Starting phenix.real_space_refine
on Tue Jan 14 07:53:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyi_42807/01_2025/8uyi_42807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyi_42807/01_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_42807/01_2025/8uyi_42807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyi_42807/01_2025/8uyi_42807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyi_42807/01_2025/8uyi_42807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyi_42807/01_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-5571/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: 4.41, per 1000 atoms: 0.74
  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: 1.69
  Conformation dependent library (CDL) restraints added in 871.8 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: 1.73

  Time building geometry restraints manager: 1.68 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:             1.020
  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:         0.060
  Set scattering table:                    0.070
  Process input model:                     17.630
  Find NCS groups from input model:        0.230
  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:2.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.650
-------------------------------------------------------------------------------
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  : 0.688 
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: 0.2097
  time to fit residues: 52.8136
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  : 0.772 
-------------------------------------------------------------------------------
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 = 36)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.168564 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  : 0.762 
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: 0.6589 (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: 0.1982
  time to fit residues: 38.6550
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  : 0.725 
-------------------------------------------------------------------------------
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:    4.9990
   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:    0.0570
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.9100

-------------------------------------------------------------------------------
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 = 0.4116 r_free = 0.4116 target = 0.190403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.167106 restraints weight = 6896.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.89
r_work: 0.3788 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6095  Z= 0.181
  Angle     :  0.558   6.284   8265  Z= 0.266
  Chirality :  0.040   0.130    932
  Planarity :  0.004   0.035   1029
  Dihedral  :  8.944 129.307    824
  Min Nonbonded Distance : 1.965

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:  1.14 (0.32), residues: 698
  helix:  1.84 (0.30), residues: 303
  sheet: -0.22 (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  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7980 (mt) cc_final: 0.7689 (mm)
REVERT: A  199 ASP cc_start: 0.8443 (m-30) cc_final: 0.8139 (m-30)
REVERT: A  236 PHE cc_start: 0.7331 (m-80) cc_final: 0.7064 (m-80)
REVERT: A  318 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8535 (tt)
REVERT: A  384 ARG cc_start: 0.8391 (mtm110) cc_final: 0.8152 (mtm110)
REVERT: A  452 PHE cc_start: 0.7627 (t80) cc_final: 0.7355 (t80)
REVERT: A  570 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7751 (tt0)
REVERT: B  129 TRP cc_start: 0.7522 (t60) cc_final: 0.7182 (t60)
REVERT: B  213 ARG cc_start: 0.8336 (mtt180) cc_final: 0.8116 (mtt-85)
REVERT: B  436 LYS cc_start: 0.7619 (tttt) cc_final: 0.6311 (mppt)
REVERT: B  573 ILE cc_start: 0.7407 (tp) cc_final: 0.7094 (pt)
  outliers start: 16
  outliers final: 10
  residues processed: 137
  average time/residue: 0.2096
  time to fit residues: 36.7066
Evaluate side-chains
  131 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  398 THR
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:    0.0970
   chunk 2 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 60 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.188050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.164203 restraints weight = 7092.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 1.95
r_work: 0.3755 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6095  Z= 0.251
  Angle     :  0.603  13.815   8265  Z= 0.284
  Chirality :  0.041   0.131    932
  Planarity :  0.004   0.037   1029
  Dihedral  :  8.329 122.991    824
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 13.54 %
    Favored  : 83.08 %
  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:  1.10 (0.33), residues: 698
  helix:  1.87 (0.30), residues: 303
  sheet: -0.37 (0.47), residues: 101
  loop :  0.03 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 505 
 HIS   0.004   0.001   HIS A 243 
 PHE   0.008   0.001   PHE A 552 
 TYR   0.016   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
  146 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8035 (mt) cc_final: 0.7715 (mm)
REVERT: A  199 ASP cc_start: 0.8394 (m-30) cc_final: 0.8160 (m-30)
REVERT: A  318 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8516 (tt)
REVERT: A  384 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8191 (mtm110)
REVERT: A  570 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7724 (tt0)
REVERT: B  129 TRP cc_start: 0.7589 (t60) cc_final: 0.7240 (t60)
REVERT: B  213 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8181 (mtt-85)
REVERT: B  249 MET cc_start: 0.8138 (ttm) cc_final: 0.7885 (ttm)
REVERT: B  436 LYS cc_start: 0.7676 (tttt) cc_final: 0.6240 (mppt)
REVERT: B  558 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8264 (mp)
REVERT: B  573 ILE cc_start: 0.7377 (tp) cc_final: 0.7107 (pt)
  outliers start: 22
  outliers final: 14
  residues processed: 139
  average time/residue: 0.2260
  time to fit residues: 39.9227
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  : 0.701 
-------------------------------------------------------------------------------
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  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 A residue  558 LEU
Chi-restraints excluded: chain B residue  195 MET
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:    0.4980
   chunk 41 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.188835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.165203 restraints weight = 6959.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 1.92
r_work: 0.3767 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6095  Z= 0.213
  Angle     :  0.588  14.934   8265  Z= 0.278
  Chirality :  0.041   0.157    932
  Planarity :  0.004   0.036   1029
  Dihedral  :  8.016 119.997    824
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.15 %
    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:  1.23 (0.33), residues: 698
  helix:  2.00 (0.30), residues: 303
  sheet:  0.16 (0.51), residues: 91
  loop : -0.12 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.005   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
  142 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8035 (mt) cc_final: 0.7721 (mm)
REVERT: A  199 ASP cc_start: 0.8361 (m-30) cc_final: 0.8146 (m-30)
REVERT: A  318 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8572 (tt)
REVERT: A  384 ARG cc_start: 0.8446 (mtm110) cc_final: 0.8183 (mtm110)
REVERT: B  129 TRP cc_start: 0.7593 (t60) cc_final: 0.7255 (t60)
REVERT: B  213 ARG cc_start: 0.8414 (mtt180) cc_final: 0.8167 (mtt-85)
REVERT: B  379 ASP cc_start: 0.7403 (p0) cc_final: 0.6737 (t0)
REVERT: B  436 LYS cc_start: 0.7690 (tttt) cc_final: 0.6232 (mppt)
REVERT: B  558 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8333 (mp)
  outliers start: 22
  outliers final: 18
  residues processed: 133
  average time/residue: 0.1986
  time to fit residues: 34.0114
Evaluate side-chains
  135 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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  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  195 MET
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:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0870
   chunk 6 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7962

-------------------------------------------------------------------------------
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 = 0.190288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.166599 restraints weight = 6875.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.92
r_work: 0.3778 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3633 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6095  Z= 0.173
  Angle     :  0.569  15.398   8265  Z= 0.266
  Chirality :  0.040   0.148    932
  Planarity :  0.004   0.035   1029
  Dihedral  :  7.778 117.044    824
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  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:  1.26 (0.33), residues: 698
  helix:  2.11 (0.31), residues: 303
  sheet: -0.43 (0.47), residues: 109
  loop :  0.05 (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   0.009   0.001   PHE A 253 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.004   0.000   ARG B 292 

*********************** 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
  143 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8060 (mt) cc_final: 0.7742 (mm)
REVERT: A  199 ASP cc_start: 0.8339 (m-30) cc_final: 0.8097 (m-30)
REVERT: A  318 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8564 (tt)
REVERT: B  129 TRP cc_start: 0.7582 (t60) cc_final: 0.7248 (t60)
REVERT: B  436 LYS cc_start: 0.7669 (tttt) cc_final: 0.6220 (mppt)
  outliers start: 20
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1922
  time to fit residues: 33.7605
Evaluate side-chains
  134 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0030
   chunk 68 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 52 optimal weight:    0.2980
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.192199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.168350 restraints weight = 6917.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 1.94
r_work: 0.3799 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3655 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
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      :  0.002   0.040   6095  Z= 0.148
  Angle     :  0.568  16.155   8265  Z= 0.263
  Chirality :  0.040   0.143    932
  Planarity :  0.004   0.034   1029
  Dihedral  :  7.499 114.077    824
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.54 %
    Favored  : 81.69 %
  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:  2.24 (0.31), residues: 303
  sheet: -0.32 (0.47), residues: 109
  loop :  0.14 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 567 
 HIS   0.002   0.000   HIS A 243 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.015   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
  138 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7988 (mt) cc_final: 0.7702 (mm)
REVERT: A  199 ASP cc_start: 0.8300 (m-30) cc_final: 0.8080 (m-30)
REVERT: A  318 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8548 (tt)
REVERT: A  384 ARG cc_start: 0.8355 (mtm110) cc_final: 0.8118 (mtm110)
REVERT: B  129 TRP cc_start: 0.7571 (t60) cc_final: 0.7286 (t60)
REVERT: B  376 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5540 (tt0)
REVERT: B  436 LYS cc_start: 0.7608 (tttt) cc_final: 0.6159 (mppt)
  outliers start: 18
  outliers final: 12
  residues processed: 131
  average time/residue: 0.2013
  time to fit residues: 33.7677
Evaluate side-chains
  130 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
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  318 LEU
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  376 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    0.0470
   chunk 60 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   overall best weight:    0.7480

-------------------------------------------------------------------------------
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 = 0.191584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.167731 restraints weight = 6854.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.92
r_work: 0.3793 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6095  Z= 0.168
  Angle     :  0.578  15.883   8265  Z= 0.270
  Chirality :  0.040   0.143    932
  Planarity :  0.004   0.038   1029
  Dihedral  :  7.423 112.304    824
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.85 %
    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 (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:  1.45 (0.33), residues: 698
  helix:  2.28 (0.30), residues: 303
  sheet:  0.04 (0.50), residues: 99
  loop : -0.04 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.002   0.000   HIS A 243 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.016   0.001   TYR A 221 
 ARG   0.010   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
  137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7982 (mt) cc_final: 0.7696 (mm)
REVERT: A  199 ASP cc_start: 0.8261 (m-30) cc_final: 0.8031 (m-30)
REVERT: A  318 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8552 (tt)
REVERT: B  129 TRP cc_start: 0.7563 (t60) cc_final: 0.7276 (t60)
REVERT: B  423 ASP cc_start: 0.8021 (t0) cc_final: 0.7074 (m-30)
REVERT: B  436 LYS cc_start: 0.7615 (tttt) cc_final: 0.6135 (mppt)
  outliers start: 18
  outliers final: 14
  residues processed: 131
  average time/residue: 0.2053
  time to fit residues: 34.3917
Evaluate side-chains
  131 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0980
   chunk 55 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.192000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.168532 restraints weight = 6926.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.89
r_work: 0.3797 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6095  Z= 0.166
  Angle     :  0.589  16.199   8265  Z= 0.277
  Chirality :  0.040   0.144    932
  Planarity :  0.004   0.039   1029
  Dihedral  :  7.379 109.959    824
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.08 %
    Favored  : 82.00 %
  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:  1.49 (0.33), residues: 698
  helix:  2.28 (0.30), residues: 303
  sheet:  0.07 (0.50), residues: 99
  loop :  0.01 (0.39), residues: 296

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   0.010   0.001   PHE A 253 
 TYR   0.015   0.001   TYR A 482 
 ARG   0.010   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
  137 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7047 (mp0)
REVERT: A  161 LEU cc_start: 0.7977 (mt) cc_final: 0.7705 (mm)
REVERT: A  199 ASP cc_start: 0.8286 (m-30) cc_final: 0.8072 (m-30)
REVERT: A  318 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8574 (tt)
REVERT: B  129 TRP cc_start: 0.7578 (t60) cc_final: 0.7326 (t60)
REVERT: B  379 ASP cc_start: 0.7510 (p0) cc_final: 0.6244 (t70)
REVERT: B  423 ASP cc_start: 0.8014 (t0) cc_final: 0.7073 (m-30)
REVERT: B  436 LYS cc_start: 0.7652 (tttt) cc_final: 0.6212 (mppt)
  outliers start: 19
  outliers final: 16
  residues processed: 129
  average time/residue: 0.1981
  time to fit residues: 33.0914
Evaluate side-chains
  133 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  155 ASN
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:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0050
   chunk 30 optimal weight:    0.0470
   chunk 59 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 60 optimal weight:    0.4980
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.3292

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.193158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.169944 restraints weight = 6949.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 1.90
r_work: 0.3821 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6095  Z= 0.146
  Angle     :  0.582  16.429   8265  Z= 0.273
  Chirality :  0.040   0.142    932
  Planarity :  0.004   0.041   1029
  Dihedral  :  7.292 108.438    824
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.00 %
    Favored  : 81.69 %
  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:  1.57 (0.33), residues: 698
  helix:  2.35 (0.30), residues: 303
  sheet:  0.04 (0.49), residues: 99
  loop :  0.09 (0.39), residues: 296

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   0.010   0.001   PHE A 253 
 TYR   0.014   0.001   TYR A 482 
 ARG   0.010   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
  132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.8013 (mt) cc_final: 0.7751 (mm)
REVERT: A  199 ASP cc_start: 0.8268 (m-30) cc_final: 0.8042 (m-30)
REVERT: A  318 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8574 (tt)
REVERT: B  129 TRP cc_start: 0.7575 (t60) cc_final: 0.7357 (t60)
REVERT: B  393 ASN cc_start: 0.8544 (m110) cc_final: 0.8130 (m110)
REVERT: B  423 ASP cc_start: 0.7999 (t0) cc_final: 0.7081 (m-30)
REVERT: B  436 LYS cc_start: 0.7627 (tttt) cc_final: 0.6213 (mppt)
REVERT: B  440 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7527 (mt-10)
  outliers start: 15
  outliers final: 13
  residues processed: 126
  average time/residue: 0.1971
  time to fit residues: 32.1915
Evaluate side-chains
  130 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  318 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  456 ASN
Chi-restraints excluded: chain A residue  500 ASN
Chi-restraints excluded: chain A residue  558 LEU
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  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:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.191812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.168345 restraints weight = 6964.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 1.91
r_work: 0.3796 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3651 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3497

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= 0.186
  Angle     :  0.604  16.556   8265  Z= 0.285
  Chirality :  0.041   0.155    932
  Planarity :  0.004   0.036   1029
  Dihedral  :  7.294 107.267    824
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.85 %
    Favored  : 81.69 %
  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:  1.55 (0.33), residues: 698
  helix:  2.31 (0.30), residues: 303
  sheet:  0.09 (0.49), residues: 99
  loop :  0.07 (0.39), residues: 296

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   0.012   0.001   PHE A 287 
 TYR   0.014   0.001   TYR A 482 
 ARG   0.009   0.000   ARG B 213 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3259.13 seconds
wall clock time: 59 minutes 15.68 seconds (3555.68 seconds total)