Starting phenix.real_space_refine
on Fri Jul 25 11:17:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nll_12465/07_2025/7nll_12465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nll_12465/07_2025/7nll_12465.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2025/7nll_12465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2025/7nll_12465.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2025/7nll_12465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2025/7nll_12465.cif"
  }
  resolution = 2.89
  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
-------------------------------------------------------------------------------
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=   0.078 sd=   0.125
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2915 atoms to isotropic.
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      22      5.16       5
     C    3220      2.51       5
     N     829      2.21       5
     O     985      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5056
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1501
          Classifications: {'peptide': 196}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "D"
      Number of atoms: 1494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1494
          Classifications: {'peptide': 195}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1021
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 5, 'TRANS': 127}
    Chain: "C"
      Number of atoms: 1012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1012
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 5, 'TRANS': 126}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'RTV': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'RTV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.51, per 1000 atoms: 0.69
  Number of scatterers: 5056
  At special positions: 0
  Unit cell: (92.92, 57.57, 105.04, 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      22     16.00
     O     985      8.00
     N     829      7.00
     C    3220      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 391 " - pdb=" SG  CYS D 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 480 " - pdb=" SG  CYS D 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " 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: 1.18
  Conformation dependent library (CDL) restraints added in 579.2 milliseconds
  

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1184

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 10 sheets defined
      15.2% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.597A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 371
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 4.330A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 4.330A  pdb=" N   ARG B 408 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN B 409 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'D' and resid 337 through 343
      removed outlier: 3.597A  pdb=" N   VAL D 341 " --> pdb=" O   PRO D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 371
    Processing helix  chain 'D' and resid 383 through 388
      removed outlier: 4.329A  pdb=" N   ASN D 388 " --> pdb=" O   PRO D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 410
      removed outlier: 4.329A  pdb=" N   ARG D 408 " --> pdb=" O   GLY D 404 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLN D 409 " --> pdb=" O   ASP D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 422
    Processing helix  chain 'D' and resid 438 through 443
    Processing helix  chain 'A' and resid 87 through 91
    Processing helix  chain 'A' and resid 114 through 118
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'C' and resid 114 through 118
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.614A  pdb=" N   TYR C 109 " --> pdb=" O   CYS B 379 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'D' and resid 354 through 358
    Processing sheet with id=AA5, first strand: chain 'D' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'D' and resid 473 through 474
    Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.753A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.753A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)

    171 hydrogen bonds defined for protein.
    417 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: 1.28

  Time building geometry restraints manager: 1.39 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: 1620
        1.34 -     1.46: 1413
        1.46 -     1.58: 2139
        1.58 -     1.70: 0
        1.70 -     1.81: 24
  Bond restraints: 5196
  Sorted by residual:
  bond pdb=" C5  RTV D1001 "
       pdb=" O5  RTV D1001 "
    ideal  model  delta    sigma   weight residual
    1.411  1.436 -0.025 2.00e-02 2.50e+03 1.52e+00
  bond pdb=" C5  RTV B1001 "
       pdb=" O5  RTV B1001 "
    ideal  model  delta    sigma   weight residual
    1.411  1.435 -0.024 2.00e-02 2.50e+03 1.49e+00
  bond pdb=" C1  RTV B1001 "
       pdb=" O5  RTV B1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.428 -0.022 2.00e-02 2.50e+03 1.17e+00
  bond pdb=" C2  RTV B1001 "
       pdb=" C3  RTV B1001 "
    ideal  model  delta    sigma   weight residual
    1.547  1.525  0.022 2.00e-02 2.50e+03 1.17e+00
  bond pdb=" C4  RTV B1001 "
       pdb=" C5  RTV B1001 "
    ideal  model  delta    sigma   weight residual
    1.547  1.526  0.021 2.00e-02 2.50e+03 1.12e+00
  ... (remaining 5191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.88: 6519
        0.88 -     1.77: 434
        1.77 -     2.65: 85
        2.65 -     3.53: 36
        3.53 -     4.42: 8
  Bond angle restraints: 7082
  Sorted by residual:
  angle pdb=" N   TYR C 109 "
        pdb=" CA  TYR C 109 "
        pdb=" C   TYR C 109 "
      ideal   model   delta    sigma   weight residual
     108.34  105.46    2.88 1.64e+00 3.72e-01 3.09e+00
  angle pdb=" N   TYR A 109 "
        pdb=" CA  TYR A 109 "
        pdb=" C   TYR A 109 "
      ideal   model   delta    sigma   weight residual
     108.34  105.46    2.88 1.64e+00 3.72e-01 3.08e+00
  angle pdb=" CA  TYR B 369 "
        pdb=" CB  TYR B 369 "
        pdb=" CG  TYR B 369 "
      ideal   model   delta    sigma   weight residual
     113.90  116.98   -3.08 1.80e+00 3.09e-01 2.93e+00
  angle pdb=" CA  TYR D 369 "
        pdb=" CB  TYR D 369 "
        pdb=" CG  TYR D 369 "
      ideal   model   delta    sigma   weight residual
     113.90  116.95   -3.05 1.80e+00 3.09e-01 2.87e+00
  angle pdb=" N   ASP A 119 "
        pdb=" CA  ASP A 119 "
        pdb=" C   ASP A 119 "
      ideal   model   delta    sigma   weight residual
     111.36  113.10   -1.74 1.09e+00 8.42e-01 2.54e+00
  ... (remaining 7077 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.37: 2892
       22.37 -    44.73: 96
       44.73 -    67.10: 14
       67.10 -    89.47: 12
       89.47 -   111.84: 14
  Dihedral angle restraints: 3028
    sinusoidal: 1140
      harmonic: 1888
  Sorted by residual:
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  96 "
           pdb=" CB  CYS C  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.00   36.00     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CB  CYS A  22 "
           pdb=" SG  CYS A  22 "
           pdb=" SG  CYS A  96 "
           pdb=" CB  CYS A  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.02   35.98     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" C2  RTV D1001 "
           pdb=" C3  RTV D1001 "
           pdb=" C4  RTV D1001 "
           pdb=" C5  RTV D1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.83   54.01 -111.84     1      3.00e+01 1.11e-03 1.46e+01
  ... (remaining 3025 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.000: 745
       1.000 -    2.000: 0
       2.000 -    3.001: 0
       3.001 -    4.001: 0
       4.001 -    5.001: 2
  Chirality restraints: 747
  Sorted by residual:
  chirality pdb=" C2  RTV D1001 "
            pdb=" C1  RTV D1001 "
            pdb=" C3  RTV D1001 "
            pdb=" N2  RTV D1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50   -2.50    5.00 2.00e-01 2.50e+01 6.25e+02
  chirality pdb=" C2  RTV B1001 "
            pdb=" C1  RTV B1001 "
            pdb=" C3  RTV B1001 "
            pdb=" N2  RTV B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50   -2.50    5.00 2.00e-01 2.50e+01 6.25e+02
  chirality pdb=" CA  ILE A  51 "
            pdb=" N   ILE A  51 "
            pdb=" C   ILE A  51 "
            pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.56e-01
  ... (remaining 744 not shown)

  Planarity restraints: 927
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 116 "    0.010 2.00e-02 2.50e+03   7.11e-03 1.27e+00
        pdb=" CG  TRP C 116 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 116 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 116 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 116 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 116 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 116 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 116 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 116 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 116 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 116 "   -0.010 2.00e-02 2.50e+03   6.98e-03 1.22e+00
        pdb=" CG  TRP A 116 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 116 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 116 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 116 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 116 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 116 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 116 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 116 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 116 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 109 "   -0.006 2.00e-02 2.50e+03   6.69e-03 8.94e-01
        pdb=" CG  TYR C 109 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 109 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 109 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 109 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 109 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 109 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 109 "    0.001 2.00e-02 2.50e+03
  ... (remaining 924 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1059
        2.78 -     3.31: 4439
        3.31 -     3.84: 8558
        3.84 -     4.37: 10483
        4.37 -     4.90: 17832
  Nonbonded interactions: 42371
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 343 "
            pdb=" O7  RTV B1001 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" N   GLY C  15 "
            pdb=" O   LEU C  86 "
     model   vdw
     2.557 3.120
  nonbonded pdb=" N   GLY A  15 "
            pdb=" O   LEU A  86 "
     model   vdw
     2.557 3.120
  nonbonded pdb=" N   GLN C  13 "
            pdb=" OE1 GLN C  13 "
     model   vdw
     2.571 3.120
  nonbonded pdb=" N   GLN A  13 "
            pdb=" OE1 GLN A  13 "
     model   vdw
     2.572 3.120
  ... (remaining 42366 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 2 through 133)
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'B' and (resid 333 through 381 or (resid 382 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 383 through 527 or resid 1001))
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.590
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
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   0.028   5206  Z= 0.121
  Angle     :  0.550   4.419   7102  Z= 0.304
  Chirality :  0.263   5.001    747
  Planarity :  0.004   0.023    927
  Dihedral  : 15.471 111.836   1814
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.31), residues: 648
  helix: -0.59 (0.84), residues: 36
  sheet:  2.74 (0.37), residues: 164
  loop :  0.35 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 116 
 HIS   0.000   0.000   HIS B 519 
 PHE   0.012   0.001   PHE B 347 
 TYR   0.016   0.001   TYR C 109 
 ARG   0.002   0.000   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23601 (  171)
  hydrogen bonds       : angle       9.26000 (  417)
  SS BOND              : bond        0.00204 (   10)
  SS BOND              : angle       0.71170 (   20)
  covalent geometry    : bond        0.00274 ( 5196)
  covalent geometry    : angle       0.54912 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8321 (m-30) cc_final: 0.8049 (m-30)
REVERT: B  483 VAL cc_start: 0.8283 (t) cc_final: 0.8058 (m)
REVERT: D  493 GLN cc_start: 0.8064 (tp40) cc_final: 0.7738 (tp40)
REVERT: A   73 ASP cc_start: 0.8075 (t0) cc_final: 0.7862 (t0)
REVERT: C   32 TYR cc_start: 0.9068 (m-80) cc_final: 0.8781 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.9839
  time to fit residues: 167.8566
Evaluate side-chains
  116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 48 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:   20.0000
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 394 ASN
** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 487 ASN
A  74 ASN
C  39 GLN
C  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.096964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.081725 restraints weight = 8624.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.74
r_work: 0.3053 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5206  Z= 0.229
  Angle     :  0.627   6.909   7102  Z= 0.333
  Chirality :  0.049   0.288    747
  Planarity :  0.005   0.036    927
  Dihedral  :  6.573  43.843    770
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.41 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.31), residues: 648
  helix: -0.99 (0.79), residues: 38
  sheet:  1.65 (0.36), residues: 193
  loop :  0.07 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 116 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.016   0.002   PHE D 347 
 TYR   0.019   0.002   TYR B 495 
 ARG   0.003   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  171)
  hydrogen bonds       : angle       7.04313 (  417)
  SS BOND              : bond        0.00372 (   10)
  SS BOND              : angle       1.61831 (   20)
  covalent geometry    : bond        0.00529 ( 5196)
  covalent geometry    : angle       0.62215 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8815 (m-30) cc_final: 0.8564 (m-30)
REVERT: D  340 GLU cc_start: 0.8429 (tt0) cc_final: 0.8142 (tm-30)
REVERT: D  420 ASP cc_start: 0.8935 (m-30) cc_final: 0.8625 (m-30)
REVERT: D  493 GLN cc_start: 0.8542 (tp40) cc_final: 0.8215 (tp40)
REVERT: D  498 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8369 (mp10)
REVERT: A    6 GLU cc_start: 0.8026 (mp0) cc_final: 0.7637 (mp0)
REVERT: A   31 ASP cc_start: 0.8342 (t0) cc_final: 0.8112 (t0)
REVERT: A   46 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8180 (pt0)
REVERT: A   73 ASP cc_start: 0.8160 (t0) cc_final: 0.7925 (t0)
REVERT: A   89 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8170 (mp0)
REVERT: C   32 TYR cc_start: 0.9206 (m-80) cc_final: 0.8836 (m-80)
REVERT: C   90 ASP cc_start: 0.8116 (m-30) cc_final: 0.7822 (m-30)
REVERT: C   95 TYR cc_start: 0.9376 (m-80) cc_final: 0.8995 (m-80)
  outliers start: 18
  outliers final: 6
  residues processed: 138
  average time/residue: 0.8514
  time to fit residues: 124.1964
Evaluate side-chains
  127 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   65 LYS
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   79 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 31 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 37 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
B 501 ASN
D 487 ASN
A  74 ASN
A  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.099211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.083735 restraints weight = 8548.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.79
r_work: 0.3030 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5206  Z= 0.194
  Angle     :  0.576   8.215   7102  Z= 0.306
  Chirality :  0.044   0.160    747
  Planarity :  0.004   0.036    927
  Dihedral  :  5.779  40.919    770
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 16.48 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.31), residues: 648
  helix: -1.20 (0.78), residues: 37
  sheet:  1.48 (0.36), residues: 186
  loop : -0.18 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 116 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.010   0.001   PHE A  68 
 TYR   0.017   0.002   TYR B 369 
 ARG   0.007   0.001   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  171)
  hydrogen bonds       : angle       6.73556 (  417)
  SS BOND              : bond        0.00278 (   10)
  SS BOND              : angle       1.23689 (   20)
  covalent geometry    : bond        0.00447 ( 5196)
  covalent geometry    : angle       0.57286 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  418 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8110 (mm)
REVERT: B  420 ASP cc_start: 0.8843 (m-30) cc_final: 0.8550 (m-30)
REVERT: B  493 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7756 (tm-30)
REVERT: D  340 GLU cc_start: 0.8482 (tt0) cc_final: 0.8158 (tm-30)
REVERT: D  420 ASP cc_start: 0.8963 (m-30) cc_final: 0.8657 (m-30)
REVERT: D  493 GLN cc_start: 0.8614 (tp40) cc_final: 0.8295 (tp40)
REVERT: D  498 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8349 (mp10)
REVERT: A    6 GLU cc_start: 0.8174 (mp0) cc_final: 0.7638 (mp0)
REVERT: A   46 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8345 (pt0)
REVERT: A   73 ASP cc_start: 0.8233 (t0) cc_final: 0.7954 (t0)
REVERT: A   76 LYS cc_start: 0.8256 (mtpm) cc_final: 0.8054 (mtpm)
REVERT: A  103 SER cc_start: 0.8687 (m) cc_final: 0.8431 (p)
REVERT: C   32 TYR cc_start: 0.9218 (m-80) cc_final: 0.8919 (m-80)
REVERT: C   90 ASP cc_start: 0.8177 (m-30) cc_final: 0.7847 (m-30)
REVERT: C   95 TYR cc_start: 0.9365 (m-80) cc_final: 0.9016 (m-80)
  outliers start: 23
  outliers final: 10
  residues processed: 133
  average time/residue: 0.7723
  time to fit residues: 108.8878
Evaluate side-chains
  126 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 60 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 2 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 49 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0370
   overall best weight:    6.2066

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
A  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.098677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.083237 restraints weight = 8793.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.84
r_work: 0.3014 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5206  Z= 0.179
  Angle     :  0.558   9.524   7102  Z= 0.294
  Chirality :  0.044   0.161    747
  Planarity :  0.004   0.033    927
  Dihedral  :  5.601  40.268    770
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 17.05 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.31), residues: 648
  helix: -1.43 (0.85), residues: 31
  sheet:  1.15 (0.36), residues: 187
  loop : -0.32 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 436 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.010   0.001   PHE A  68 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.004   0.000   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  171)
  hydrogen bonds       : angle       6.53866 (  417)
  SS BOND              : bond        0.00280 (   10)
  SS BOND              : angle       1.12908 (   20)
  covalent geometry    : bond        0.00412 ( 5196)
  covalent geometry    : angle       0.55581 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8826 (m-30) cc_final: 0.8607 (m-30)
REVERT: B  493 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7618 (tm-30)
REVERT: D  340 GLU cc_start: 0.8549 (tt0) cc_final: 0.8125 (tm-30)
REVERT: D  420 ASP cc_start: 0.8946 (m-30) cc_final: 0.8628 (m-30)
REVERT: D  493 GLN cc_start: 0.8621 (tp40) cc_final: 0.8336 (tp40)
REVERT: D  498 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8404 (mp10)
REVERT: A    6 GLU cc_start: 0.8303 (mp0) cc_final: 0.7751 (mp0)
REVERT: A   46 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8380 (pt0)
REVERT: A   73 ASP cc_start: 0.8152 (t0) cc_final: 0.7837 (t0)
REVERT: A  103 SER cc_start: 0.8886 (m) cc_final: 0.8670 (p)
REVERT: C   32 TYR cc_start: 0.9217 (m-80) cc_final: 0.8956 (m-80)
REVERT: C   46 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: C   90 ASP cc_start: 0.8208 (m-30) cc_final: 0.7850 (m-30)
REVERT: C   95 TYR cc_start: 0.9380 (m-80) cc_final: 0.8993 (m-80)
  outliers start: 30
  outliers final: 20
  residues processed: 133
  average time/residue: 0.8008
  time to fit residues: 112.8285
Evaluate side-chains
  136 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  430 THR
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   65 LYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 13 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 49 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0040
   overall best weight:    6.2000

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
A  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.097923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.082572 restraints weight = 8694.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.79
r_work: 0.3008 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   5206  Z= 0.178
  Angle     :  0.563  10.735   7102  Z= 0.294
  Chirality :  0.044   0.157    747
  Planarity :  0.004   0.034    927
  Dihedral  :  5.483  39.966    770
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 17.43 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.31), residues: 648
  helix: -1.57 (0.83), residues: 31
  sheet:  0.94 (0.36), residues: 187
  loop : -0.41 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 116 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.009   0.001   PHE A  68 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.003   0.000   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  171)
  hydrogen bonds       : angle       6.46020 (  417)
  SS BOND              : bond        0.00310 (   10)
  SS BOND              : angle       1.02276 (   20)
  covalent geometry    : bond        0.00411 ( 5196)
  covalent geometry    : angle       0.56143 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 114
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8815 (m-30) cc_final: 0.8486 (m-30)
REVERT: B  493 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7643 (tm-30)
REVERT: D  340 GLU cc_start: 0.8641 (tt0) cc_final: 0.8186 (tm-30)
REVERT: D  420 ASP cc_start: 0.8930 (m-30) cc_final: 0.8613 (m-30)
REVERT: D  493 GLN cc_start: 0.8620 (tp40) cc_final: 0.8287 (tp40)
REVERT: D  498 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8390 (mp10)
REVERT: A    6 GLU cc_start: 0.8384 (mp0) cc_final: 0.7886 (mp0)
REVERT: A   46 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8383 (pt0)
REVERT: A   73 ASP cc_start: 0.8197 (t0) cc_final: 0.7851 (t0)
REVERT: A   76 LYS cc_start: 0.8274 (mtpm) cc_final: 0.7956 (mtmm)
REVERT: C   32 TYR cc_start: 0.9234 (m-80) cc_final: 0.8968 (m-80)
REVERT: C   46 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8110 (pt0)
REVERT: C   90 ASP cc_start: 0.8295 (m-30) cc_final: 0.7946 (m-30)
REVERT: C   95 TYR cc_start: 0.9380 (m-80) cc_final: 0.8952 (m-80)
  outliers start: 36
  outliers final: 24
  residues processed: 131
  average time/residue: 0.7563
  time to fit residues: 105.0969
Evaluate side-chains
  136 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  430 THR
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   65 LYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0040
   chunk 10 optimal weight:   20.0000
   chunk 52 optimal weight:    7.9990
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   overall best weight:    7.2000

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.097151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.081906 restraints weight = 8760.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.76
r_work: 0.2994 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   5206  Z= 0.200
  Angle     :  0.581  11.474   7102  Z= 0.301
  Chirality :  0.044   0.164    747
  Planarity :  0.004   0.037    927
  Dihedral  :  5.563  39.208    770
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 18.58 %
    Favored  : 74.52 %
  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: -0.23 (0.31), residues: 648
  helix: -1.67 (0.83), residues: 30
  sheet:  0.76 (0.36), residues: 187
  loop : -0.45 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 436 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.010   0.001   PHE A  68 
 TYR   0.015   0.001   TYR B 369 
 ARG   0.003   0.000   ARG D 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  171)
  hydrogen bonds       : angle       6.51575 (  417)
  SS BOND              : bond        0.00320 (   10)
  SS BOND              : angle       1.05187 (   20)
  covalent geometry    : bond        0.00464 ( 5196)
  covalent geometry    : angle       0.57921 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 114
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8815 (m-30) cc_final: 0.8483 (m-30)
REVERT: B  493 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7665 (tm-30)
REVERT: B  498 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8444 (mp10)
REVERT: D  340 GLU cc_start: 0.8665 (tt0) cc_final: 0.8205 (tm-30)
REVERT: D  420 ASP cc_start: 0.8933 (m-30) cc_final: 0.8614 (m-30)
REVERT: D  493 GLN cc_start: 0.8624 (tp40) cc_final: 0.8312 (tp40)
REVERT: D  498 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8410 (mp10)
REVERT: D  517 LEU cc_start: 0.8202 (tp) cc_final: 0.7979 (tt)
REVERT: A    6 GLU cc_start: 0.8423 (mp0) cc_final: 0.7893 (mp0)
REVERT: A   31 ASP cc_start: 0.8407 (t0) cc_final: 0.8034 (t0)
REVERT: A   45 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7816 (mtt180)
REVERT: A   46 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8389 (pt0)
REVERT: A   73 ASP cc_start: 0.8185 (t0) cc_final: 0.7838 (t0)
REVERT: A   76 LYS cc_start: 0.8311 (mtpm) cc_final: 0.7960 (mtmm)
REVERT: C   32 TYR cc_start: 0.9248 (m-80) cc_final: 0.8965 (m-80)
REVERT: C   46 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8182 (pt0)
REVERT: C   90 ASP cc_start: 0.8317 (m-30) cc_final: 0.7948 (m-30)
REVERT: C   95 TYR cc_start: 0.9378 (m-80) cc_final: 0.8989 (m-80)
  outliers start: 36
  outliers final: 21
  residues processed: 130
  average time/residue: 0.7859
  time to fit residues: 108.3265
Evaluate side-chains
  138 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  430 THR
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   65 LYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 42 optimal weight:    0.4980
   chunk 3 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0060
   chunk 1 optimal weight:    0.7980
   overall best weight:    2.6600

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.100964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.085689 restraints weight = 8458.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.73
r_work: 0.3071 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5206  Z= 0.109
  Angle     :  0.527  10.522   7102  Z= 0.272
  Chirality :  0.042   0.134    747
  Planarity :  0.004   0.035    927
  Dihedral  :  4.941  41.172    770
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 19.92 %
    Favored  : 74.52 %
  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: -0.06 (0.31), residues: 648
  helix: -1.57 (0.87), residues: 31
  sheet:  1.25 (0.37), residues: 167
  loop : -0.43 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 436 
 HIS   0.000   0.000   HIS D 519 
 PHE   0.005   0.001   PHE B 490 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.003   0.000   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02949 (  171)
  hydrogen bonds       : angle       6.17225 (  417)
  SS BOND              : bond        0.00184 (   10)
  SS BOND              : angle       0.73561 (   20)
  covalent geometry    : bond        0.00247 ( 5196)
  covalent geometry    : angle       0.52645 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8820 (m-30) cc_final: 0.8598 (m-30)
REVERT: B  493 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7684 (tm-30)
REVERT: B  498 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8312 (mp10)
REVERT: D  340 GLU cc_start: 0.8746 (tt0) cc_final: 0.8231 (tm-30)
REVERT: D  420 ASP cc_start: 0.8881 (m-30) cc_final: 0.8576 (m-30)
REVERT: D  493 GLN cc_start: 0.8633 (tp40) cc_final: 0.8323 (tp40)
REVERT: D  498 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8244 (mp10)
REVERT: D  517 LEU cc_start: 0.8129 (tp) cc_final: 0.7913 (tt)
REVERT: A    6 GLU cc_start: 0.8353 (mp0) cc_final: 0.7658 (mp0)
REVERT: A   31 ASP cc_start: 0.8295 (t0) cc_final: 0.7848 (t0)
REVERT: A   45 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7744 (mtt180)
REVERT: A   73 ASP cc_start: 0.8146 (t0) cc_final: 0.7768 (t0)
REVERT: A   76 LYS cc_start: 0.8299 (mtpm) cc_final: 0.7967 (mtmm)
REVERT: A  123 GLN cc_start: 0.8340 (pp30) cc_final: 0.7320 (pp30)
REVERT: C   32 TYR cc_start: 0.9169 (m-80) cc_final: 0.8945 (m-80)
REVERT: C   90 ASP cc_start: 0.8284 (m-30) cc_final: 0.7893 (m-30)
REVERT: C   95 TYR cc_start: 0.9364 (m-80) cc_final: 0.9045 (m-80)
  outliers start: 29
  outliers final: 20
  residues processed: 137
  average time/residue: 0.8053
  time to fit residues: 116.6371
Evaluate side-chains
  136 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  430 THR
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 30 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 60 optimal weight:   30.0000
   chunk 57 optimal weight:    0.0050
   chunk 14 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   overall best weight:    3.5200

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.100285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.085000 restraints weight = 8641.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.77
r_work: 0.3052 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5206  Z= 0.124
  Angle     :  0.571  16.399   7102  Z= 0.284
  Chirality :  0.042   0.140    747
  Planarity :  0.004   0.033    927
  Dihedral  :  4.944  40.694    770
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 21.84 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.31), residues: 648
  helix: -1.53 (0.89), residues: 31
  sheet:  1.21 (0.37), residues: 167
  loop : -0.44 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 436 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.006   0.001   PHE C  68 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.002   0.000   ARG D 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  171)
  hydrogen bonds       : angle       6.12870 (  417)
  SS BOND              : bond        0.00239 (   10)
  SS BOND              : angle       0.84955 (   20)
  covalent geometry    : bond        0.00283 ( 5196)
  covalent geometry    : angle       0.56998 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  493 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7697 (tm-30)
REVERT: B  498 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8340 (mp10)
REVERT: D  340 GLU cc_start: 0.8711 (tt0) cc_final: 0.8204 (tm-30)
REVERT: D  420 ASP cc_start: 0.8898 (m-30) cc_final: 0.8576 (m-30)
REVERT: D  493 GLN cc_start: 0.8647 (tp40) cc_final: 0.8345 (tp40)
REVERT: D  498 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8242 (mp10)
REVERT: D  517 LEU cc_start: 0.8095 (tp) cc_final: 0.7891 (tt)
REVERT: A    6 GLU cc_start: 0.7783 (mp0) cc_final: 0.7408 (mp0)
REVERT: A   31 ASP cc_start: 0.8297 (t0) cc_final: 0.7808 (t0)
REVERT: A   45 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7724 (mtt180)
REVERT: A   73 ASP cc_start: 0.8085 (t0) cc_final: 0.7712 (t0)
REVERT: A   76 LYS cc_start: 0.8268 (mtpm) cc_final: 0.7943 (mtmm)
REVERT: C   32 TYR cc_start: 0.9164 (m-80) cc_final: 0.8925 (m-80)
REVERT: C   46 GLU cc_start: 0.8499 (pt0) cc_final: 0.8282 (pt0)
REVERT: C   90 ASP cc_start: 0.8267 (m-30) cc_final: 0.7832 (m-30)
  outliers start: 25
  outliers final: 21
  residues processed: 127
  average time/residue: 0.8049
  time to fit residues: 108.5888
Evaluate side-chains
  137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  418 ILE
Chi-restraints excluded: chain D residue  430 THR
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 47 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 60 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.097449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.082280 restraints weight = 8552.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.71
r_work: 0.3004 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5206  Z= 0.198
  Angle     :  0.593  12.188   7102  Z= 0.305
  Chirality :  0.044   0.157    747
  Planarity :  0.004   0.033    927
  Dihedral  :  5.386  38.879    770
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 22.22 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.31), residues: 648
  helix: -1.51 (1.05), residues: 24
  sheet:  0.65 (0.36), residues: 187
  loop : -0.52 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 436 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.010   0.001   PHE A  68 
 TYR   0.015   0.001   TYR B 369 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (  171)
  hydrogen bonds       : angle       6.39551 (  417)
  SS BOND              : bond        0.00319 (   10)
  SS BOND              : angle       1.05191 (   20)
  covalent geometry    : bond        0.00459 ( 5196)
  covalent geometry    : angle       0.59144 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  493 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7667 (tm-30)
REVERT: B  498 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8438 (mp10)
REVERT: D  340 GLU cc_start: 0.8762 (tt0) cc_final: 0.8186 (tm-30)
REVERT: D  493 GLN cc_start: 0.8635 (tp40) cc_final: 0.8340 (tp40)
REVERT: D  498 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8383 (mp10)
REVERT: A    6 GLU cc_start: 0.7942 (mp0) cc_final: 0.7574 (mp0)
REVERT: A   31 ASP cc_start: 0.8309 (t0) cc_final: 0.7792 (t0)
REVERT: A   45 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7750 (mtt180)
REVERT: A   73 ASP cc_start: 0.8147 (t0) cc_final: 0.7776 (t0)
REVERT: C   32 TYR cc_start: 0.9240 (m-80) cc_final: 0.8957 (m-80)
REVERT: C   46 GLU cc_start: 0.8664 (pt0) cc_final: 0.8454 (pt0)
REVERT: C   82 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7654 (tm-30)
REVERT: C   90 ASP cc_start: 0.8364 (m-30) cc_final: 0.7970 (m-30)
  outliers start: 27
  outliers final: 18
  residues processed: 126
  average time/residue: 0.7568
  time to fit residues: 101.4242
Evaluate side-chains
  132 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  430 THR
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   82 GLN
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 14 optimal weight:    0.0070
   chunk 24 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   overall best weight:    5.0006

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.098487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.083314 restraints weight = 8560.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.75
r_work: 0.3024 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5206  Z= 0.156
  Angle     :  0.579  11.759   7102  Z= 0.295
  Chirality :  0.043   0.145    747
  Planarity :  0.004   0.034    927
  Dihedral  :  5.137  39.809    770
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 22.99 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.31), residues: 648
  helix: -1.62 (1.05), residues: 24
  sheet:  0.63 (0.36), residues: 187
  loop : -0.55 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 436 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.007   0.001   PHE B 490 
 TYR   0.018   0.001   TYR C  95 
 ARG   0.002   0.000   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03206 (  171)
  hydrogen bonds       : angle       6.30014 (  417)
  SS BOND              : bond        0.00250 (   10)
  SS BOND              : angle       0.96932 (   20)
  covalent geometry    : bond        0.00361 ( 5196)
  covalent geometry    : angle       0.57789 ( 7082)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  493 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7640 (tm-30)
REVERT: B  498 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8329 (mp10)
REVERT: D  340 GLU cc_start: 0.8772 (tt0) cc_final: 0.8554 (tt0)
REVERT: D  420 ASP cc_start: 0.8918 (m-30) cc_final: 0.8585 (m-30)
REVERT: D  493 GLN cc_start: 0.8623 (tp40) cc_final: 0.8317 (tp40)
REVERT: D  498 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8308 (mp10)
REVERT: A    6 GLU cc_start: 0.7812 (mp0) cc_final: 0.7360 (mp0)
REVERT: A   31 ASP cc_start: 0.8289 (t0) cc_final: 0.7759 (t0)
REVERT: A   45 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7722 (mtt180)
REVERT: A   73 ASP cc_start: 0.8118 (t0) cc_final: 0.7749 (t0)
REVERT: A   76 LYS cc_start: 0.8301 (mtpm) cc_final: 0.7971 (mtmm)
REVERT: C   32 TYR cc_start: 0.9222 (m-80) cc_final: 0.8955 (m-80)
REVERT: C   46 GLU cc_start: 0.8612 (pt0) cc_final: 0.8400 (pt0)
REVERT: C   90 ASP cc_start: 0.8320 (m-30) cc_final: 0.7909 (m-30)
  outliers start: 24
  outliers final: 19
  residues processed: 124
  average time/residue: 0.7553
  time to fit residues: 99.4644
Evaluate side-chains
  132 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain D residue  333 THR
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 VAL
Chi-restraints excluded: chain D residue  430 THR
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  480 CYS
Chi-restraints excluded: chain D residue  498 GLN
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   45 ARG
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0170
   chunk 58 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    3.1824

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.099429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.084262 restraints weight = 8676.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.73
r_work: 0.3044 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.4236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5206  Z= 0.124
  Angle     :  0.571  12.340   7102  Z= 0.290
  Chirality :  0.042   0.137    747
  Planarity :  0.004   0.033    927
  Dihedral  :  4.996  40.619    770
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 23.18 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.31), residues: 648
  helix: -1.54 (1.07), residues: 24
  sheet:  0.86 (0.37), residues: 177
  loop : -0.53 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 436 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.009   0.001   PHE D 486 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.002   0.000   ARG B 408 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03005 (  171)
  hydrogen bonds       : angle       6.18510 (  417)
  SS BOND              : bond        0.00208 (   10)
  SS BOND              : angle       0.82496 (   20)
  covalent geometry    : bond        0.00283 ( 5196)
  covalent geometry    : angle       0.57005 ( 7082)

===============================================================================
Job complete
usr+sys time: 3862.26 seconds
wall clock time: 67 minutes 1.73 seconds (4021.73 seconds total)