Starting phenix.real_space_refine
on Wed Mar 12 07:32:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nll_12465/03_2025/7nll_12465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nll_12465/03_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_12465/03_2025/7nll_12465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nll_12465/03_2025/7nll_12465.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nll_12465/03_2025/7nll_12465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nll_12465/03_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-5624/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: 3.22, per 1000 atoms: 0.64
  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: 1.31
  Conformation dependent library (CDL) restraints added in 635.7 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: 0.65
  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: 1.40

  Time building geometry restraints manager: 1.50 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:             0.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.180
  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:16.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.810
-------------------------------------------------------------------------------
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   5196  Z= 0.176
  Angle     :  0.549   4.419   7082  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 

*********************** 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  : 0.574 
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: 0.9897
  time to fit residues: 169.0087
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  : 0.622 
-------------------------------------------------------------------------------
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:   20.0000
   overall best weight:   10.1992

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.095596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080448 restraints weight = 8738.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.74
r_work: 0.3022 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   5196  Z= 0.424
  Angle     :  0.652   7.606   7082  Z= 0.348
  Chirality :  0.050   0.302    747
  Planarity :  0.005   0.035    927
  Dihedral  :  6.811  43.896    770
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 12.84 %
    Favored  : 82.95 %
  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:  0.55 (0.31), residues: 648
  helix: -0.94 (0.79), residues: 37
  sheet:  1.30 (0.37), residues: 201
  loop :  0.07 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 116 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.017   0.002   PHE D 347 
 TYR   0.022   0.002   TYR B 495 
 ARG   0.004   0.001   ARG C  19 

*********************** 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
  151 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8770 (m-30) cc_final: 0.8467 (m-30)
REVERT: D  340 GLU cc_start: 0.8420 (tt0) cc_final: 0.8136 (tm-30)
REVERT: D  420 ASP cc_start: 0.8917 (m-30) cc_final: 0.8579 (m-30)
REVERT: D  493 GLN cc_start: 0.8537 (tp40) cc_final: 0.8219 (tp40)
REVERT: D  498 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8402 (mp10)
REVERT: A    6 GLU cc_start: 0.8070 (mp0) cc_final: 0.7675 (mp0)
REVERT: A   31 ASP cc_start: 0.8307 (t0) cc_final: 0.8067 (t0)
REVERT: A   46 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8195 (pt0)
REVERT: A   73 ASP cc_start: 0.8223 (t0) cc_final: 0.8001 (t0)
REVERT: A  108 THR cc_start: 0.9431 (m) cc_final: 0.9122 (p)
REVERT: A  128 THR cc_start: 0.8806 (m) cc_final: 0.8563 (p)
REVERT: C   32 TYR cc_start: 0.9218 (m-80) cc_final: 0.8890 (m-80)
REVERT: C   84 ASN cc_start: 0.8743 (m110) cc_final: 0.8538 (m-40)
REVERT: C   90 ASP cc_start: 0.8137 (m-30) cc_final: 0.7834 (m-30)
REVERT: C   95 TYR cc_start: 0.9363 (m-80) cc_final: 0.8913 (m-80)
  outliers start: 22
  outliers final: 5
  residues processed: 136
  average time/residue: 0.8011
  time to fit residues: 115.5011
Evaluate side-chains
  118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  500 THR
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 C residue   57 SER
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:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 409 GLN
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 = 0.3428 r_free = 0.3428 target = 0.097008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.081887 restraints weight = 8630.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.73
r_work: 0.3045 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   5196  Z= 0.231
  Angle     :  0.551   8.193   7082  Z= 0.292
  Chirality :  0.044   0.155    747
  Planarity :  0.004   0.035    927
  Dihedral  :  5.704  41.487    770
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.01 %
    Favored  : 78.54 %
  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:  0.29 (0.31), residues: 648
  helix: -1.24 (0.77), residues: 37
  sheet:  1.36 (0.36), residues: 187
  loop : -0.19 (0.28), residues: 424

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   0.008   0.001   PHE A  68 
 TYR   0.017   0.001   TYR B 369 
 ARG   0.008   0.001   ARG B 403 

*********************** 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
  137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: B  418 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8074 (mm)
REVERT: B  420 ASP cc_start: 0.8821 (m-30) cc_final: 0.8559 (m-30)
REVERT: B  493 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7708 (tm-30)
REVERT: D  340 GLU cc_start: 0.8495 (tt0) cc_final: 0.8174 (tm-30)
REVERT: D  420 ASP cc_start: 0.8944 (m-30) cc_final: 0.8648 (m-30)
REVERT: D  493 GLN cc_start: 0.8606 (tp40) cc_final: 0.8287 (tp40)
REVERT: D  498 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8345 (mp10)
REVERT: A    6 GLU cc_start: 0.8152 (mp0) cc_final: 0.7606 (mp0)
REVERT: A   46 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8260 (pt0)
REVERT: A   73 ASP cc_start: 0.8186 (t0) cc_final: 0.7927 (t0)
REVERT: A  103 SER cc_start: 0.8680 (m) cc_final: 0.8429 (p)
REVERT: C   32 TYR cc_start: 0.9197 (m-80) cc_final: 0.8883 (m-80)
REVERT: C   46 GLU cc_start: 0.8589 (pt0) cc_final: 0.8376 (pt0)
REVERT: C   84 ASN cc_start: 0.8717 (m110) cc_final: 0.8467 (m-40)
REVERT: C   90 ASP cc_start: 0.8171 (m-30) cc_final: 0.7864 (m-30)
REVERT: C   95 TYR cc_start: 0.9360 (m-80) cc_final: 0.9066 (m-80)
  outliers start: 18
  outliers final: 9
  residues processed: 128
  average time/residue: 0.8056
  time to fit residues: 109.0585
Evaluate side-chains
  126 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
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 D residue  333 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   46 GLU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  112 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:   20.0000
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.098935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.083519 restraints weight = 8787.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.83
r_work: 0.3020 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   5196  Z= 0.255
  Angle     :  0.548   9.126   7082  Z= 0.289
  Chirality :  0.044   0.160    747
  Planarity :  0.004   0.033    927
  Dihedral  :  5.556  40.498    770
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 17.05 %
    Favored  : 77.39 %
  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:  0.07 (0.31), residues: 648
  helix: -1.37 (0.86), residues: 31
  sheet:  1.09 (0.36), residues: 187
  loop : -0.31 (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   0.010   0.001   PHE A  68 
 TYR   0.017   0.001   TYR B 369 
 ARG   0.004   0.000   ARG B 403 

*********************** 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
  145 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8816 (m-30) cc_final: 0.8603 (m-30)
REVERT: B  493 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7636 (tm-30)
REVERT: D  340 GLU cc_start: 0.8580 (tt0) cc_final: 0.8154 (tm-30)
REVERT: D  420 ASP cc_start: 0.8945 (m-30) cc_final: 0.8652 (m-30)
REVERT: D  493 GLN cc_start: 0.8603 (tp40) cc_final: 0.8320 (tp40)
REVERT: D  498 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8387 (mp10)
REVERT: A    6 GLU cc_start: 0.8299 (mp0) cc_final: 0.7739 (mp0)
REVERT: A   46 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8367 (pt0)
REVERT: A   73 ASP cc_start: 0.8198 (t0) cc_final: 0.7930 (t0)
REVERT: A   76 LYS cc_start: 0.8193 (mtpm) cc_final: 0.7932 (mtmm)
REVERT: A  103 SER cc_start: 0.8886 (m) cc_final: 0.8670 (p)
REVERT: C   32 TYR cc_start: 0.9219 (m-80) cc_final: 0.8930 (m-80)
REVERT: C   84 ASN cc_start: 0.8684 (m110) cc_final: 0.8459 (m-40)
REVERT: C   90 ASP cc_start: 0.8210 (m-30) cc_final: 0.7866 (m-30)
REVERT: C   95 TYR cc_start: 0.9374 (m-80) cc_final: 0.8974 (m-80)
  outliers start: 29
  outliers final: 19
  residues processed: 132
  average time/residue: 0.7948
  time to fit residues: 111.1416
Evaluate side-chains
  133 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   69 THR
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:   20.0000
   chunk 8 optimal weight:   20.0000
   chunk 13 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0980
   chunk 29 optimal weight:    6.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    4.5386

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.099937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.084537 restraints weight = 8594.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.77
r_work: 0.3046 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5196  Z= 0.212
  Angle     :  0.535  10.274   7082  Z= 0.279
  Chirality :  0.043   0.148    747
  Planarity :  0.004   0.033    927
  Dihedral  :  5.281  40.738    770
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 19.35 %
    Favored  : 75.29 %
  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: -0.01 (0.31), residues: 648
  helix: -1.47 (0.85), residues: 31
  sheet:  0.98 (0.36), residues: 187
  loop : -0.33 (0.28), residues: 430

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 A  68 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.003   0.000   ARG B 403 

*********************** 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: 28
    poor density    : 122
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  493 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7691 (tm-30)
REVERT: B  498 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8435 (mp10)
REVERT: D  340 GLU cc_start: 0.8670 (tt0) cc_final: 0.8201 (tm-30)
REVERT: D  420 ASP cc_start: 0.8923 (m-30) cc_final: 0.8613 (m-30)
REVERT: D  493 GLN cc_start: 0.8610 (tp40) cc_final: 0.8278 (tp40)
REVERT: D  498 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8327 (mp10)
REVERT: A    6 GLU cc_start: 0.8346 (mp0) cc_final: 0.7807 (mp0)
REVERT: A   46 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8383 (pt0)
REVERT: C   32 TYR cc_start: 0.9198 (m-80) cc_final: 0.8922 (m-80)
REVERT: C   84 ASN cc_start: 0.8724 (m110) cc_final: 0.8499 (m-40)
REVERT: C   90 ASP cc_start: 0.8265 (m-30) cc_final: 0.7924 (m-30)
REVERT: C   95 TYR cc_start: 0.9359 (m-80) cc_final: 0.9006 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 135
  average time/residue: 0.7888
  time to fit residues: 113.0578
Evaluate side-chains
  142 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
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  492 LEU
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  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   69 THR
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  129 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    0.0370
   chunk 38 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    5.8066

-------------------------------------------------------------------------------
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 = 0.3402 r_free = 0.3402 target = 0.098706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.083398 restraints weight = 8636.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.76
r_work: 0.3023 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   5196  Z= 0.256
  Angle     :  0.553  11.501   7082  Z= 0.287
  Chirality :  0.043   0.155    747
  Planarity :  0.004   0.035    927
  Dihedral  :  5.354  39.960    770
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 18.58 %
    Favored  : 74.71 %
  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: -0.13 (0.31), residues: 648
  helix: -1.60 (0.84), residues: 31
  sheet:  0.85 (0.36), residues: 187
  loop : -0.38 (0.28), residues: 430

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   0.009   0.001   PHE A  68 
 TYR   0.015   0.001   TYR B 369 
 ARG   0.002   0.000   ARG D 457 

*********************** 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
  149 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  493 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7607 (tm-30)
REVERT: B  498 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8535 (mp10)
REVERT: D  340 GLU cc_start: 0.8677 (tt0) cc_final: 0.8187 (tm-30)
REVERT: D  420 ASP cc_start: 0.8899 (m-30) cc_final: 0.8578 (m-30)
REVERT: D  493 GLN cc_start: 0.8615 (tp40) cc_final: 0.8288 (tp40)
REVERT: D  498 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8348 (mp10)
REVERT: D  517 LEU cc_start: 0.8145 (tp) cc_final: 0.7933 (tt)
REVERT: A    6 GLU cc_start: 0.8384 (mp0) cc_final: 0.7849 (mp0)
REVERT: A   31 ASP cc_start: 0.8401 (t0) cc_final: 0.8065 (t0)
REVERT: A   45 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7758 (mtt180)
REVERT: A   46 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8396 (pt0)
REVERT: C   32 TYR cc_start: 0.9202 (m-80) cc_final: 0.8894 (m-80)
REVERT: C   46 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8281 (pt0)
REVERT: C   84 ASN cc_start: 0.8671 (m110) cc_final: 0.8461 (m-40)
REVERT: C   90 ASP cc_start: 0.8272 (m-30) cc_final: 0.7939 (m-30)
REVERT: C   95 TYR cc_start: 0.9352 (m-80) cc_final: 0.8937 (m-80)
  outliers start: 35
  outliers final: 22
  residues processed: 134
  average time/residue: 0.8272
  time to fit residues: 117.1882
Evaluate side-chains
  139 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  417 LYS
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  492 LEU
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   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   69 THR
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   46 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 28 optimal weight:    8.9990
   chunk 42 optimal weight:    0.3980
   chunk 3 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0770
   chunk 55 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    4.8944

-------------------------------------------------------------------------------
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**
A  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.099153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.083790 restraints weight = 8549.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.74
r_work: 0.3029 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5196  Z= 0.227
  Angle     :  0.574  14.565   7082  Z= 0.289
  Chirality :  0.043   0.148    747
  Planarity :  0.004   0.035    927
  Dihedral  :  5.220  40.269    770
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 21.07 %
    Favored  : 73.18 %
  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: -0.17 (0.31), residues: 648
  helix: -1.62 (0.84), residues: 31
  sheet:  0.79 (0.36), residues: 187
  loop : -0.39 (0.28), residues: 430

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 A  68 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.002   0.000   ARG D 457 

*********************** 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
  143 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  408 ARG cc_start: 0.9127 (tmm160) cc_final: 0.8824 (ptm-80)
REVERT: B  493 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7635 (tm-30)
REVERT: B  498 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8476 (mp10)
REVERT: D  340 GLU cc_start: 0.8703 (tt0) cc_final: 0.8206 (tm-30)
REVERT: D  420 ASP cc_start: 0.8902 (m-30) cc_final: 0.8595 (m-30)
REVERT: D  493 GLN cc_start: 0.8614 (tp40) cc_final: 0.8311 (tp40)
REVERT: D  498 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8342 (mp10)
REVERT: D  517 LEU cc_start: 0.8170 (tp) cc_final: 0.7970 (tt)
REVERT: A    6 GLU cc_start: 0.7866 (mp0) cc_final: 0.7489 (mp0)
REVERT: A   31 ASP cc_start: 0.8344 (t0) cc_final: 0.7912 (t0)
REVERT: A   45 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7763 (mtt180)
REVERT: A   46 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8383 (pt0)
REVERT: A   76 LYS cc_start: 0.8289 (mtmm) cc_final: 0.8023 (ptpp)
REVERT: C   32 TYR cc_start: 0.9226 (m-80) cc_final: 0.8920 (m-80)
REVERT: C   46 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8265 (pt0)
REVERT: C   90 ASP cc_start: 0.8302 (m-30) cc_final: 0.7931 (m-30)
REVERT: C   95 TYR cc_start: 0.9356 (m-80) cc_final: 0.8965 (m-80)
  outliers start: 30
  outliers final: 21
  residues processed: 131
  average time/residue: 0.8110
  time to fit residues: 112.7018
Evaluate side-chains
  137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  417 LYS
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  492 LEU
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   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   69 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   46 GLU
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:   10.0000
   chunk 35 optimal weight:    0.0670
   chunk 4 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   chunk 60 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   overall best weight:    5.4126

-------------------------------------------------------------------------------
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**
A  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.098702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.083281 restraints weight = 8701.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.78
r_work: 0.3018 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5196  Z= 0.245
  Angle     :  0.565  10.854   7082  Z= 0.292
  Chirality :  0.043   0.149    747
  Planarity :  0.004   0.034    927
  Dihedral  :  5.255  39.858    770
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.46 %
    Favored  : 73.56 %
  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: -1.54 (1.02), residues: 24
  sheet:  0.72 (0.36), residues: 187
  loop : -0.45 (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 A  68 
 TYR   0.015   0.001   TYR B 369 
 ARG   0.002   0.000   ARG D 457 

*********************** 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: 26
    poor density    : 111
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  408 ARG cc_start: 0.9104 (tmm160) cc_final: 0.8798 (ptm-80)
REVERT: B  493 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7643 (tm-30)
REVERT: B  498 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8473 (mp10)
REVERT: D  340 GLU cc_start: 0.8739 (tt0) cc_final: 0.8501 (tt0)
REVERT: D  420 ASP cc_start: 0.8835 (m-30) cc_final: 0.8530 (m-30)
REVERT: D  493 GLN cc_start: 0.8613 (tp40) cc_final: 0.8307 (tp40)
REVERT: D  498 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8347 (mp10)
REVERT: A    6 GLU cc_start: 0.7875 (mp0) cc_final: 0.7494 (mp0)
REVERT: A   31 ASP cc_start: 0.8298 (t0) cc_final: 0.7824 (t0)
REVERT: A   45 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7772 (mtt180)
REVERT: A   46 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8411 (pt0)
REVERT: C   32 TYR cc_start: 0.9237 (m-80) cc_final: 0.8985 (m-80)
REVERT: C   46 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8275 (pt0)
REVERT: C   82 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7645 (tm-30)
REVERT: C   90 ASP cc_start: 0.8292 (m-30) cc_final: 0.7922 (m-30)
  outliers start: 26
  outliers final: 19
  residues processed: 128
  average time/residue: 0.7820
  time to fit residues: 106.2681
Evaluate side-chains
  136 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  417 LYS
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  492 LEU
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  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   45 ARG
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   46 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 47 optimal weight:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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**
A  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.098170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.083013 restraints weight = 8544.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.72
r_work: 0.3017 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5196  Z= 0.252
  Angle     :  0.571  11.467   7082  Z= 0.295
  Chirality :  0.043   0.149    747
  Planarity :  0.004   0.034    927
  Dihedral  :  5.245  39.643    770
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 21.65 %
    Favored  : 73.18 %
  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: -0.28 (0.31), residues: 648
  helix: -1.57 (1.01), residues: 24
  sheet:  0.68 (0.36), residues: 187
  loop : -0.49 (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 A  68 
 TYR   0.015   0.001   TYR B 369 
 ARG   0.002   0.000   ARG D 457 

*********************** 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
  138 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  408 ARG cc_start: 0.9059 (tmm160) cc_final: 0.8822 (ptm-80)
REVERT: B  493 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7641 (tm-30)
REVERT: B  498 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8466 (mp10)
REVERT: D  340 GLU cc_start: 0.8734 (tt0) cc_final: 0.8524 (tt0)
REVERT: D  405 ASP cc_start: 0.8887 (m-30) cc_final: 0.8685 (m-30)
REVERT: D  420 ASP cc_start: 0.8833 (m-30) cc_final: 0.8522 (m-30)
REVERT: D  493 GLN cc_start: 0.8610 (tp40) cc_final: 0.8312 (tp40)
REVERT: D  498 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8327 (mp10)
REVERT: A    6 GLU cc_start: 0.7843 (mp0) cc_final: 0.7452 (mp0)
REVERT: A   31 ASP cc_start: 0.8286 (t0) cc_final: 0.7789 (t0)
REVERT: A   45 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7760 (mtt180)
REVERT: A   46 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8397 (pt0)
REVERT: C   32 TYR cc_start: 0.9232 (m-80) cc_final: 0.8966 (m-80)
REVERT: C   46 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8266 (pt0)
REVERT: C   82 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7673 (tm-30)
REVERT: C   90 ASP cc_start: 0.8302 (m-30) cc_final: 0.7930 (m-30)
REVERT: C   95 TYR cc_start: 0.9341 (m-80) cc_final: 0.9104 (m-80)
  outliers start: 27
  outliers final: 20
  residues processed: 127
  average time/residue: 0.7451
  time to fit residues: 100.6178
Evaluate side-chains
  138 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  417 LYS
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  492 LEU
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  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   46 GLU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   46 GLU
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:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 11 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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**
A  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.098704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.083431 restraints weight = 8603.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.72
r_work: 0.3023 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5196  Z= 0.227
  Angle     :  0.563  10.474   7082  Z= 0.292
  Chirality :  0.043   0.145    747
  Planarity :  0.004   0.033    927
  Dihedral  :  5.181  39.970    770
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.65 %
    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: -0.28 (0.31), residues: 648
  helix: -1.56 (1.02), residues: 24
  sheet:  0.63 (0.36), residues: 187
  loop : -0.47 (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 A  68 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.002   0.000   ARG D 457 

********************** 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
  139 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  408 ARG cc_start: 0.9007 (tmm160) cc_final: 0.8794 (ptm-80)
REVERT: B  493 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7662 (tm-30)
REVERT: D  340 GLU cc_start: 0.8778 (tt0) cc_final: 0.8565 (tt0)
REVERT: D  409 GLN cc_start: 0.8684 (tt0) cc_final: 0.8422 (tt0)
REVERT: D  420 ASP cc_start: 0.8830 (m-30) cc_final: 0.8525 (m-30)
REVERT: D  493 GLN cc_start: 0.8608 (tp40) cc_final: 0.8321 (tp40)
REVERT: D  498 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8313 (mp10)
REVERT: A    6 GLU cc_start: 0.7780 (mp0) cc_final: 0.7378 (mp0)
REVERT: A   31 ASP cc_start: 0.8226 (t0) cc_final: 0.7689 (t0)
REVERT: A   45 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7753 (mtt180)
REVERT: A   46 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (pt0)
REVERT: C   32 TYR cc_start: 0.9246 (m-80) cc_final: 0.8988 (m-80)
REVERT: C   46 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8256 (pt0)
REVERT: C   82 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7619 (tm-30)
REVERT: C   90 ASP cc_start: 0.8316 (m-30) cc_final: 0.7944 (m-30)
REVERT: C   95 TYR cc_start: 0.9353 (m-80) cc_final: 0.9113 (m-80)
  outliers start: 26
  outliers final: 21
  residues processed: 129
  average time/residue: 0.7858
  time to fit residues: 107.6145
Evaluate side-chains
  138 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  417 LYS
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  492 LEU
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain D residue  333 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   46 GLU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   46 GLU
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  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:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 12 optimal weight:    9.9990
   chunk 55 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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**
A  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.098988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.083783 restraints weight = 8705.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.74
r_work: 0.3027 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5196  Z= 0.216
  Angle     :  0.554  10.133   7082  Z= 0.288
  Chirality :  0.043   0.142    747
  Planarity :  0.004   0.033    927
  Dihedral  :  5.110  40.098    770
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  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: -0.26 (0.31), residues: 648
  helix: -1.52 (1.03), residues: 24
  sheet:  0.78 (0.37), residues: 177
  loop : -0.49 (0.27), residues: 447

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 A  68 
 TYR   0.016   0.001   TYR B 369 
 ARG   0.002   0.000   ARG D 457 

===============================================================================
Job complete
usr+sys time: 3847.02 seconds
wall clock time: 66 minutes 10.46 seconds (3970.46 seconds total)