Starting phenix.real_space_refine
on Wed Mar  4 08:33:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qpb_4612/03_2026/6qpb_4612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qpb_4612/03_2026/6qpb_4612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qpb_4612/03_2026/6qpb_4612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qpb_4612/03_2026/6qpb_4612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qpb_4612/03_2026/6qpb_4612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qpb_4612/03_2026/6qpb_4612.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      80      5.16       5
     C    8000      2.51       5
     N    1938      2.21       5
     O    2134      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12154
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 731, 6039
          Classifications: {'peptide': 731}
          Link IDs: {'PTRANS': 34, 'TRANS': 696}
          Chain breaks: 6
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 38
          Unusual residues: {'P1O': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.39, per 1000 atoms: 0.44
  Number of scatterers: 12154
  At special positions: 0
  Unit cell: (88.044, 114.356, 116.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      80     16.00
     P       2     15.00
     O    2134      8.00
     N    1938      7.00
     C    8000      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 807 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 338 " - pdb=" SG  CYS B 365 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 349 " - pdb=" SG  CYS B 807 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 601 " 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: 0.82
  Conformation dependent library (CDL) restraints added in 564.0 milliseconds
  

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2788

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      63.2% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 109
    Processing helix  chain 'A' and resid 131 through 143
    Processing helix  chain 'A' and resid 205 through 220
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 264 through 273
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.633A  pdb=" N   ILE A 279 " --> pdb=" O   PRO A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 327
      removed outlier: 7.497A  pdb=" N   GLU A 294 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 9.456A  pdb=" N   LYS A 295 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ILE A 296 " --> pdb=" O   TYR A 292 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   TYR A 299 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 338
      removed outlier: 3.980A  pdb=" N   LYS A 335 " --> pdb=" O   CYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.523A  pdb=" N   GLN A 345 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 375
      removed outlier: 4.711A  pdb=" N   ILE A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE A 374 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 408
      removed outlier: 3.805A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 427
    Processing helix  chain 'A' and resid 448 through 489
    Processing helix  chain 'A' and resid 504 through 539
    Processing helix  chain 'A' and resid 543 through 573
      removed outlier: 5.111A  pdb=" N   SER A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   CYS A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 624
    Processing helix  chain 'A' and resid 625 through 632
      removed outlier: 3.538A  pdb=" N   TRP A 629 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 664 through 680
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 3.806A  pdb=" N   ARG A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 747
      removed outlier: 4.007A  pdb=" N   VAL A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 760
      removed outlier: 3.552A  pdb=" N   PHE A 760 " --> pdb=" O   TYR A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 781
      removed outlier: 3.521A  pdb=" N   ASN A 779 " --> pdb=" O   GLY A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 857
    Processing helix  chain 'A' and resid 861 through 877
      removed outlier: 3.576A  pdb=" N   LYS A 877 " --> pdb=" O   TYR A 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 109
    Processing helix  chain 'B' and resid 131 through 143
    Processing helix  chain 'B' and resid 205 through 220
    Processing helix  chain 'B' and resid 233 through 240
    Processing helix  chain 'B' and resid 264 through 273
    Processing helix  chain 'B' and resid 275 through 279
      removed outlier: 3.633A  pdb=" N   ILE B 279 " --> pdb=" O   PRO B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 327
      removed outlier: 7.496A  pdb=" N   GLU B 294 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
      removed outlier: 9.456A  pdb=" N   LYS B 295 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ILE B 296 " --> pdb=" O   TYR B 292 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE B 298 " --> pdb=" O   GLU B 294 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR B 299 " --> pdb=" O   LYS B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 338
      removed outlier: 3.980A  pdb=" N   LYS B 335 " --> pdb=" O   CYS B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 346
      removed outlier: 3.523A  pdb=" N   GLN B 345 " --> pdb=" O   ILE B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 375
      removed outlier: 4.712A  pdb=" N   ILE B 373 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B 374 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 408
      removed outlier: 3.806A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 427
    Processing helix  chain 'B' and resid 448 through 489
    Processing helix  chain 'B' and resid 504 through 539
    Processing helix  chain 'B' and resid 543 through 573
      removed outlier: 5.111A  pdb=" N   SER B 566 " --> pdb=" O   ASN B 562 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   CYS B 567 " --> pdb=" O   TYR B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 624
    Processing helix  chain 'B' and resid 625 through 632
      removed outlier: 3.538A  pdb=" N   TRP B 629 " --> pdb=" O   VAL B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 655
    Processing helix  chain 'B' and resid 664 through 680
    Processing helix  chain 'B' and resid 687 through 709
      removed outlier: 3.807A  pdb=" N   ARG B 701 " --> pdb=" O   ILE B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 747
      removed outlier: 4.006A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 760
      removed outlier: 3.552A  pdb=" N   PHE B 760 " --> pdb=" O   TYR B 756 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 781
      removed outlier: 3.521A  pdb=" N   ASN B 779 " --> pdb=" O   GLY B 775 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 857
    Processing helix  chain 'B' and resid 861 through 877
      removed outlier: 3.577A  pdb=" N   LYS B 877 " --> pdb=" O   TYR B 873 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 78
    Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 785
    Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 78
    Processing sheet with id=AA4, first strand: chain 'B' and resid 782 through 785

    720 hydrogen bonds defined for protein.
    2130 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: 1.79

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 2150
        1.33 -     1.46: 4100
        1.46 -     1.59: 6114
        1.59 -     1.72: 2
        1.72 -     1.85: 122
  Bond restraints: 12488
  Sorted by residual:
  bond pdb=" O3  P1O B1001 "
       pdb=" P1  P1O B1001 "
    ideal  model  delta    sigma   weight residual
    1.648  1.777 -0.129 2.00e-02 2.50e+03 4.17e+01
  bond pdb=" O3  P1O A1001 "
       pdb=" P1  P1O A1001 "
    ideal  model  delta    sigma   weight residual
    1.648  1.776 -0.128 2.00e-02 2.50e+03 4.13e+01
  bond pdb=" C19 P1O A1001 "
       pdb=" C20 P1O A1001 "
    ideal  model  delta    sigma   weight residual
    1.502  1.579 -0.077 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" C19 P1O B1001 "
       pdb=" C20 P1O B1001 "
    ideal  model  delta    sigma   weight residual
    1.502  1.578 -0.076 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" C7  P1O B1001 "
       pdb=" C8  P1O B1001 "
    ideal  model  delta    sigma   weight residual
    1.515  1.588 -0.073 2.00e-02 2.50e+03 1.35e+01
  ... (remaining 12483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 16388
        2.15 -     4.30: 452
        4.30 -     6.45: 60
        6.45 -     8.60: 18
        8.60 -    10.75: 10
  Bond angle restraints: 16928
  Sorted by residual:
  angle pdb=" N   PRO B 763 "
        pdb=" CA  PRO B 763 "
        pdb=" C   PRO B 763 "
      ideal   model   delta    sigma   weight residual
     110.70  117.03   -6.33 1.22e+00 6.72e-01 2.69e+01
  angle pdb=" N   PRO A 763 "
        pdb=" CA  PRO A 763 "
        pdb=" C   PRO A 763 "
      ideal   model   delta    sigma   weight residual
     110.70  116.99   -6.29 1.22e+00 6.72e-01 2.66e+01
  angle pdb=" C   GLY A 589 "
        pdb=" N   LYS A 590 "
        pdb=" CA  LYS A 590 "
      ideal   model   delta    sigma   weight residual
     121.54  130.89   -9.35 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   GLY B 589 "
        pdb=" N   LYS B 590 "
        pdb=" CA  LYS B 590 "
      ideal   model   delta    sigma   weight residual
     121.54  130.87   -9.33 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C   TRP A 408 "
        pdb=" N   ASP A 409 "
        pdb=" CA  ASP A 409 "
      ideal   model   delta    sigma   weight residual
     122.46  128.69   -6.23 1.41e+00 5.03e-01 1.95e+01
  ... (remaining 16923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.60: 6848
       22.60 -    45.21: 468
       45.21 -    67.81: 50
       67.81 -    90.41: 12
       90.41 -   113.02: 2
  Dihedral angle restraints: 7380
    sinusoidal: 3048
      harmonic: 4332
  Sorted by residual:
  dihedral pdb=" CB  CYS A 338 "
           pdb=" SG  CYS A 338 "
           pdb=" SG  CYS A 365 "
           pdb=" CB  CYS A 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    3.54   89.46     1      1.00e+01 1.00e-02 9.51e+01
  dihedral pdb=" CB  CYS B 338 "
           pdb=" SG  CYS B 338 "
           pdb=" SG  CYS B 365 "
           pdb=" CB  CYS B 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    3.56   89.44     1      1.00e+01 1.00e-02 9.51e+01
  dihedral pdb=" CB  CYS A 596 "
           pdb=" SG  CYS A 596 "
           pdb=" SG  CYS A 601 "
           pdb=" CB  CYS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.79  -61.79     1      1.00e+01 1.00e-02 5.06e+01
  ... (remaining 7377 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.009: 1832
       1.009 -    2.018: 0
       2.018 -    3.026: 0
       3.026 -    4.035: 0
       4.035 -    5.044: 2
  Chirality restraints: 1834
  Sorted by residual:
  chirality pdb=" C7  P1O B1001 "
            pdb=" C6  P1O B1001 "
            pdb=" C8  P1O B1001 "
            pdb=" O7  P1O B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.35    2.69   -5.04 2.00e-01 2.50e+01 6.36e+02
  chirality pdb=" C7  P1O A1001 "
            pdb=" C6  P1O A1001 "
            pdb=" C8  P1O A1001 "
            pdb=" O7  P1O A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.35    2.69   -5.04 2.00e-01 2.50e+01 6.36e+02
  chirality pdb=" CB  ILE A 197 "
            pdb=" CA  ILE A 197 "
            pdb=" CG1 ILE A 197 "
            pdb=" CG2 ILE A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.29 2.00e-01 2.50e+01 2.07e+00
  ... (remaining 1831 not shown)

  Planarity restraints: 2100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 763 "    0.056 5.00e-02 4.00e+02   8.45e-02 1.14e+01
        pdb=" N   PRO A 764 "   -0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 764 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 764 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 763 "   -0.056 5.00e-02 4.00e+02   8.44e-02 1.14e+01
        pdb=" N   PRO B 764 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO B 764 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 764 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 762 "    0.052 5.00e-02 4.00e+02   7.71e-02 9.51e+00
        pdb=" N   PRO B 763 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B 763 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 763 "    0.041 5.00e-02 4.00e+02
  ... (remaining 2097 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 146
        2.65 -     3.21: 10548
        3.21 -     3.77: 19389
        3.77 -     4.34: 25524
        4.34 -     4.90: 42313
  Nonbonded interactions: 97920
  Sorted by model distance:
  nonbonded pdb=" O   THR A 364 "
            pdb=" OG  SER A 367 "
     model   vdw
     2.084 3.040
  nonbonded pdb=" O   THR B 364 "
            pdb=" OG  SER B 367 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   ASP A  46 "
            pdb=" OG  SER A 103 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ASP B  46 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ILE A 744 "
            pdb=" OG  SER A 748 "
     model   vdw
     2.339 3.040
  ... (remaining 97915 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.360
  Find NCS groups from input model:        0.090
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.129  12494  Z= 0.292
  Angle     :  0.879  10.753  16940  Z= 0.488
  Chirality :  0.174   5.044   1834
  Planarity :  0.009   0.085   2100
  Dihedral  : 14.703 113.018   4574
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.17), residues: 1434
  helix: -1.45 (0.13), residues: 854
  sheet: -1.18 (0.55), residues: 64
  loop : -2.58 (0.22), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.020   0.002   TYR A 222 
 PHE   0.028   0.002   PHE B  73 
 TRP   0.012   0.002   TRP A 619 
 HIS   0.007   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 (12488)
  covalent geometry    : angle       0.87614 (16928)
  SS BOND              : bond        0.01003 (    6)
  SS BOND              : angle       2.88560 (   12)
  hydrogen bonds       : bond        0.12221 (  720)
  hydrogen bonds       : angle       6.10700 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  381 ILE cc_start: 0.8655 (mt) cc_final: 0.8301 (mm)
REVERT: A  384 VAL cc_start: 0.9064 (t) cc_final: 0.8829 (m)
REVERT: A  522 MET cc_start: 0.7545 (mmm) cc_final: 0.7083 (mmm)
REVERT: A  811 ASP cc_start: 0.7920 (t0) cc_final: 0.7532 (m-30)
REVERT: A  851 PHE cc_start: 0.7787 (m-80) cc_final: 0.7506 (m-10)
REVERT: B   60 ASP cc_start: 0.7902 (p0) cc_final: 0.7643 (p0)
REVERT: B  381 ILE cc_start: 0.8629 (mt) cc_final: 0.8300 (mm)
REVERT: B  384 VAL cc_start: 0.9107 (t) cc_final: 0.8880 (m)
REVERT: B  522 MET cc_start: 0.7531 (mmm) cc_final: 0.7252 (mmm)
REVERT: B  706 LYS cc_start: 0.8924 (mttt) cc_final: 0.8702 (mtmt)
REVERT: B  810 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7605 (ttt90)
REVERT: B  811 ASP cc_start: 0.7862 (t0) cc_final: 0.7492 (m-30)
REVERT: B  851 PHE cc_start: 0.7863 (m-80) cc_final: 0.7535 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1034
  time to fit residues: 31.0433
Evaluate side-chains
  136 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    0.0170
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.4024

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN
A 418 GLN
A 623 GLN
A 796 ASN
B 401 GLN
B 418 GLN
B 623 GLN
B 674 GLN
B 796 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.136300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.109230 restraints weight = 17285.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.109161 restraints weight = 13418.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110187 restraints weight = 11378.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110664 restraints weight = 9378.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110968 restraints weight = 8742.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12494  Z= 0.151
  Angle     :  0.606  10.226  16940  Z= 0.323
  Chirality :  0.042   0.213   1834
  Planarity :  0.006   0.072   2100
  Dihedral  :  8.581 149.118   1676
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.85 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.20), residues: 1434
  helix:  0.47 (0.16), residues: 878
  sheet: -0.71 (0.61), residues: 64
  loop : -1.82 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 266 
 TYR   0.020   0.001   TYR B 855 
 PHE   0.017   0.001   PHE B 558 
 TRP   0.011   0.001   TRP A 619 
 HIS   0.006   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (12488)
  covalent geometry    : angle       0.59283 (16928)
  SS BOND              : bond        0.00300 (    6)
  SS BOND              : angle       4.74050 (   12)
  hydrogen bonds       : bond        0.05385 (  720)
  hydrogen bonds       : angle       4.60342 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   47 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6475 (t80)
REVERT: A  759 SER cc_start: 0.9036 (m) cc_final: 0.8768 (p)
REVERT: A  811 ASP cc_start: 0.8052 (t0) cc_final: 0.7554 (m-30)
REVERT: A  851 PHE cc_start: 0.7761 (m-80) cc_final: 0.7532 (m-10)
REVERT: B  354 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6986 (tpt-90)
REVERT: B  524 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8702 (mp)
REVERT: B  811 ASP cc_start: 0.8021 (t0) cc_final: 0.7527 (m-30)
REVERT: B  851 PHE cc_start: 0.7842 (m-80) cc_final: 0.7591 (m-10)
  outliers start: 22
  outliers final: 9
  residues processed: 177
  average time/residue: 0.0986
  time to fit residues: 25.9386
Evaluate side-chains
  151 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 PHE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue   47 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  734 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 140 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 132 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 129 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 696 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.130077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.104228 restraints weight = 17473.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.104146 restraints weight = 13770.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.104782 restraints weight = 11493.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.104998 restraints weight = 10217.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.105259 restraints weight = 9669.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  12494  Z= 0.212
  Angle     :  0.633   9.466  16940  Z= 0.335
  Chirality :  0.044   0.192   1834
  Planarity :  0.006   0.067   2100
  Dihedral  :  8.239 135.997   1676
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.73 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.21), residues: 1434
  helix:  1.04 (0.16), residues: 862
  sheet: -0.74 (0.64), residues: 64
  loop : -1.53 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  70 
 TYR   0.017   0.002   TYR A 580 
 PHE   0.015   0.002   PHE A 558 
 TRP   0.011   0.001   TRP A 619 
 HIS   0.007   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (12488)
  covalent geometry    : angle       0.62532 (16928)
  SS BOND              : bond        0.00699 (    6)
  SS BOND              : angle       3.85832 (   12)
  hydrogen bonds       : bond        0.05661 (  720)
  hydrogen bonds       : angle       4.58018 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6961 (t80)
REVERT: A  384 VAL cc_start: 0.9041 (t) cc_final: 0.8821 (m)
REVERT: A  524 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8693 (mp)
REVERT: B  108 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7325 (t-90)
REVERT: B  851 PHE cc_start: 0.7854 (m-80) cc_final: 0.7628 (m-10)
  outliers start: 33
  outliers final: 20
  residues processed: 162
  average time/residue: 0.0998
  time to fit residues: 23.9413
Evaluate side-chains
  148 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 PHE
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  330 ASN
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain B residue   47 PHE
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  667 GLU
Chi-restraints excluded: chain B residue  734 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 141 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.133203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.105962 restraints weight = 16992.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.106117 restraints weight = 15161.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.108315 restraints weight = 12582.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.108814 restraints weight = 8515.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108953 restraints weight = 7848.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12494  Z= 0.155
  Angle     :  0.577  10.072  16940  Z= 0.304
  Chirality :  0.042   0.195   1834
  Planarity :  0.005   0.067   2100
  Dihedral  :  8.018 132.054   1676
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.10 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.21), residues: 1434
  helix:  1.46 (0.17), residues: 854
  sheet: -0.49 (0.64), residues: 64
  loop : -1.41 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  70 
 TYR   0.021   0.001   TYR B 855 
 PHE   0.015   0.001   PHE A 558 
 TRP   0.010   0.001   TRP B 333 
 HIS   0.005   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12488)
  covalent geometry    : angle       0.56887 (16928)
  SS BOND              : bond        0.00597 (    6)
  SS BOND              : angle       3.75472 (   12)
  hydrogen bonds       : bond        0.05223 (  720)
  hydrogen bonds       : angle       4.35880 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 138
  time to evaluate  : 0.568 
Fit side-chains
REVERT: A   47 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7166 (t80)
REVERT: A  294 GLU cc_start: 0.7732 (mp0) cc_final: 0.7514 (mp0)
REVERT: A  384 VAL cc_start: 0.9002 (t) cc_final: 0.8785 (m)
REVERT: A  773 MET cc_start: 0.9340 (mmm) cc_final: 0.8986 (tpp)
REVERT: B   47 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7088 (t80)
REVERT: B  851 PHE cc_start: 0.7801 (m-80) cc_final: 0.7582 (m-10)
  outliers start: 36
  outliers final: 20
  residues processed: 165
  average time/residue: 0.0899
  time to fit residues: 22.9174
Evaluate side-chains
  154 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 PHE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  330 ASN
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain B residue   47 PHE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  330 ASN
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  770 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 126 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 117 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   chunk 6 optimal weight:   20.0000
   chunk 105 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.6984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.133183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.105979 restraints weight = 17084.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.107996 restraints weight = 12377.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.109132 restraints weight = 10015.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.109363 restraints weight = 7855.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.109487 restraints weight = 7394.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12494  Z= 0.158
  Angle     :  0.577  10.165  16940  Z= 0.300
  Chirality :  0.042   0.193   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.957 130.157   1676
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.24 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.22), residues: 1434
  helix:  1.63 (0.17), residues: 848
  sheet: -0.46 (0.62), residues: 64
  loop : -1.27 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  70 
 TYR   0.018   0.001   TYR B 855 
 PHE   0.014   0.001   PHE B 558 
 TRP   0.010   0.001   TRP A 333 
 HIS   0.004   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12488)
  covalent geometry    : angle       0.56846 (16928)
  SS BOND              : bond        0.00523 (    6)
  SS BOND              : angle       3.68015 (   12)
  hydrogen bonds       : bond        0.05174 (  720)
  hydrogen bonds       : angle       4.29474 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  384 VAL cc_start: 0.8994 (t) cc_final: 0.8772 (m)
REVERT: A  524 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8625 (mp)
REVERT: A  773 MET cc_start: 0.9243 (mmm) cc_final: 0.8707 (tpp)
REVERT: B   47 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7196 (t80)
REVERT: B  138 TYR cc_start: 0.7803 (m-80) cc_final: 0.7570 (m-80)
REVERT: B  524 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: B  851 PHE cc_start: 0.7787 (m-80) cc_final: 0.7552 (m-10)
  outliers start: 37
  outliers final: 23
  residues processed: 168
  average time/residue: 0.0940
  time to fit residues: 24.1306
Evaluate side-chains
  161 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  770 TYR
Chi-restraints excluded: chain B residue   47 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  770 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9980
   chunk 141 optimal weight:    0.7980
   overall best weight:    1.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.134653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.107772 restraints weight = 16900.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.108299 restraints weight = 14432.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.110170 restraints weight = 11884.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.110592 restraints weight = 8270.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.110920 restraints weight = 7819.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12494  Z= 0.157
  Angle     :  0.570  10.381  16940  Z= 0.297
  Chirality :  0.042   0.190   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.938 129.408   1676
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.92 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.22), residues: 1434
  helix:  1.72 (0.17), residues: 850
  sheet: -0.67 (0.61), residues: 62
  loop : -1.18 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 219 
 TYR   0.017   0.001   TYR B 855 
 PHE   0.013   0.001   PHE A 558 
 TRP   0.009   0.001   TRP A 650 
 HIS   0.004   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (12488)
  covalent geometry    : angle       0.56117 (16928)
  SS BOND              : bond        0.00528 (    6)
  SS BOND              : angle       3.73043 (   12)
  hydrogen bonds       : bond        0.05102 (  720)
  hydrogen bonds       : angle       4.27007 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  384 VAL cc_start: 0.9005 (t) cc_final: 0.8785 (m)
REVERT: A  773 MET cc_start: 0.9158 (mmm) cc_final: 0.8617 (tpp)
REVERT: A  842 MET cc_start: 0.8053 (ttt) cc_final: 0.7797 (ttp)
REVERT: B  138 TYR cc_start: 0.7851 (m-80) cc_final: 0.7597 (m-80)
REVERT: B  851 PHE cc_start: 0.7775 (m-80) cc_final: 0.7549 (m-10)
  outliers start: 38
  outliers final: 28
  residues processed: 163
  average time/residue: 0.0947
  time to fit residues: 23.5701
Evaluate side-chains
  157 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue  143 HIS
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain B residue  143 HIS
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  770 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 133 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 129 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 HIS ** 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 = 0.3595 r_free = 0.3595 target = 0.136833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.109724 restraints weight = 17254.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109717 restraints weight = 13863.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111364 restraints weight = 11866.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.111718 restraints weight = 8759.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112226 restraints weight = 8072.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12494  Z= 0.123
  Angle     :  0.537  10.712  16940  Z= 0.278
  Chirality :  0.041   0.175   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.741 129.087   1676
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.21 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.22), residues: 1434
  helix:  1.97 (0.17), residues: 850
  sheet: -0.53 (0.59), residues: 64
  loop : -1.08 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 219 
 TYR   0.016   0.001   TYR A 855 
 PHE   0.014   0.001   PHE B 558 
 TRP   0.011   0.001   TRP B 650 
 HIS   0.003   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12488)
  covalent geometry    : angle       0.52916 (16928)
  SS BOND              : bond        0.00496 (    6)
  SS BOND              : angle       3.39601 (   12)
  hydrogen bonds       : bond        0.04698 (  720)
  hydrogen bonds       : angle       4.17576 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A  553 MET cc_start: 0.8268 (tpp) cc_final: 0.7999 (tpp)
REVERT: A  555 MET cc_start: 0.8475 (tpt) cc_final: 0.8222 (mmt)
REVERT: A  773 MET cc_start: 0.9198 (mmm) cc_final: 0.8632 (tpp)
REVERT: B   54 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6177 (pp20)
REVERT: B  555 MET cc_start: 0.8486 (tpt) cc_final: 0.8204 (mmt)
REVERT: B  773 MET cc_start: 0.9383 (mmm) cc_final: 0.9124 (tpp)
REVERT: B  851 PHE cc_start: 0.7750 (m-80) cc_final: 0.7503 (m-10)
  outliers start: 30
  outliers final: 22
  residues processed: 167
  average time/residue: 0.0934
  time to fit residues: 23.9307
Evaluate side-chains
  157 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0000
   chunk 29 optimal weight:    1.9990
   chunk 117 optimal weight:    6.9990
   chunk 43 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 123 optimal weight:   10.0000
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 696 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.108567 restraints weight = 17197.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109745 restraints weight = 12187.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110708 restraints weight = 10033.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.111219 restraints weight = 8174.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.111356 restraints weight = 7481.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12494  Z= 0.131
  Angle     :  0.553  10.637  16940  Z= 0.286
  Chirality :  0.041   0.175   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.691 128.849   1676
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.66 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.22), residues: 1434
  helix:  2.03 (0.17), residues: 850
  sheet: -0.48 (0.58), residues: 64
  loop : -1.05 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.018   0.001   TYR B 138 
 PHE   0.013   0.001   PHE B 558 
 TRP   0.009   0.001   TRP B 333 
 HIS   0.003   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (12488)
  covalent geometry    : angle       0.54508 (16928)
  SS BOND              : bond        0.00468 (    6)
  SS BOND              : angle       3.44883 (   12)
  hydrogen bonds       : bond        0.04728 (  720)
  hydrogen bonds       : angle       4.18202 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 138
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.7828 (tppt) cc_final: 0.7535 (mtmt)
REVERT: A  696 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.7751 (t0)
REVERT: A  773 MET cc_start: 0.9213 (mmm) cc_final: 0.8657 (tpp)
REVERT: B   54 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6265 (pp20)
REVERT: B   93 LYS cc_start: 0.7831 (tppt) cc_final: 0.7534 (mtmt)
REVERT: B  773 MET cc_start: 0.9381 (mmm) cc_final: 0.9065 (tpp)
REVERT: B  851 PHE cc_start: 0.7736 (m-80) cc_final: 0.7518 (m-10)
  outliers start: 33
  outliers final: 25
  residues processed: 161
  average time/residue: 0.0848
  time to fit residues: 21.0003
Evaluate side-chains
  157 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 116 optimal weight:    0.6980
   chunk 73 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 105 optimal weight:    8.9990
   chunk 130 optimal weight:    0.0770
   chunk 110 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.9540

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.109801 restraints weight = 17149.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110407 restraints weight = 12186.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.111481 restraints weight = 10446.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.111988 restraints weight = 8346.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.112178 restraints weight = 7695.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12494  Z= 0.125
  Angle     :  0.543  10.640  16940  Z= 0.281
  Chirality :  0.040   0.173   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.639 128.599   1676
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.20 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.22), residues: 1434
  helix:  2.08 (0.17), residues: 850
  sheet: -0.47 (0.59), residues: 64
  loop : -1.01 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.016   0.001   TYR A 855 
 PHE   0.014   0.001   PHE B 558 
 TRP   0.009   0.001   TRP A 333 
 HIS   0.003   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (12488)
  covalent geometry    : angle       0.53581 (16928)
  SS BOND              : bond        0.00462 (    6)
  SS BOND              : angle       3.35033 (   12)
  hydrogen bonds       : bond        0.04626 (  720)
  hydrogen bonds       : angle       4.17410 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  773 MET cc_start: 0.9223 (mmm) cc_final: 0.8664 (tpp)
REVERT: B   54 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6272 (pp20)
REVERT: B  773 MET cc_start: 0.9335 (mmm) cc_final: 0.8737 (tpp)
REVERT: B  851 PHE cc_start: 0.7698 (m-80) cc_final: 0.7476 (m-10)
  outliers start: 31
  outliers final: 25
  residues processed: 153
  average time/residue: 0.0872
  time to fit residues: 20.7867
Evaluate side-chains
  152 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 94 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 138 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 145 optimal weight:   10.0000
   chunk 130 optimal weight:    0.1980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 696 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.134065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.107064 restraints weight = 17252.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.109332 restraints weight = 12618.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.109593 restraints weight = 9885.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.109872 restraints weight = 8555.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110443 restraints weight = 7913.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12494  Z= 0.143
  Angle     :  0.554  10.283  16940  Z= 0.288
  Chirality :  0.041   0.176   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.704 128.685   1676
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.20 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.22), residues: 1434
  helix:  2.01 (0.17), residues: 850
  sheet: -0.52 (0.59), residues: 64
  loop : -0.99 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.018   0.001   TYR B 138 
 PHE   0.013   0.001   PHE B 558 
 TRP   0.009   0.001   TRP A 333 
 HIS   0.004   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12488)
  covalent geometry    : angle       0.54621 (16928)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       3.49234 (   12)
  hydrogen bonds       : bond        0.04838 (  720)
  hydrogen bonds       : angle       4.21750 ( 2130)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A  773 MET cc_start: 0.9180 (mmm) cc_final: 0.8638 (tpp)
REVERT: B   54 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6279 (pp20)
REVERT: B  773 MET cc_start: 0.9222 (mmm) cc_final: 0.8637 (tpp)
REVERT: B  851 PHE cc_start: 0.7768 (m-80) cc_final: 0.7540 (m-10)
  outliers start: 29
  outliers final: 25
  residues processed: 148
  average time/residue: 0.0876
  time to fit residues: 20.5182
Evaluate side-chains
  153 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  375 ASP
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 95 optimal weight:    0.0870
   chunk 93 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    1.1762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108416 restraints weight = 17294.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110700 restraints weight = 12780.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.111588 restraints weight = 9704.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.111862 restraints weight = 7738.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.111956 restraints weight = 7343.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.160  12494  Z= 0.182
  Angle     :  0.820  59.107  16940  Z= 0.476
  Chirality :  0.046   0.856   1834
  Planarity :  0.005   0.073   2100
  Dihedral  :  7.718 128.679   1676
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.50 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.22), residues: 1434
  helix:  1.98 (0.17), residues: 850
  sheet: -0.52 (0.59), residues: 64
  loop : -0.98 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.017   0.001   TYR B 138 
 PHE   0.013   0.001   PHE B 558 
 TRP   0.008   0.001   TRP A 333 
 HIS   0.004   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (12488)
  covalent geometry    : angle       0.81525 (16928)
  SS BOND              : bond        0.00474 (    6)
  SS BOND              : angle       3.47886 (   12)
  hydrogen bonds       : bond        0.04861 (  720)
  hydrogen bonds       : angle       4.23317 ( 2130)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1547.67 seconds
wall clock time: 27 minutes 40.36 seconds (1660.36 seconds total)