (mptt)
REVERT: B  439 LYS cc_start: 0.7546 (mttt) cc_final: 0.7313 (mtpt)
REVERT: B  442 ASP cc_start: 0.8205 (m-30) cc_final: 0.7741 (m-30)
REVERT: B  471 ASP cc_start: 0.7209 (m-30) cc_final: 0.6912 (m-30)
REVERT: B  501 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7540 (mt-10)
REVERT: B  541 ARG cc_start: 0.5720 (mtt-85) cc_final: 0.5463 (mtm-85)
REVERT: B  566 LYS cc_start: 0.8027 (tttt) cc_final: 0.7765 (ttpp)
  outliers start: 7
  outliers final: 2
  residues processed: 199
  average time/residue: 0.2033
  time to fit residues: 51.3361
Evaluate side-chains
  145 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 142
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain B residue  500 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 GLN
B 328 HIS
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.191890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.168563 restraints weight = 6835.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 1.99
r_work: 0.3801 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6095  Z= 0.207
  Angle     :  0.584   6.293   8265  Z= 0.282
  Chirality :  0.041   0.129    932
  Planarity :  0.004   0.036   1029
  Dihedral  :  9.790 144.274    827
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.00 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.31), residues: 698
  helix:  1.21 (0.29), residues: 302
  sheet: -0.25 (0.49), residues: 101
  loop :  0.02 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.013   0.002   HIS A 559 
 PHE   0.008   0.001   PHE A 452 
 TYR   0.015   0.001   TYR A 482 
 ARG   0.002   0.000   ARG A 302 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7987 (mt) cc_final: 0.7685 (mm)
REVERT: A  204 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8450 (m)
REVERT: A  318 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8458 (tt)
REVERT: A  418 GLU cc_start: 0.6403 (mt-10) cc_final: 0.5922 (mt-10)
REVERT: A  572 HIS cc_start: 0.6588 (m-70) cc_final: 0.6287 (m170)
REVERT: B  129 TRP cc_start: 0.7497 (t60) cc_final: 0.7125 (t60)
REVERT: B  213 ARG cc_start: 0.8355 (mtt180) cc_final: 0.8105 (mtt-85)
REVERT: B  423 ASP cc_start: 0.7959 (m-30) cc_final: 0.7696 (t70)
REVERT: B  436 LYS cc_start: 0.7519 (tttt) cc_final: 0.6184 (mppt)
  outliers start: 14
  outliers final: 8
  residues processed: 151
  average time/residue: 0.1949
  time to fit residues: 38.2544
Evaluate side-chains
  131 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 559 HIS
B 569 GLN
B 572 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.190287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.166982 restraints weight = 6899.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.89
r_work: 0.3792 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6095  Z= 0.180
  Angle     :  0.555   6.239   8265  Z= 0.265
  Chirality :  0.040   0.130    932
  Planarity :  0.004   0.035   1029
  Dihedral  :  8.988 129.865    824
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.08 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.32), residues: 698
  helix:  1.82 (0.30), residues: 303
  sheet: -0.23 (0.48), residues: 101
  loop :  0.07 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.011   0.001   HIS A 559 
 PHE   0.011   0.001   PHE B 399 
 TYR   0.015   0.001   TYR A 350 
 ARG   0.002   0.000   ARG A 384 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7981 (mt) cc_final: 0.7691 (mm)
REVERT: A  199 ASP cc_start: 0.8441 (m-30) cc_final: 0.8139 (m-30)
REVERT: A  236 PHE cc_start: 0.7336 (m-80) cc_final: 0.7068 (m-80)
REVERT: A  318 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8538 (tt)
REVERT: A  384 ARG cc_start: 0.8392 (mtm110) cc_final: 0.8151 (mtm110)
REVERT: A  570 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7746 (tt0)
REVERT: B  129 TRP cc_start: 0.7534 (t60) cc_final: 0.7185 (t60)
REVERT: B  213 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8116 (mtt-85)
REVERT: B  436 LYS cc_start: 0.7615 (tttt) cc_final: 0.6310 (mppt)
REVERT: B  573 ILE cc_start: 0.7331 (tp) cc_final: 0.7026 (pt)
  outliers start: 16
  outliers final: 9
  residues processed: 138
  average time/residue: 0.1937
  time to fit residues: 34.2348
Evaluate side-chains
  130 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0980
   chunk 2 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 326 ASN
A 421 ASN
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.189091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.165496 restraints weight = 7069.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 1.94
r_work: 0.3770 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6095  Z= 0.212
  Angle     :  0.585  13.267   8265  Z= 0.275
  Chirality :  0.041   0.130    932
  Planarity :  0.004   0.036   1029
  Dihedral  :  8.236 121.130    824
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 13.85 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.33), residues: 698
  helix:  1.94 (0.30), residues: 303
  sheet: -0.35 (0.47), residues: 101
  loop :  0.06 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.004   0.001   HIS A 243 
 PHE   0.008   0.001   PHE A 253 
 TYR   0.017   0.001   TYR A 482 
 ARG   0.006   0.000   ARG B 292 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8024 (mt) cc_final: 0.7712 (mm)
REVERT: A  199 ASP cc_start: 0.8384 (m-30) cc_final: 0.8160 (m-30)
REVERT: A  318 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8531 (tt)
REVERT: A  384 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8162 (mtm110)
REVERT: A  452 PHE cc_start: 0.7609 (t80) cc_final: 0.7388 (t80)
REVERT: A  570 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7752 (tt0)
REVERT: B  129 TRP cc_start: 0.7576 (t60) cc_final: 0.7232 (t60)
REVERT: B  213 ARG cc_start: 0.8395 (mtt180) cc_final: 0.8172 (mtt-85)
REVERT: B  249 MET cc_start: 0.8030 (ttm) cc_final: 0.7823 (ttm)
REVERT: B  436 LYS cc_start: 0.7656 (tttt) cc_final: 0.6253 (mppt)
REVERT: B  558 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8272 (mp)
REVERT: B  573 ILE cc_start: 0.7408 (tp) cc_final: 0.7125 (pt)
  outliers start: 19
  outliers final: 11
  residues processed: 139
  average time/residue: 0.2089
  time to fit residues: 36.8064
Evaluate side-chains
  127 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 44 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 58 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.191156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.167654 restraints weight = 6935.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.91
r_work: 0.3797 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3653 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6095  Z= 0.166
  Angle     :  0.571  15.134   8265  Z= 0.267
  Chirality :  0.040   0.149    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.884 116.763    824
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 13.85 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.33), residues: 698
  helix:  2.10 (0.30), residues: 303
  sheet: -0.44 (0.46), residues: 109
  loop :  0.05 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 567 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.015   0.001   TYR A 482 
 ARG   0.004   0.000   ARG B 292 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8024 (mt) cc_final: 0.7706 (mm)
REVERT: A  199 ASP cc_start: 0.8317 (m-30) cc_final: 0.8082 (m-30)
REVERT: A  290 MET cc_start: 0.8954 (mtm) cc_final: 0.8663 (mtm)
REVERT: A  318 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8547 (tt)
REVERT: A  384 ARG cc_start: 0.8373 (mtm110) cc_final: 0.8125 (mtm110)
REVERT: B  129 TRP cc_start: 0.7548 (t60) cc_final: 0.7217 (t60)
REVERT: B  436 LYS cc_start: 0.7648 (tttt) cc_final: 0.6225 (mppt)
REVERT: B  558 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8307 (mp)
  outliers start: 19
  outliers final: 14
  residues processed: 135
  average time/residue: 0.1928
  time to fit residues: 33.5740
Evaluate side-chains
  131 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 68 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.190479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.166775 restraints weight = 6880.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.90
r_work: 0.3781 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6095  Z= 0.194
  Angle     :  0.578  15.651   8265  Z= 0.271
  Chirality :  0.040   0.139    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.754 115.556    824
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 14.31 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.33), residues: 698
  helix:  2.13 (0.30), residues: 303
  sheet: -0.40 (0.47), residues: 109
  loop :  0.08 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.006   0.000   ARG B 213 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8042 (mt) cc_final: 0.7749 (mm)
REVERT: A  199 ASP cc_start: 0.8336 (m-30) cc_final: 0.8088 (m-30)
REVERT: A  318 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8572 (tt)
REVERT: A  384 ARG cc_start: 0.8374 (mtm110) cc_final: 0.8120 (mtm110)
REVERT: B  129 TRP cc_start: 0.7567 (t60) cc_final: 0.7244 (t60)
REVERT: B  436 LYS cc_start: 0.7669 (tttt) cc_final: 0.6213 (mppt)
REVERT: B  558 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8293 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2057
  time to fit residues: 35.5975
Evaluate side-chains
  137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.189976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.166051 restraints weight = 6923.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.93
r_work: 0.3775 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3632 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6095  Z= 0.201
  Angle     :  0.586  15.706   8265  Z= 0.274
  Chirality :  0.041   0.142    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.648 115.134    824
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.77 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.33), residues: 698
  helix:  2.13 (0.30), residues: 303
  sheet: -0.42 (0.47), residues: 109
  loop :  0.11 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.008   0.001   PHE A 253 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.006   0.000   ARG B 213 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8021 (mt) cc_final: 0.7736 (mm)
REVERT: A  199 ASP cc_start: 0.8333 (m-30) cc_final: 0.8108 (m-30)
REVERT: A  318 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8566 (tt)
REVERT: B  129 TRP cc_start: 0.7576 (t60) cc_final: 0.7258 (t60)
REVERT: B  436 LYS cc_start: 0.7675 (tttt) cc_final: 0.6227 (mppt)
  outliers start: 19
  outliers final: 16
  residues processed: 132
  average time/residue: 0.1891
  time to fit residues: 32.2958
Evaluate side-chains
  133 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    0.0970
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   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 189 GLN
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.191522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.167847 restraints weight = 6881.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 1.92
r_work: 0.3797 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6095  Z= 0.163
  Angle     :  0.571  16.197   8265  Z= 0.267
  Chirality :  0.040   0.138    932
  Planarity :  0.004   0.033   1029
  Dihedral  :  7.490 113.092    824
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.46 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.33), residues: 698
  helix:  2.25 (0.30), residues: 302
  sheet: -0.37 (0.47), residues: 109
  loop :  0.11 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 567 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.008   0.001   PHE A 253 
 TYR   0.015   0.001   TYR A 482 
 ARG   0.008   0.000   ARG B 213 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7992 (mt) cc_final: 0.7710 (mm)
REVERT: A  199 ASP cc_start: 0.8259 (m-30) cc_final: 0.8031 (m-30)
REVERT: A  318 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8553 (tt)
REVERT: A  450 ILE cc_start: 0.7998 (mt) cc_final: 0.7727 (tt)
REVERT: B  129 TRP cc_start: 0.7566 (t60) cc_final: 0.7268 (t60)
REVERT: B  393 ASN cc_start: 0.8556 (m110) cc_final: 0.8083 (m110)
REVERT: B  423 ASP cc_start: 0.8024 (t0) cc_final: 0.7127 (m-30)
REVERT: B  436 LYS cc_start: 0.7681 (tttt) cc_final: 0.6278 (mppt)
  outliers start: 20
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1905
  time to fit residues: 34.2180
Evaluate side-chains
  135 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0770
   chunk 23 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 456 ASN
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.191864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.168638 restraints weight = 6996.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.89
r_work: 0.3803 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3660 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6095  Z= 0.163
  Angle     :  0.583  15.971   8265  Z= 0.274
  Chirality :  0.040   0.139    932
  Planarity :  0.004   0.033   1029
  Dihedral  :  7.402 110.343    824
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.08 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.33), residues: 698
  helix:  2.28 (0.31), residues: 302
  sheet: -0.02 (0.49), residues: 99
  loop : -0.04 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 567 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.008   0.001   PHE A 253 
 TYR   0.015   0.001   TYR A 482 
 ARG   0.007   0.000   ARG B 213 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8003 (mt) cc_final: 0.7721 (mm)
REVERT: A  199 ASP cc_start: 0.8258 (m-30) cc_final: 0.8030 (m-30)
REVERT: A  318 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8566 (tt)
REVERT: B  129 TRP cc_start: 0.7573 (t60) cc_final: 0.7339 (t60)
REVERT: B  393 ASN cc_start: 0.8564 (m110) cc_final: 0.8127 (m110)
REVERT: B  423 ASP cc_start: 0.7997 (t0) cc_final: 0.7106 (m-30)
REVERT: B  436 LYS cc_start: 0.7663 (tttt) cc_final: 0.6251 (mppt)
  outliers start: 20
  outliers final: 17
  residues processed: 134
  average time/residue: 0.1981
  time to fit residues: 34.2285
Evaluate side-chains
  134 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  456 ASN
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Chi-restraints excluded: chain B residue  492 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 60 optimal weight:    0.8980
   chunk 62 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 456 ASN
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.192592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.169378 restraints weight = 6959.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 1.87
r_work: 0.3817 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6095  Z= 0.158
  Angle     :  0.590  16.412   8265  Z= 0.280
  Chirality :  0.040   0.139    932
  Planarity :  0.004   0.033   1029
  Dihedral  :  7.358 109.024    824
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.92 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.33), residues: 698
  helix:  2.33 (0.30), residues: 302
  sheet:  0.09 (0.49), residues: 99
  loop : -0.02 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 567 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.011   0.001   PHE A 452 
 TYR   0.021   0.001   TYR A 221 
 ARG   0.007   0.000   ARG B 213 

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8051 (mt) cc_final: 0.7782 (mm)
REVERT: A  199 ASP cc_start: 0.8247 (m-30) cc_final: 0.8014 (m-30)
REVERT: A  318 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8521 (tt)
REVERT: B  129 TRP cc_start: 0.7562 (t60) cc_final: 0.7318 (t60)
REVERT: B  393 ASN cc_start: 0.8556 (m110) cc_final: 0.8116 (m110)
REVERT: B  423 ASP cc_start: 0.8019 (t0) cc_final: 0.7093 (m-30)
REVERT: B  436 LYS cc_start: 0.7581 (tttt) cc_final: 0.6144 (mppt)
  outliers start: 18
  outliers final: 15
  residues processed: 129
  average time/residue: 0.2171
  time to fit residues: 36.0037
Evaluate side-chains
  132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  456 ASN
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  467 ASN
Chi-restraints excluded: chain B residue  473 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.187399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.163263 restraints weight = 7054.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 1.96
r_work: 0.3744 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6095  Z= 0.308
  Angle     :  0.661  16.276   8265  Z= 0.318
  Chirality :  0.043   0.144    932
  Planarity :  0.004   0.036   1029
  Dihedral  :  7.556 107.865    824
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.77 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.33), residues: 698
  helix:  2.03 (0.30), residues: 302
  sheet: -0.07 (0.50), residues: 99
  loop : -0.13 (0.38), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.005   0.001   HIS A 243 
 PHE   0.012   0.002   PHE A 552 
 TYR   0.020   0.002   TYR A 221 
 ARG   0.007   0.001   ARG B 213 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3593.92 seconds
wall clock time: 62 minutes 8.31 seconds (3728.31 seconds total)