Starting phenix.real_space_refine
on Sun May 11 11:52:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y5x_38955/05_2025/8y5x_38955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y5x_38955/05_2025/8y5x_38955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y5x_38955/05_2025/8y5x_38955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y5x_38955/05_2025/8y5x_38955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y5x_38955/05_2025/8y5x_38955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y5x_38955/05_2025/8y5x_38955.cif"
  }
  resolution = 3.25
  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=   0.044
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: 5
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     Na      2      4.78       5
     C    5394      2.51       5
     N    1222      2.21       5
     O    1358      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8032
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4010
          Classifications: {'peptide': 512}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 481}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 4010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4010
          Classifications: {'peptide': 512}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 481}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' NA': 1, 'SO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' NA': 1, 'SO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.53, per 1000 atoms: 0.69
  Number of scatterers: 8032
  At special positions: 0
  Unit cell: (116.399, 92.9514, 80.3904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     Na      2     11.00
     O    1358      8.00
     N    1222      7.00
     C    5394      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: 2.20
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 0 sheets defined
      81.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 10 through 23
      removed outlier: 3.597A  pdb=" N   LEU A  23 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 29
    Processing helix  chain 'A' and resid 32 through 51
      removed outlier: 3.547A  pdb=" N   GLU A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 70
      Proline residue:  A  62  - end of helix
      Proline residue:  A  67  - end of helix
    Processing helix  chain 'A' and resid 73 through 81
    Processing helix  chain 'A' and resid 83 through 102
      removed outlier: 3.668A  pdb=" N   LEU A  87 " --> pdb=" O   LYS A  83 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TRP A 102 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 117
      removed outlier: 3.511A  pdb=" N   ARG A 107 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 136
    Processing helix  chain 'A' and resid 139 through 161
      Proline residue:  A 149  - end of helix
    Processing helix  chain 'A' and resid 231 through 254
      removed outlier: 3.850A  pdb=" N   THR A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR A 254 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 258
    Processing helix  chain 'A' and resid 259 through 273
    Processing helix  chain 'A' and resid 280 through 307
      Proline residue:  A 290  - end of helix
    Processing helix  chain 'A' and resid 323 through 341
      removed outlier: 3.527A  pdb=" N   GLY A 341 " --> pdb=" O   TYR A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 364
    Processing helix  chain 'A' and resid 370 through 376
      removed outlier: 3.917A  pdb=" N   LEU A 375 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   PHE A 376 " --> pdb=" O   TRP A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 396
      removed outlier: 3.614A  pdb=" N   VAL A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 429
      removed outlier: 3.652A  pdb=" N   SER A 429 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 452
    Processing helix  chain 'A' and resid 453 through 463
    Processing helix  chain 'A' and resid 464 through 468
      removed outlier: 3.566A  pdb=" N   SER A 467 " --> pdb=" O   PRO A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 485
    Processing helix  chain 'A' and resid 489 through 508
      Proline residue:  A 499  - end of helix
      Proline residue:  A 503  - end of helix
    Processing helix  chain 'A' and resid 511 through 524
      removed outlier: 3.830A  pdb=" N   ILE A 515 " --> pdb=" O   ASN A 511 " (cutoff:3.500A)
      Proline residue:  A 518  - end of helix
      removed outlier: 4.180A  pdb=" N   SER A 524 " --> pdb=" O   THR A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 541
    Processing helix  chain 'A' and resid 546 through 572
    Processing helix  chain 'A' and resid 573 through 578
    Processing helix  chain 'B' and resid 3 through 10
    Processing helix  chain 'B' and resid 10 through 23
      removed outlier: 3.588A  pdb=" N   LEU B  23 " --> pdb=" O   THR B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 32 through 51
    Processing helix  chain 'B' and resid 54 through 61
    Processing helix  chain 'B' and resid 61 through 69
      Proline residue:  B  67  - end of helix
    Processing helix  chain 'B' and resid 73 through 81
    Processing helix  chain 'B' and resid 83 through 102
      removed outlier: 3.666A  pdb=" N   LEU B  87 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TRP B 102 " --> pdb=" O   SER B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 117
      removed outlier: 3.510A  pdb=" N   ARG B 107 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 136
    Processing helix  chain 'B' and resid 139 through 161
      Proline residue:  B 149  - end of helix
    Processing helix  chain 'B' and resid 231 through 254
      removed outlier: 3.883A  pdb=" N   THR B 249 " --> pdb=" O   ALA B 245 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   THR B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 258
    Processing helix  chain 'B' and resid 259 through 273
    Processing helix  chain 'B' and resid 280 through 307
      Proline residue:  B 290  - end of helix
    Processing helix  chain 'B' and resid 323 through 341
    Processing helix  chain 'B' and resid 344 through 364
    Processing helix  chain 'B' and resid 370 through 376
      removed outlier: 3.909A  pdb=" N   LEU B 375 " --> pdb=" O   GLY B 371 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   PHE B 376 " --> pdb=" O   TRP B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 396
      removed outlier: 3.667A  pdb=" N   VAL B 388 " --> pdb=" O   THR B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 429
      removed outlier: 3.651A  pdb=" N   SER B 429 " --> pdb=" O   LYS B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 452
    Processing helix  chain 'B' and resid 453 through 463
    Processing helix  chain 'B' and resid 464 through 468
      removed outlier: 3.593A  pdb=" N   SER B 467 " --> pdb=" O   PRO B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 485
    Processing helix  chain 'B' and resid 489 through 508
      Proline residue:  B 499  - end of helix
      Proline residue:  B 503  - end of helix
    Processing helix  chain 'B' and resid 511 through 524
      removed outlier: 3.813A  pdb=" N   ILE B 515 " --> pdb=" O   ASN B 511 " (cutoff:3.500A)
      Proline residue:  B 518  - end of helix
      removed outlier: 4.138A  pdb=" N   SER B 524 " --> pdb=" O   THR B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 533 through 541
    Processing helix  chain 'B' and resid 546 through 572
    Processing helix  chain 'B' and resid 573 through 578

    546 hydrogen bonds defined for protein.
    1626 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: 2.34

  Time building geometry restraints manager: 2.57 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: 2307
        1.34 -     1.46: 1890
        1.46 -     1.58: 3979
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 8264
  Sorted by residual:
  bond pdb=" O4  SO4 A 601 "
       pdb=" S   SO4 A 601 "
    ideal  model  delta    sigma   weight residual
    1.499  1.458  0.041 2.00e-02 2.50e+03 4.28e+00
  bond pdb=" O1  SO4 B 601 "
       pdb=" S   SO4 B 601 "
    ideal  model  delta    sigma   weight residual
    1.498  1.457  0.041 2.00e-02 2.50e+03 4.17e+00
  bond pdb=" O3  SO4 A 601 "
       pdb=" S   SO4 A 601 "
    ideal  model  delta    sigma   weight residual
    1.499  1.458  0.041 2.00e-02 2.50e+03 4.16e+00
  bond pdb=" O4  SO4 B 601 "
       pdb=" S   SO4 B 601 "
    ideal  model  delta    sigma   weight residual
    1.499  1.458  0.041 2.00e-02 2.50e+03 4.10e+00
  bond pdb=" O1  SO4 A 601 "
       pdb=" S   SO4 A 601 "
    ideal  model  delta    sigma   weight residual
    1.498  1.458  0.040 2.00e-02 2.50e+03 4.06e+00
  ... (remaining 8259 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 10854
        1.38 -     2.76: 330
        2.76 -     4.14: 68
        4.14 -     5.52: 28
        5.52 -     6.90: 10
  Bond angle restraints: 11290
  Sorted by residual:
  angle pdb=" N   VAL A 487 "
        pdb=" CA  VAL A 487 "
        pdb=" C   VAL A 487 "
      ideal   model   delta    sigma   weight residual
     112.96  109.62    3.34 1.00e+00 1.00e+00 1.11e+01
  angle pdb=" C   THR B 286 "
        pdb=" N   PHE B 287 "
        pdb=" CA  PHE B 287 "
      ideal   model   delta    sigma   weight residual
     122.54  117.08    5.46 1.65e+00 3.67e-01 1.09e+01
  angle pdb=" C   THR A 286 "
        pdb=" N   PHE A 287 "
        pdb=" CA  PHE A 287 "
      ideal   model   delta    sigma   weight residual
     122.54  117.11    5.43 1.65e+00 3.67e-01 1.08e+01
  angle pdb=" N   VAL B 487 "
        pdb=" CA  VAL B 487 "
        pdb=" C   VAL B 487 "
      ideal   model   delta    sigma   weight residual
     112.96  109.77    3.19 1.00e+00 1.00e+00 1.02e+01
  angle pdb=" C   ALA A 505 "
        pdb=" N   GLU A 506 "
        pdb=" CA  GLU A 506 "
      ideal   model   delta    sigma   weight residual
     122.38  117.20    5.18 1.81e+00 3.05e-01 8.19e+00
  ... (remaining 11285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 4437
       17.59 -    35.19: 297
       35.19 -    52.78: 40
       52.78 -    70.38: 8
       70.38 -    87.97: 8
  Dihedral angle restraints: 4790
    sinusoidal: 1806
      harmonic: 2984
  Sorted by residual:
  dihedral pdb=" CA  VAL B  29 "
           pdb=" C   VAL B  29 "
           pdb=" N   LEU B  30 "
           pdb=" CA  LEU B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.57   29.43     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  VAL A  29 "
           pdb=" C   VAL A  29 "
           pdb=" N   LEU A  30 "
           pdb=" CA  LEU A  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.01   28.99     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  ARG A 364 "
           pdb=" C   ARG A 364 "
           pdb=" N   ASP A 365 "
           pdb=" CA  ASP A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.93  -18.07     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 4787 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 779
       0.027 -    0.053: 357
       0.053 -    0.080: 126
       0.080 -    0.106: 67
       0.106 -    0.133: 21
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CA  GLU B 506 "
            pdb=" N   GLU B 506 "
            pdb=" C   GLU B 506 "
            pdb=" CB  GLU B 506 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  GLU A 506 "
            pdb=" N   GLU A 506 "
            pdb=" C   GLU A 506 "
            pdb=" CB  GLU A 506 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  ILE B 422 "
            pdb=" N   ILE B 422 "
            pdb=" C   ILE B 422 "
            pdb=" CB  ILE B 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 1347 not shown)

  Planarity restraints: 1342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  24 "   -0.035 5.00e-02 4.00e+02   5.30e-02 4.49e+00
        pdb=" N   PRO A  25 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A  25 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  25 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  24 "    0.035 5.00e-02 4.00e+02   5.23e-02 4.37e+00
        pdb=" N   PRO B  25 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B  25 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  25 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  26 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A  27 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1339 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 762
        2.74 -     3.28: 8557
        3.28 -     3.82: 14094
        3.82 -     4.36: 15919
        4.36 -     4.90: 28131
  Nonbonded interactions: 67463
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  59 "
            pdb=" OH  TYR A  81 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OD1 ASP B  84 "
            pdb=" OG  SER B 386 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" NH2 ARG A 107 "
            pdb=" O   GLY A 341 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" NH2 ARG B 107 "
            pdb=" O   GLY B 341 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OH  TYR B 268 "
            pdb=" OE2 GLU B 450 "
     model   vdw
     2.302 3.040
  ... (remaining 67458 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.620
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8264  Z= 0.158
  Angle     :  0.637   6.904  11290  Z= 0.340
  Chirality :  0.040   0.133   1350
  Planarity :  0.005   0.053   1342
  Dihedral  : 12.538  87.975   2854
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.36 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.27), residues: 1012
  helix:  1.89 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.00 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 424 
 HIS   0.006   0.001   HIS B 509 
 PHE   0.018   0.001   PHE A 127 
 TYR   0.006   0.001   TYR A 514 
 ARG   0.004   0.000   ARG B 344 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11632 (  546)
  hydrogen bonds       : angle       4.85591 ( 1626)
  covalent geometry    : bond        0.00348 ( 8264)
  covalent geometry    : angle       0.63657 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.7572 (tt0) cc_final: 0.7165 (tt0)
REVERT: A  573 ILE cc_start: 0.8816 (mm) cc_final: 0.8542 (mm)
REVERT: B  157 GLN cc_start: 0.7574 (tt0) cc_final: 0.7198 (tt0)
REVERT: B  234 HIS cc_start: 0.7043 (t-90) cc_final: 0.6822 (t70)
REVERT: B  573 ILE cc_start: 0.8807 (mm) cc_final: 0.8535 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1663
  time to fit residues: 35.6328
Evaluate side-chains
  126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 234 HIS
A 326 GLN
** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 GLN
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.143171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.117351 restraints weight = 12941.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.22
r_work: 0.3328 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8264  Z= 0.179
  Angle     :  0.626   6.711  11290  Z= 0.320
  Chirality :  0.042   0.133   1350
  Planarity :  0.005   0.051   1342
  Dihedral  :  4.471  29.486   1064
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.06 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  7.50 %
    Favored  : 91.70 %
  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:  1.67 (0.27), residues: 1012
  helix:  2.06 (0.19), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.76 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 424 
 HIS   0.004   0.001   HIS B 544 
 PHE   0.021   0.002   PHE B 287 
 TYR   0.008   0.001   TYR A 514 
 ARG   0.003   0.001   ARG B 344 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04849 (  546)
  hydrogen bonds       : angle       4.12089 ( 1626)
  covalent geometry    : bond        0.00426 ( 8264)
  covalent geometry    : angle       0.62568 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.8123 (tt0) cc_final: 0.7737 (tt0)
REVERT: A  326 GLN cc_start: 0.8517 (mt0) cc_final: 0.8247 (mt0)
REVERT: A  573 ILE cc_start: 0.8831 (mm) cc_final: 0.8572 (mm)
REVERT: B    6 TYR cc_start: 0.6535 (m-80) cc_final: 0.6282 (m-10)
REVERT: B  114 MET cc_start: 0.8337 (mtp) cc_final: 0.8113 (mtp)
REVERT: B  234 HIS cc_start: 0.7596 (t-90) cc_final: 0.7265 (t70)
REVERT: B  573 ILE cc_start: 0.8819 (mm) cc_final: 0.8562 (mm)
  outliers start: 7
  outliers final: 3
  residues processed: 141
  average time/residue: 0.1596
  time to fit residues: 32.4526
Evaluate side-chains
  133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 76 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 2 optimal weight:    0.0070
   chunk 98 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.145520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.120184 restraints weight = 13073.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.22
r_work: 0.3373 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8264  Z= 0.124
  Angle     :  0.564   6.145  11290  Z= 0.288
  Chirality :  0.039   0.129   1350
  Planarity :  0.005   0.051   1342
  Dihedral  :  4.330  28.947   1064
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.11 %
    Favored  : 88.64 %
  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:  2.05 (0.27), residues: 1012
  helix:  2.34 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.52 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 572 
 HIS   0.004   0.001   HIS B 544 
 PHE   0.018   0.001   PHE B 287 
 TYR   0.010   0.001   TYR A 514 
 ARG   0.002   0.001   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04098 (  546)
  hydrogen bonds       : angle       3.86552 ( 1626)
  covalent geometry    : bond        0.00276 ( 8264)
  covalent geometry    : angle       0.56432 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.7889 (tt0) cc_final: 0.7606 (tt0)
REVERT: A  450 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7036 (mm-30)
REVERT: A  573 ILE cc_start: 0.8734 (mm) cc_final: 0.8472 (mm)
REVERT: B  157 GLN cc_start: 0.7997 (mt0) cc_final: 0.7668 (tt0)
REVERT: B  234 HIS cc_start: 0.7383 (t-90) cc_final: 0.7122 (t70)
REVERT: B  297 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: B  450 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6957 (mm-30)
REVERT: B  573 ILE cc_start: 0.8716 (mm) cc_final: 0.8455 (mm)
  outliers start: 11
  outliers final: 5
  residues processed: 152
  average time/residue: 0.1533
  time to fit residues: 34.4062
Evaluate side-chains
  139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  379 TYR
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 326 GLN
** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.143666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.118334 restraints weight = 12928.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.19
r_work: 0.3350 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8264  Z= 0.148
  Angle     :  0.587   6.634  11290  Z= 0.297
  Chirality :  0.040   0.147   1350
  Planarity :  0.005   0.049   1342
  Dihedral  :  4.343  28.744   1064
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.82 %
    Favored  : 86.70 %
  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:  2.09 (0.27), residues: 1012
  helix:  2.36 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.48 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 585 
 HIS   0.005   0.001   HIS A 544 
 PHE   0.016   0.001   PHE B 287 
 TYR   0.010   0.001   TYR B   6 
 ARG   0.002   0.000   ARG B 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04259 (  546)
  hydrogen bonds       : angle       3.86838 ( 1626)
  covalent geometry    : bond        0.00346 ( 8264)
  covalent geometry    : angle       0.58746 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.6617 (m-80) cc_final: 0.6310 (m-10)
REVERT: A  486 GLU cc_start: 0.6450 (mp0) cc_final: 0.6112 (mp0)
REVERT: B  234 HIS cc_start: 0.7516 (t-90) cc_final: 0.7207 (t70)
REVERT: B  268 TYR cc_start: 0.8054 (t80) cc_final: 0.7804 (t80)
REVERT: B  297 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8797 (mm)
REVERT: B  450 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6966 (mp0)
  outliers start: 13
  outliers final: 7
  residues processed: 150
  average time/residue: 0.1564
  time to fit residues: 34.3302
Evaluate side-chains
  144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 71 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 234 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.144359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.118987 restraints weight = 12782.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.19
r_work: 0.3359 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8264  Z= 0.133
  Angle     :  0.568   6.518  11290  Z= 0.287
  Chirality :  0.039   0.127   1350
  Planarity :  0.005   0.049   1342
  Dihedral  :  4.277  28.333   1064
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.05 %
    Favored  : 86.36 %
  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:  2.14 (0.28), residues: 1012
  helix:  2.40 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.45 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 572 
 HIS   0.004   0.001   HIS A 544 
 PHE   0.016   0.001   PHE A 287 
 TYR   0.010   0.001   TYR B   6 
 ARG   0.002   0.000   ARG B 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  546)
  hydrogen bonds       : angle       3.79055 ( 1626)
  covalent geometry    : bond        0.00305 ( 8264)
  covalent geometry    : angle       0.56798 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.6567 (m-80) cc_final: 0.6257 (m-10)
REVERT: A  450 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7176 (mm-30)
REVERT: A  486 GLU cc_start: 0.6450 (mp0) cc_final: 0.5982 (mp0)
REVERT: A  573 ILE cc_start: 0.8830 (mm) cc_final: 0.8487 (mm)
REVERT: A  578 ASP cc_start: 0.7306 (t0) cc_final: 0.6920 (t70)
REVERT: B  234 HIS cc_start: 0.7499 (t-90) cc_final: 0.7240 (t70)
REVERT: B  268 TYR cc_start: 0.8075 (t80) cc_final: 0.7828 (t80)
REVERT: B  297 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8762 (mm)
REVERT: B  450 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6931 (mp0)
REVERT: B  573 ILE cc_start: 0.8822 (mm) cc_final: 0.8474 (mm)
  outliers start: 14
  outliers final: 7
  residues processed: 154
  average time/residue: 0.1541
  time to fit residues: 34.8177
Evaluate side-chains
  148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 80 optimal weight:    0.2980
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 234 HIS
A 326 GLN
** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 GLN
B 544 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.142741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.117199 restraints weight = 12933.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.19
r_work: 0.3327 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8264  Z= 0.164
  Angle     :  0.596   6.873  11290  Z= 0.301
  Chirality :  0.041   0.167   1350
  Planarity :  0.005   0.048   1342
  Dihedral  :  4.356  28.537   1064
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.93 %
    Favored  : 86.93 %
  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:  1.96 (0.27), residues: 1012
  helix:  2.24 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.58 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 585 
 HIS   0.004   0.001   HIS B 544 
 PHE   0.016   0.001   PHE B 287 
 TYR   0.011   0.001   TYR B   6 
 ARG   0.002   0.000   ARG B 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  546)
  hydrogen bonds       : angle       3.84700 ( 1626)
  covalent geometry    : bond        0.00390 ( 8264)
  covalent geometry    : angle       0.59619 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.6581 (m-80) cc_final: 0.6298 (m-10)
REVERT: A  345 TYR cc_start: 0.5786 (m-80) cc_final: 0.5567 (m-80)
REVERT: A  450 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7249 (mm-30)
REVERT: A  486 GLU cc_start: 0.6509 (mp0) cc_final: 0.6026 (mp0)
REVERT: A  573 ILE cc_start: 0.8832 (mm) cc_final: 0.8461 (mm)
REVERT: A  578 ASP cc_start: 0.7412 (t0) cc_final: 0.6978 (t70)
REVERT: B  234 HIS cc_start: 0.7548 (t-90) cc_final: 0.7277 (t70)
REVERT: B  268 TYR cc_start: 0.8090 (t80) cc_final: 0.7726 (t80)
REVERT: B  297 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8747 (mm)
REVERT: B  573 ILE cc_start: 0.8821 (mm) cc_final: 0.8447 (mm)
REVERT: B  578 ASP cc_start: 0.7464 (t0) cc_final: 0.7029 (t70)
  outliers start: 10
  outliers final: 6
  residues processed: 142
  average time/residue: 0.1522
  time to fit residues: 31.7138
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 93 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 234 HIS
** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 HIS
B 157 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.143630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.118073 restraints weight = 13010.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.21
r_work: 0.3340 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8264  Z= 0.143
  Angle     :  0.581   6.841  11290  Z= 0.293
  Chirality :  0.040   0.223   1350
  Planarity :  0.005   0.049   1342
  Dihedral  :  4.309  28.329   1064
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.27 %
    Favored  : 86.25 %
  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:  1.94 (0.27), residues: 1012
  helix:  2.22 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.56 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 424 
 HIS   0.005   0.001   HIS A 544 
 PHE   0.015   0.001   PHE B 287 
 TYR   0.012   0.001   TYR B   6 
 ARG   0.002   0.000   ARG B 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  546)
  hydrogen bonds       : angle       3.81568 ( 1626)
  covalent geometry    : bond        0.00336 ( 8264)
  covalent geometry    : angle       0.58091 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  345 TYR cc_start: 0.5484 (m-80) cc_final: 0.5269 (m-80)
REVERT: A  450 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7040 (mm-30)
REVERT: A  573 ILE cc_start: 0.8743 (mm) cc_final: 0.8385 (mm)
REVERT: A  578 ASP cc_start: 0.7398 (t0) cc_final: 0.6931 (t70)
REVERT: B  268 TYR cc_start: 0.7996 (t80) cc_final: 0.7729 (t80)
REVERT: B  297 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8647 (mm)
REVERT: B  347 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: B  450 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6714 (mp0)
REVERT: B  529 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7926 (mt)
REVERT: B  573 ILE cc_start: 0.8729 (mm) cc_final: 0.8377 (mm)
REVERT: B  578 ASP cc_start: 0.7389 (t0) cc_final: 0.6980 (t70)
  outliers start: 13
  outliers final: 8
  residues processed: 147
  average time/residue: 0.1457
  time to fit residues: 31.5553
Evaluate side-chains
  142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 234 HIS
B 157 GLN
B 234 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.144132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.118514 restraints weight = 13008.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.21
r_work: 0.3347 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8264  Z= 0.138
  Angle     :  0.582   6.830  11290  Z= 0.294
  Chirality :  0.040   0.258   1350
  Planarity :  0.005   0.048   1342
  Dihedral  :  4.289  28.172   1064
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.39 %
    Favored  : 85.80 %
  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:  1.98 (0.27), residues: 1012
  helix:  2.27 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.57 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 424 
 HIS   0.003   0.001   HIS A 544 
 PHE   0.014   0.001   PHE B 287 
 TYR   0.018   0.001   TYR A   6 
 ARG   0.004   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  546)
  hydrogen bonds       : angle       3.80921 ( 1626)
  covalent geometry    : bond        0.00321 ( 8264)
  covalent geometry    : angle       0.58250 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A  345 TYR cc_start: 0.5486 (m-80) cc_final: 0.5276 (m-80)
REVERT: A  450 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7042 (mm-30)
REVERT: A  573 ILE cc_start: 0.8720 (mm) cc_final: 0.8385 (mm)
REVERT: A  578 ASP cc_start: 0.7434 (t0) cc_final: 0.6911 (t70)
REVERT: B  243 CYS cc_start: 0.8593 (p) cc_final: 0.8186 (p)
REVERT: B  268 TYR cc_start: 0.7995 (t80) cc_final: 0.7720 (t80)
REVERT: B  297 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8643 (mm)
REVERT: B  450 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6741 (mp0)
REVERT: B  529 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7930 (mt)
REVERT: B  573 ILE cc_start: 0.8709 (mm) cc_final: 0.8372 (mm)
REVERT: B  578 ASP cc_start: 0.7415 (t0) cc_final: 0.6915 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 148
  average time/residue: 0.1678
  time to fit residues: 36.6796
Evaluate side-chains
  148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    0.1980
   chunk 85 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0770
   chunk 49 optimal weight:    0.7980
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 234 HIS
A 326 GLN
B 157 GLN
B 234 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.143546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.117763 restraints weight = 13182.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.23
r_work: 0.3335 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8264  Z= 0.152
  Angle     :  0.611  15.269  11290  Z= 0.305
  Chirality :  0.041   0.258   1350
  Planarity :  0.005   0.048   1342
  Dihedral  :  4.320  28.323   1064
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.39 %
    Favored  : 85.80 %
  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:  1.91 (0.27), residues: 1012
  helix:  2.16 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.46 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 424 
 HIS   0.003   0.001   HIS B 544 
 PHE   0.014   0.001   PHE B 287 
 TYR   0.021   0.001   TYR A   6 
 ARG   0.003   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  546)
  hydrogen bonds       : angle       3.85123 ( 1626)
  covalent geometry    : bond        0.00357 ( 8264)
  covalent geometry    : angle       0.61071 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A  345 TYR cc_start: 0.5508 (m-80) cc_final: 0.5297 (m-80)
REVERT: A  450 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7073 (mm-30)
REVERT: A  573 ILE cc_start: 0.8709 (mm) cc_final: 0.8354 (mm)
REVERT: A  578 ASP cc_start: 0.7476 (t0) cc_final: 0.6972 (t0)
REVERT: B  243 CYS cc_start: 0.8612 (p) cc_final: 0.8195 (p)
REVERT: B  268 TYR cc_start: 0.8008 (t80) cc_final: 0.7705 (t80)
REVERT: B  297 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8652 (mm)
REVERT: B  450 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6740 (mp0)
REVERT: B  529 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7970 (mt)
REVERT: B  573 ILE cc_start: 0.8698 (mm) cc_final: 0.8340 (mm)
REVERT: B  578 ASP cc_start: 0.7456 (t0) cc_final: 0.6892 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 142
  average time/residue: 0.1510
  time to fit residues: 31.7937
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 234 HIS
B 234 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.144305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.118896 restraints weight = 12830.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.18
r_work: 0.3355 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8264  Z= 0.137
  Angle     :  0.608  15.528  11290  Z= 0.302
  Chirality :  0.040   0.255   1350
  Planarity :  0.005   0.048   1342
  Dihedral  :  4.277  28.162   1064
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.73 %
    Favored  : 85.45 %
  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:  1.97 (0.28), residues: 1012
  helix:  2.22 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.44 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 424 
 HIS   0.003   0.001   HIS B 544 
 PHE   0.013   0.001   PHE B 287 
 TYR   0.023   0.001   TYR A   6 
 ARG   0.003   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  546)
  hydrogen bonds       : angle       3.83024 ( 1626)
  covalent geometry    : bond        0.00314 ( 8264)
  covalent geometry    : angle       0.60826 (11290)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: A  450 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7178 (mm-30)
REVERT: A  573 ILE cc_start: 0.8741 (mm) cc_final: 0.8385 (mm)
REVERT: A  578 ASP cc_start: 0.7613 (t0) cc_final: 0.7083 (t0)
REVERT: B  243 CYS cc_start: 0.8819 (p) cc_final: 0.8380 (p)
REVERT: B  268 TYR cc_start: 0.8117 (t80) cc_final: 0.7820 (t80)
REVERT: B  297 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8721 (mm)
REVERT: B  347 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8182 (mt-10)
REVERT: B  450 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6880 (mp0)
REVERT: B  529 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7939 (mt)
REVERT: B  573 ILE cc_start: 0.8724 (mm) cc_final: 0.8354 (mm)
REVERT: B  578 ASP cc_start: 0.7605 (t0) cc_final: 0.6981 (t70)
  outliers start: 16
  outliers final: 12
  residues processed: 150
  average time/residue: 0.1495
  time to fit residues: 32.8544
Evaluate side-chains
  152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  569 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 76 optimal weight:   30.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
B 234 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.143295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.117721 restraints weight = 12949.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.19
r_work: 0.3332 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8264  Z= 0.154
  Angle     :  0.619  15.262  11290  Z= 0.309
  Chirality :  0.041   0.252   1350
  Planarity :  0.005   0.048   1342
  Dihedral  :  4.327  28.515   1064
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.73 %
    Favored  : 85.45 %
  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:  1.91 (0.27), residues: 1012
  helix:  2.18 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.46 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 424 
 HIS   0.003   0.001   HIS A 105 
 PHE   0.013   0.001   PHE A 287 
 TYR   0.022   0.001   TYR A   6 
 ARG   0.003   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  546)
  hydrogen bonds       : angle       3.88570 ( 1626)
  covalent geometry    : bond        0.00361 ( 8264)
  covalent geometry    : angle       0.61939 (11290)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3823.97 seconds
wall clock time: 66 minutes 59.21 seconds (4019.21 seconds total)