Starting phenix.real_space_refine
on Tue Feb 11 10:08:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9co9_45774/02_2025/9co9_45774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9co9_45774/02_2025/9co9_45774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9co9_45774/02_2025/9co9_45774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9co9_45774/02_2025/9co9_45774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9co9_45774/02_2025/9co9_45774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9co9_45774/02_2025/9co9_45774.cif"
  }
  resolution = 3.44
  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=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    3305      2.51       5
     N     882      2.21       5
     O     985      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5198
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1608
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
    Chain: "A"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1634
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 14, 'TRANS': 188}
    Chain: "D"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 978
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
    Chain: "E"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 978
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
  Time building chain proxies: 4.35, per 1000 atoms: 0.84
  Number of scatterers: 5198
  At special positions: 0
  Unit cell: (82.336, 109.781, 118.635, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O     985      8.00
     N     882      7.00
     C    3305      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 376 " - pdb=" SG  CYS B 429 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 388 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 521 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  50 " - pdb=" SG  CYS D 104 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  50 " - pdb=" SG  CYS E 104 " distance=2.03

  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: 1.19
  Conformation dependent library (CDL) restraints added in 654.2 milliseconds
  

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1206

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 10 sheets defined
      10.4% alpha, 24.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'B' and resid 334 through 340
      removed outlier: 3.765A  pdb=" N   VAL B 338 " --> pdb=" O   PRO B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 407
      removed outlier: 3.759A  pdb=" N   VAL B 404 " --> pdb=" O   GLY B 401 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   SER B 405 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 419
    Processing helix  chain 'B' and resid 498 through 502
      removed outlier: 3.551A  pdb=" N   GLN B 502 " --> pdb=" O   VAL B 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 340
    Processing helix  chain 'A' and resid 380 through 384
      removed outlier: 3.879A  pdb=" N   LEU A 384 " --> pdb=" O   PRO A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 407
      removed outlier: 3.587A  pdb=" N   VAL A 404 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   SER A 405 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 419
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.600A  pdb=" N   ASP D  90 " --> pdb=" O   LYS D  87 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR D  91 " --> pdb=" O   LEU D  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 87 through 91'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.986A  pdb=" N   THR E  91 " --> pdb=" O   LEU E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 351 through 355
      removed outlier: 3.979A  pdb=" N   ASN B 351 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL B 392 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY B 428 " --> pdb=" O   TYR B 377 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TYR B 377 " --> pdb=" O   GLY B 428 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL B 430 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 449 through 451
    Processing sheet with id=AA3, first strand: chain 'B' and resid 470 through 471
      removed outlier: 3.514A  pdb=" N   TYR B 470 " --> pdb=" O   TYR B 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 355
      removed outlier: 3.537A  pdb=" N   ASN A 351 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE A 355 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   VAL A 392 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ASN A 391 " --> pdb=" O   GLU A 512 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   GLU A 512 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.504A  pdb=" N   VAL D  79 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   THR D  78 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASP D  73 " --> pdb=" O   THR D  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12
      removed outlier: 4.167A  pdb=" N   GLY D  10 " --> pdb=" O   GLN D 124 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   THR D 126 " --> pdb=" O   GLY D  10 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL D  12 " --> pdb=" O   THR D 126 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL D  93 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   THR D  34 " --> pdb=" O   CYS D  50 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   CYS D  50 " --> pdb=" O   THR D  34 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.633A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 126 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR E  34 " --> pdb=" O   CYS E  50 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   CYS E  50 " --> pdb=" O   THR E  34 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)

    131 hydrogen bonds defined for protein.
    315 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: 1.41

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1668
        1.35 -     1.47: 1458
        1.47 -     1.60: 2192
        1.60 -     1.73: 0
        1.73 -     1.85: 28
  Bond restraints: 5346
  Sorted by residual:
  bond pdb=" C   PHE B 326 "
       pdb=" N   PRO B 327 "
    ideal  model  delta    sigma   weight residual
    1.331  1.374 -0.043 1.28e-02 6.10e+03 1.12e+01
  bond pdb=" N   GLY A 473 "
       pdb=" CA  GLY A 473 "
    ideal  model  delta    sigma   weight residual
    1.445  1.475 -0.031 9.90e-03 1.02e+04 9.66e+00
  bond pdb=" N   TYR D 110 "
       pdb=" CA  TYR D 110 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.040 1.36e-02 5.41e+03 8.63e+00
  bond pdb=" N   GLN A 489 "
       pdb=" CA  GLN A 489 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.18e-02 7.18e+03 8.43e+00
  bond pdb=" N   HIS D  32 "
       pdb=" CA  HIS D  32 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.034 1.18e-02 7.18e+03 8.15e+00
  ... (remaining 5341 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 6948
        2.33 -     4.66: 259
        4.66 -     6.99: 42
        6.99 -     9.32: 12
        9.32 -    11.65: 2
  Bond angle restraints: 7263
  Sorted by residual:
  angle pdb=" N   HIS D  30 "
        pdb=" CA  HIS D  30 "
        pdb=" C   HIS D  30 "
      ideal   model   delta    sigma   weight residual
     114.64  102.99   11.65 1.52e+00 4.33e-01 5.88e+01
  angle pdb=" CA  PHE A 339 "
        pdb=" CB  PHE A 339 "
        pdb=" CG  PHE A 339 "
      ideal   model   delta    sigma   weight residual
     113.80  120.08   -6.28 1.00e+00 1.00e+00 3.95e+01
  angle pdb=" CA  TYR D 110 "
        pdb=" CB  TYR D 110 "
        pdb=" CG  TYR D 110 "
      ideal   model   delta    sigma   weight residual
     113.90  123.49   -9.59 1.80e+00 3.09e-01 2.84e+01
  angle pdb=" N   THR D  31 "
        pdb=" CA  THR D  31 "
        pdb=" C   THR D  31 "
      ideal   model   delta    sigma   weight residual
     114.12  107.44    6.68 1.39e+00 5.18e-01 2.31e+01
  angle pdb=" O   TYR D 109 "
        pdb=" C   TYR D 109 "
        pdb=" N   TYR D 110 "
      ideal   model   delta    sigma   weight residual
     123.27  117.86    5.41 1.16e+00 7.43e-01 2.18e+01
  ... (remaining 7258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 2839
       17.97 -    35.93: 251
       35.93 -    53.90: 35
       53.90 -    71.86: 8
       71.86 -    89.82: 2
  Dihedral angle restraints: 3135
    sinusoidal: 1222
      harmonic: 1913
  Sorted by residual:
  dihedral pdb=" CB  CYS B 477 "
           pdb=" SG  CYS B 477 "
           pdb=" SG  CYS B 484 "
           pdb=" CB  CYS B 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -16.00  -70.00     1      1.00e+01 1.00e-02 6.32e+01
  dihedral pdb=" CB  CYS A 388 "
           pdb=" SG  CYS A 388 "
           pdb=" SG  CYS A 521 "
           pdb=" CB  CYS A 521 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.69   54.31     1      1.00e+01 1.00e-02 4.00e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  96 "
           pdb=" CB  CYS D  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.44  -47.44     1      1.00e+01 1.00e-02 3.11e+01
  ... (remaining 3132 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 502
       0.053 -    0.106: 188
       0.106 -    0.159: 49
       0.159 -    0.213: 12
       0.213 -    0.266: 2
  Chirality restraints: 753
  Sorted by residual:
  chirality pdb=" CA  PRO A 495 "
            pdb=" N   PRO A 495 "
            pdb=" C   PRO A 495 "
            pdb=" CB  PRO A 495 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  ILE A 465 "
            pdb=" N   ILE A 465 "
            pdb=" C   ILE A 465 "
            pdb=" CB  ILE A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ASN A 391 "
            pdb=" N   ASN A 391 "
            pdb=" C   ASN A 391 "
            pdb=" CB  ASN A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 750 not shown)

  Planarity restraints: 950
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 109 "    0.021 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        pdb=" C   TYR D 109 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   TYR D 109 "    0.026 2.00e-02 2.50e+03
        pdb=" N   TYR D 110 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 494 "   -0.315 9.50e-02 1.11e+02   1.41e-01 1.22e+01
        pdb=" NE  ARG A 494 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 494 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 494 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 494 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  28 "    0.013 2.00e-02 2.50e+03   2.68e-02 7.16e+00
        pdb=" C   ALA D  28 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ALA D  28 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU D  29 "    0.015 2.00e-02 2.50e+03
  ... (remaining 947 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1747
        2.84 -     3.36: 4242
        3.36 -     3.87: 8070
        3.87 -     4.39: 9034
        4.39 -     4.90: 15888
  Nonbonded interactions: 38981
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 114 "
            pdb=" N   PHE D 116 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" O   LEU D  29 "
            pdb=" NH1 ARG D  72 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OG1 THR B 412 "
            pdb=" OD2 ASP B 417 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   SER B 510 "
            pdb=" OG  SER B 510 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" OD2 ASP A 395 "
            pdb=" OH  TYR A 420 "
     model   vdw
     2.405 3.040
  ... (remaining 38976 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 326 through 525)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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:             4.330
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.820
  Find NCS groups from input model:        0.240
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
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      :  0.006   0.049   5346  Z= 0.378
  Angle     :  1.021  11.654   7263  Z= 0.610
  Chirality :  0.059   0.266    753
  Planarity :  0.008   0.141    950
  Dihedral  : 12.974  89.824   1893
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  6.28 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  1.43 %
    Favored  : 97.85 %
  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: -2.36 (0.30), residues: 653
  helix: -4.28 (0.37), residues: 51
  sheet:  0.13 (0.45), residues: 147
  loop : -1.96 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 449 
 HIS   0.007   0.001   HIS A 336 
 PHE   0.032   0.002   PHE A 335 
 TYR   0.031   0.002   TYR D 110 
 ARG   0.014   0.001   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 209
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   80 TYR cc_start: 0.7805 (m-80) cc_final: 0.6855 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 211
  average time/residue: 0.2207
  time to fit residues: 56.3095
Evaluate side-chains
  132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0370
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
B 489 GLN
A 489 GLN
D  82 GLN
D 121 GLN
E  13 GLN
E  32 HIS
E  74 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.109999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.085066 restraints weight = 14005.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 4.26
r_work: 0.3174 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5346  Z= 0.239
  Angle     :  0.749   9.043   7263  Z= 0.383
  Chirality :  0.048   0.175    753
  Planarity :  0.005   0.047    950
  Dihedral  :  5.341  25.826    738
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.51 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.28 %
    Favored  : 81.57 %
  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: -1.89 (0.31), residues: 653
  helix: -3.83 (0.46), residues: 55
  sheet:  0.39 (0.42), residues: 172
  loop : -1.70 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 449 
 HIS   0.003   0.001   HIS B 515 
 PHE   0.021   0.001   PHE E  68 
 TYR   0.024   0.002   TYR D 110 
 ARG   0.009   0.001   ARG D  38 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8477 (tpp80)
REVERT: B  411 GLN cc_start: 0.7367 (mp10) cc_final: 0.7101 (mp10)
REVERT: B  462 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7347 (tm-30)
REVERT: A  403 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8683 (mt-10)
REVERT: A  464 ASP cc_start: 0.8414 (t0) cc_final: 0.8121 (t70)
REVERT: A  496 THR cc_start: 0.8850 (p) cc_final: 0.8566 (p)
REVERT: A  514 LEU cc_start: 0.7201 (tt) cc_final: 0.6592 (tt)
REVERT: D   36 TRP cc_start: 0.8087 (m100) cc_final: 0.7822 (m100)
REVERT: D   44 GLU cc_start: 0.8218 (tp30) cc_final: 0.7509 (tp30)
REVERT: D   59 TYR cc_start: 0.8858 (m-80) cc_final: 0.8210 (m-80)
REVERT: D   77 ASN cc_start: 0.8863 (t0) cc_final: 0.7866 (t0)
REVERT: D   95 TYR cc_start: 0.7309 (m-80) cc_final: 0.7081 (m-80)
REVERT: D  115 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7993 (p0)
REVERT: D  125 VAL cc_start: 0.9249 (t) cc_final: 0.8963 (p)
REVERT: E   13 GLN cc_start: 0.8409 (mm110) cc_final: 0.8171 (mm-40)
REVERT: E   19 ARG cc_start: 0.9049 (ttt-90) cc_final: 0.8702 (ttt-90)
REVERT: E   68 PHE cc_start: 0.7858 (m-10) cc_final: 0.7653 (m-80)
REVERT: E   87 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8203 (ttpt)
REVERT: E   89 GLU cc_start: 0.9167 (pm20) cc_final: 0.8028 (pm20)
  outliers start: 12
  outliers final: 8
  residues processed: 152
  average time/residue: 0.1860
  time to fit residues: 35.5993
Evaluate side-chains
  136 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  358 CYS
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  115 ASP
Chi-restraints excluded: chain E residue   74 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.108259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.082425 restraints weight = 13953.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.35
r_work: 0.3146 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5346  Z= 0.226
  Angle     :  0.678   8.538   7263  Z= 0.346
  Chirality :  0.046   0.170    753
  Planarity :  0.005   0.046    950
  Dihedral  :  5.003  22.356    736
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.67 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.71 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.75 (0.31), residues: 653
  helix: -3.49 (0.54), residues: 47
  sheet:  0.45 (0.40), residues: 181
  loop : -1.72 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 433 
 HIS   0.004   0.001   HIS D  32 
 PHE   0.013   0.001   PHE E  68 
 TYR   0.032   0.001   TYR D  94 
 ARG   0.004   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  343 ARG cc_start: 0.8839 (ptp90) cc_final: 0.8603 (ptp90)
REVERT: A  403 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8784 (mt-10)
REVERT: A  464 ASP cc_start: 0.8366 (t0) cc_final: 0.8130 (t70)
REVERT: A  496 THR cc_start: 0.8914 (p) cc_final: 0.8639 (p)
REVERT: D   19 ARG cc_start: 0.9208 (ttm-80) cc_final: 0.8891 (ttt90)
REVERT: D   38 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7974 (mmm-85)
REVERT: D   44 GLU cc_start: 0.8339 (tp30) cc_final: 0.7809 (tp30)
REVERT: D   59 TYR cc_start: 0.8862 (m-80) cc_final: 0.8304 (m-80)
REVERT: D   77 ASN cc_start: 0.8760 (t0) cc_final: 0.7838 (t0)
REVERT: D  113 ASP cc_start: 0.8501 (m-30) cc_final: 0.7862 (t0)
REVERT: D  125 VAL cc_start: 0.9065 (t) cc_final: 0.8841 (m)
REVERT: E    3 GLN cc_start: 0.8770 (mm110) cc_final: 0.7540 (mm-40)
  outliers start: 16
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1777
  time to fit residues: 32.7100
Evaluate side-chains
  131 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  358 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   74 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 34 optimal weight:    0.4980
   chunk 41 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN
E  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.107073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082260 restraints weight = 14221.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 4.44
r_work: 0.3112 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.4611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5346  Z= 0.244
  Angle     :  0.690   8.748   7263  Z= 0.353
  Chirality :  0.045   0.152    753
  Planarity :  0.004   0.040    950
  Dihedral  :  5.248  31.451    736
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.21 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 17.89 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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 (0.32), residues: 653
  helix: -3.25 (0.65), residues: 42
  sheet:  0.59 (0.41), residues: 183
  loop : -1.66 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 433 
 HIS   0.005   0.001   HIS B 515 
 PHE   0.024   0.001   PHE E  68 
 TYR   0.013   0.001   TYR D  94 
 ARG   0.003   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8520 (ttp80)
REVERT: B  395 ASP cc_start: 0.9070 (p0) cc_final: 0.8574 (p0)
REVERT: B  462 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: A  389 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8636 (p90)
REVERT: A  403 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8838 (mt-10)
REVERT: A  464 ASP cc_start: 0.8473 (t0) cc_final: 0.8167 (t0)
REVERT: D    4 LEU cc_start: 0.9044 (mt) cc_final: 0.8611 (pp)
REVERT: D   19 ARG cc_start: 0.9250 (ttm-80) cc_final: 0.8961 (ttt90)
REVERT: D   44 GLU cc_start: 0.8310 (tp30) cc_final: 0.7895 (tp30)
REVERT: D   59 TYR cc_start: 0.8934 (m-80) cc_final: 0.8416 (m-80)
REVERT: D   77 ASN cc_start: 0.8857 (t0) cc_final: 0.7960 (t0)
REVERT: D  113 ASP cc_start: 0.8507 (m-30) cc_final: 0.7760 (t0)
REVERT: D  117 TYR cc_start: 0.8590 (t80) cc_final: 0.7580 (t80)
REVERT: E   19 ARG cc_start: 0.9131 (ttt-90) cc_final: 0.8659 (ttt-90)
REVERT: E   44 GLU cc_start: 0.8884 (mp0) cc_final: 0.8281 (mp0)
REVERT: E   46 GLU cc_start: 0.7829 (pm20) cc_final: 0.7335 (pm20)
  outliers start: 24
  outliers final: 14
  residues processed: 142
  average time/residue: 0.1846
  time to fit residues: 33.4458
Evaluate side-chains
  139 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  352 ARG
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   74 ASN
Chi-restraints excluded: chain E residue   83 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0570
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.6902

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.106994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082179 restraints weight = 14197.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 4.41
r_work: 0.3113 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5346  Z= 0.231
  Angle     :  0.683   8.423   7263  Z= 0.349
  Chirality :  0.045   0.183    753
  Planarity :  0.004   0.038    950
  Dihedral  :  4.926  22.523    736
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.51 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 19.50 %
    Favored  : 76.74 %
  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: -1.48 (0.32), residues: 653
  helix: -3.43 (0.51), residues: 55
  sheet:  0.58 (0.41), residues: 183
  loop : -1.44 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 433 
 HIS   0.004   0.001   HIS B 515 
 PHE   0.030   0.001   PHE E  68 
 TYR   0.016   0.001   TYR D  94 
 ARG   0.003   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8183 (t80) cc_final: 0.7752 (t80)
REVERT: B  395 ASP cc_start: 0.9086 (p0) cc_final: 0.8557 (p0)
REVERT: B  512 GLU cc_start: 0.8889 (pt0) cc_final: 0.8528 (pp20)
REVERT: A  403 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8846 (mt-10)
REVERT: A  464 ASP cc_start: 0.8381 (t0) cc_final: 0.8025 (t0)
REVERT: D    3 GLN cc_start: 0.8349 (pm20) cc_final: 0.8124 (pm20)
REVERT: D    4 LEU cc_start: 0.8969 (mt) cc_final: 0.8581 (pp)
REVERT: D   19 ARG cc_start: 0.9210 (ttm-80) cc_final: 0.8922 (ttt90)
REVERT: D   44 GLU cc_start: 0.8473 (tp30) cc_final: 0.8089 (tp30)
REVERT: D   59 TYR cc_start: 0.8899 (m-80) cc_final: 0.8420 (m-80)
REVERT: D   77 ASN cc_start: 0.8880 (t0) cc_final: 0.8027 (t0)
REVERT: D   94 TYR cc_start: 0.8373 (m-10) cc_final: 0.8135 (m-10)
REVERT: D  113 ASP cc_start: 0.8457 (m-30) cc_final: 0.7573 (t0)
REVERT: D  117 TYR cc_start: 0.8659 (t80) cc_final: 0.7688 (t80)
REVERT: E   44 GLU cc_start: 0.8878 (mp0) cc_final: 0.8299 (mp0)
REVERT: E   46 GLU cc_start: 0.7879 (pm20) cc_final: 0.7398 (pm20)
REVERT: E   73 ASP cc_start: 0.9092 (t0) cc_final: 0.8857 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 135
  average time/residue: 0.1771
  time to fit residues: 30.7633
Evaluate side-chains
  130 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  115 ASP
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   74 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
D 121 GLN
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.106004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.081012 restraints weight = 14017.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 4.52
r_work: 0.3084 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5346  Z= 0.267
  Angle     :  0.691   8.296   7263  Z= 0.354
  Chirality :  0.045   0.166    753
  Planarity :  0.004   0.040    950
  Dihedral  :  4.983  22.902    736
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.82 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.29 %
    Favored  : 74.96 %
  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 (0.32), residues: 653
  helix: -3.30 (0.59), residues: 48
  sheet:  0.56 (0.41), residues: 183
  loop : -1.46 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 433 
 HIS   0.005   0.001   HIS B 515 
 PHE   0.010   0.001   PHE D  37 
 TYR   0.013   0.001   TYR D 111 
 ARG   0.003   0.000   ARG D  67 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8275 (t80) cc_final: 0.7710 (t80)
REVERT: B  395 ASP cc_start: 0.8973 (p0) cc_final: 0.8618 (p0)
REVERT: B  462 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7368 (tm-30)
REVERT: A  389 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8364 (p90)
REVERT: A  403 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8882 (mt-10)
REVERT: A  464 ASP cc_start: 0.8403 (t0) cc_final: 0.8026 (t0)
REVERT: D    3 GLN cc_start: 0.8352 (pm20) cc_final: 0.8088 (pm20)
REVERT: D    4 LEU cc_start: 0.9018 (mt) cc_final: 0.8705 (pp)
REVERT: D   19 ARG cc_start: 0.9248 (ttm-80) cc_final: 0.8931 (ttt90)
REVERT: D   44 GLU cc_start: 0.8468 (tp30) cc_final: 0.8115 (tp30)
REVERT: D   59 TYR cc_start: 0.9002 (m-80) cc_final: 0.8493 (m-80)
REVERT: D   77 ASN cc_start: 0.8973 (t0) cc_final: 0.8108 (t0)
REVERT: D   82 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8575 (tm-30)
REVERT: D  113 ASP cc_start: 0.8433 (m-30) cc_final: 0.7207 (t0)
REVERT: D  115 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7465 (p0)
REVERT: D  117 TYR cc_start: 0.8768 (t80) cc_final: 0.7779 (t80)
REVERT: E   44 GLU cc_start: 0.8936 (mp0) cc_final: 0.8367 (mp0)
REVERT: E   46 GLU cc_start: 0.8050 (pm20) cc_final: 0.7529 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1737
  time to fit residues: 29.9414
Evaluate side-chains
  134 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  115 ASP
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   76 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 62 optimal weight:    0.0870
   chunk 8 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0670
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.107260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.082683 restraints weight = 13790.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 4.30
r_work: 0.3124 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5346  Z= 0.210
  Angle     :  0.679   8.175   7263  Z= 0.346
  Chirality :  0.045   0.166    753
  Planarity :  0.004   0.042    950
  Dihedral  :  4.741  21.010    736
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.21 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.65 %
    Favored  : 74.42 %
  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: -1.44 (0.32), residues: 653
  helix: -3.29 (0.54), residues: 55
  sheet:  0.68 (0.41), residues: 175
  loop : -1.42 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 433 
 HIS   0.004   0.001   HIS B 515 
 PHE   0.010   0.001   PHE D  37 
 TYR   0.017   0.001   TYR D  94 
 ARG   0.006   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8214 (t80) cc_final: 0.7678 (t80)
REVERT: B  395 ASP cc_start: 0.8978 (p0) cc_final: 0.8599 (p0)
REVERT: B  512 GLU cc_start: 0.8933 (pt0) cc_final: 0.8587 (pp20)
REVERT: B  514 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8197 (mm)
REVERT: A  403 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8856 (mt-10)
REVERT: A  464 ASP cc_start: 0.8375 (t0) cc_final: 0.7870 (t0)
REVERT: D    4 LEU cc_start: 0.9073 (mt) cc_final: 0.8673 (pp)
REVERT: D   44 GLU cc_start: 0.8524 (tp30) cc_final: 0.8293 (tp30)
REVERT: D   59 TYR cc_start: 0.9075 (m-80) cc_final: 0.8479 (m-80)
REVERT: D   67 ARG cc_start: 0.9181 (mtm-85) cc_final: 0.8950 (mtm-85)
REVERT: D   77 ASN cc_start: 0.9068 (t0) cc_final: 0.8322 (t0)
REVERT: D   82 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8492 (tm-30)
REVERT: D  117 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: E   44 GLU cc_start: 0.8923 (mp0) cc_final: 0.8362 (mp0)
REVERT: E   46 GLU cc_start: 0.8012 (pm20) cc_final: 0.7541 (pm20)
  outliers start: 22
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1729
  time to fit residues: 30.4604
Evaluate side-chains
  135 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0170
   chunk 9 optimal weight:    8.9990
   chunk 19 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.8220

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

Flipped N/Q/H residues before XYZ refinement:
** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.106508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.081649 restraints weight = 13926.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 4.48
r_work: 0.3082 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.5410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5346  Z= 0.271
  Angle     :  0.717   8.316   7263  Z= 0.368
  Chirality :  0.046   0.171    753
  Planarity :  0.004   0.043    950
  Dihedral  :  5.001  29.256    736
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.75 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.54 %
    Favored  : 73.52 %
  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: -1.48 (0.32), residues: 653
  helix: -3.20 (0.55), residues: 55
  sheet:  0.63 (0.41), residues: 174
  loop : -1.46 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 433 
 HIS   0.004   0.001   HIS B 515 
 PHE   0.009   0.001   PHE D  37 
 TYR   0.010   0.001   TYR B 491 
 ARG   0.002   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8327 (t80) cc_final: 0.7737 (t80)
REVERT: B  390 THR cc_start: 0.9380 (p) cc_final: 0.9113 (p)
REVERT: B  395 ASP cc_start: 0.9014 (p0) cc_final: 0.8652 (p0)
REVERT: B  462 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7479 (tm-30)
REVERT: B  512 GLU cc_start: 0.9029 (pt0) cc_final: 0.8618 (pp20)
REVERT: B  514 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8137 (mm)
REVERT: A  389 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8344 (p90)
REVERT: A  403 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8889 (mt-10)
REVERT: A  464 ASP cc_start: 0.8424 (t0) cc_final: 0.7900 (t0)
REVERT: D    3 GLN cc_start: 0.8401 (pm20) cc_final: 0.8099 (pm20)
REVERT: D    4 LEU cc_start: 0.9144 (mt) cc_final: 0.8706 (pp)
REVERT: D   59 TYR cc_start: 0.9069 (m-80) cc_final: 0.8538 (m-80)
REVERT: D   67 ARG cc_start: 0.9152 (mtm-85) cc_final: 0.8733 (mtm110)
REVERT: D   77 ASN cc_start: 0.9099 (t0) cc_final: 0.8394 (t0)
REVERT: D   82 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8576 (tm-30)
REVERT: E   44 GLU cc_start: 0.8954 (mp0) cc_final: 0.8367 (mp0)
REVERT: E   46 GLU cc_start: 0.8152 (pm20) cc_final: 0.7630 (pm20)
  outliers start: 22
  outliers final: 16
  residues processed: 130
  average time/residue: 0.1769
  time to fit residues: 29.6954
Evaluate side-chains
  130 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  389 PHE
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0670
   chunk 15 optimal weight:    0.2980
   chunk 52 optimal weight:    0.0270
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.107842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.081428 restraints weight = 14002.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 4.38
r_work: 0.3131 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.5476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5346  Z= 0.212
  Angle     :  0.717   8.201   7263  Z= 0.367
  Chirality :  0.046   0.168    753
  Planarity :  0.004   0.042    950
  Dihedral  :  4.698  18.277    736
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.21 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.43 %
    Favored  : 72.99 %
  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: -1.41 (0.32), residues: 653
  helix: -3.03 (0.58), residues: 55
  sheet:  0.50 (0.40), residues: 182
  loop : -1.37 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 433 
 HIS   0.003   0.001   HIS D  32 
 PHE   0.008   0.001   PHE D  37 
 TYR   0.009   0.001   TYR D  59 
 ARG   0.005   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 PHE cc_start: 0.8214 (t80) cc_final: 0.7656 (t80)
REVERT: B  390 THR cc_start: 0.9347 (p) cc_final: 0.9046 (p)
REVERT: B  395 ASP cc_start: 0.9000 (p0) cc_final: 0.8493 (p0)
REVERT: B  462 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: B  512 GLU cc_start: 0.8996 (pt0) cc_final: 0.8600 (pp20)
REVERT: B  514 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8111 (mm)
REVERT: A  403 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8861 (mt-10)
REVERT: A  464 ASP cc_start: 0.8361 (t0) cc_final: 0.7994 (t70)
REVERT: D    3 GLN cc_start: 0.8391 (pm20) cc_final: 0.8116 (pm20)
REVERT: D    4 LEU cc_start: 0.9104 (mt) cc_final: 0.8625 (pp)
REVERT: D   59 TYR cc_start: 0.9097 (m-80) cc_final: 0.8217 (m-80)
REVERT: D   67 ARG cc_start: 0.9155 (mtm-85) cc_final: 0.8878 (mtm-85)
REVERT: D   77 ASN cc_start: 0.9104 (t0) cc_final: 0.8465 (t0)
REVERT: D   80 TYR cc_start: 0.8443 (m-80) cc_final: 0.8213 (m-80)
REVERT: D   82 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8525 (tm-30)
REVERT: D   83 MET cc_start: 0.8729 (mmm) cc_final: 0.8424 (mmm)
REVERT: E   44 GLU cc_start: 0.8921 (mp0) cc_final: 0.8316 (mp0)
REVERT: E   46 GLU cc_start: 0.8083 (pm20) cc_final: 0.7582 (pm20)
REVERT: E   76 LYS cc_start: 0.9424 (mtmm) cc_final: 0.9204 (mtmm)
  outliers start: 20
  outliers final: 17
  residues processed: 129
  average time/residue: 0.1736
  time to fit residues: 28.8361
Evaluate side-chains
  132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0670
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.107473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.082151 restraints weight = 14034.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 4.45
r_work: 0.3120 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5346  Z= 0.235
  Angle     :  0.726   8.243   7263  Z= 0.372
  Chirality :  0.046   0.168    753
  Planarity :  0.004   0.042    950
  Dihedral  :  4.729  18.260    736
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.90 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.26 %
    Favored  : 72.81 %
  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: -1.37 (0.32), residues: 653
  helix: -2.84 (0.60), residues: 55
  sheet:  0.57 (0.41), residues: 176
  loop : -1.36 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 433 
 HIS   0.004   0.001   HIS B 515 
 PHE   0.009   0.001   PHE A 389 
 TYR   0.009   0.001   TYR D 111 
 ARG   0.006   0.000   ARG B 343 

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

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

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1306 Ramachandran restraints generated.
    653 Oldfield, 0 Emsley, 653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 ARG cc_start: 0.8924 (tmm-80) cc_final: 0.8685 (ttp80)
REVERT: B  368 PHE cc_start: 0.8264 (t80) cc_final: 0.7690 (t80)
REVERT: B  390 THR cc_start: 0.9296 (p) cc_final: 0.8978 (p)
REVERT: B  395 ASP cc_start: 0.8973 (p0) cc_final: 0.8560 (p0)
REVERT: B  462 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7535 (tm-30)
REVERT: B  512 GLU cc_start: 0.9038 (pt0) cc_final: 0.8611 (pp20)
REVERT: B  514 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8077 (mm)
REVERT: A  403 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8868 (mt-10)
REVERT: A  464 ASP cc_start: 0.8376 (t0) cc_final: 0.8012 (t70)
REVERT: D    3 GLN cc_start: 0.8420 (pm20) cc_final: 0.8157 (pm20)
REVERT: D    4 LEU cc_start: 0.9103 (mt) cc_final: 0.8678 (pp)
REVERT: D   59 TYR cc_start: 0.9178 (m-80) cc_final: 0.8170 (m-80)
REVERT: D   67 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8693 (mtm110)
REVERT: D   77 ASN cc_start: 0.9140 (t0) cc_final: 0.8545 (t0)
REVERT: D   80 TYR cc_start: 0.8446 (m-80) cc_final: 0.8202 (m-80)
REVERT: D   82 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8536 (tm-30)
REVERT: E   44 GLU cc_start: 0.8936 (mp0) cc_final: 0.8337 (mp0)
REVERT: E   46 GLU cc_start: 0.8146 (pm20) cc_final: 0.7631 (pm20)
REVERT: E   76 LYS cc_start: 0.9409 (mtmm) cc_final: 0.9202 (mtmm)
  outliers start: 22
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1745
  time to fit residues: 28.7977
Evaluate side-chains
  134 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  392 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   68 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue  116 PHE
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   51 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 41 optimal weight:    0.1980
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.107281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.081023 restraints weight = 14019.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 4.39
r_work: 0.3115 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.5574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5346  Z= 0.242
  Angle     :  0.725   8.192   7263  Z= 0.372
  Chirality :  0.046   0.169    753
  Planarity :  0.004   0.042    950
  Dihedral  :  4.734  19.123    736
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.05 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.43 %
    Favored  : 73.17 %
  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: -1.37 (0.32), residues: 653
  helix: -2.82 (0.60), residues: 55
  sheet:  0.63 (0.42), residues: 175
  loop : -1.39 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 433 
 HIS   0.004   0.001   HIS B 515 
 PHE   0.013   0.001   PHE A 389 
 TYR   0.010   0.001   TYR B 491 
 ARG   0.006   0.000   ARG B 343 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3657.53 seconds
wall clock time: 65 minutes 35.84 seconds (3935.84 seconds total)