Starting phenix.real_space_refine
on Wed Jul 30 09:05:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qpb_4612/07_2025/6qpb_4612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qpb_4612/07_2025/6qpb_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_4612/07_2025/6qpb_4612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qpb_4612/07_2025/6qpb_4612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qpb_4612/07_2025/6qpb_4612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qpb_4612/07_2025/6qpb_4612.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 12.61, per 1000 atoms: 1.04
  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: 3.04
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.14
  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: 3.25

  Time building geometry restraints manager: 3.58 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: 0.06
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:             0.680
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     34.690
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.470
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (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
 TRP   0.012   0.002   TRP A 619 
 HIS   0.007   0.001   HIS B 830 
 PHE   0.028   0.002   PHE B  73 
 TYR   0.020   0.002   TYR A 222 
 ARG   0.003   0.000   ARG A 219 

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

*********************** 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  : 1.253 
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: 0.2398
  time to fit residues: 71.4373
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  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 114 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 85 optimal weight:    9.9990
   chunk 132 optimal weight:    0.7980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.137481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.112075 restraints weight = 17223.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.111222 restraints weight = 13670.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111873 restraints weight = 11718.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12494  Z= 0.139
  Angle     :  0.593  10.087  16940  Z= 0.317
  Chirality :  0.042   0.207   1834
  Planarity :  0.006   0.072   2100
  Dihedral  :  8.527 148.361   1676
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.85 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.20), residues: 1434
  helix:  0.53 (0.16), residues: 878
  sheet: -0.62 (0.60), residues: 64
  loop : -1.82 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 619 
 HIS   0.005   0.001   HIS A 830 
 PHE   0.017   0.001   PHE B 558 
 TYR   0.020   0.001   TYR B 855 
 ARG   0.003   0.000   ARG B 266 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05249 (  720)
  hydrogen bonds       : angle       4.58332 ( 2130)
  SS BOND              : bond        0.00247 (    6)
  SS BOND              : angle       4.58229 (   12)
  covalent geometry    : bond        0.00300 (12488)
  covalent geometry    : angle       0.58066 (16928)

*********************** 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
  187 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 1.249 
Fit side-chains
REVERT: A   47 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6417 (t80)
REVERT: A  759 SER cc_start: 0.9031 (m) cc_final: 0.8761 (p)
REVERT: A  810 ARG cc_start: 0.7903 (ttt180) cc_final: 0.7683 (tmm-80)
REVERT: A  811 ASP cc_start: 0.8033 (t0) cc_final: 0.7547 (m-30)
REVERT: A  851 PHE cc_start: 0.7742 (m-80) cc_final: 0.7512 (m-10)
REVERT: B  811 ASP cc_start: 0.8033 (t0) cc_final: 0.7542 (m-30)
REVERT: B  851 PHE cc_start: 0.7828 (m-80) cc_final: 0.7572 (m-10)
  outliers start: 19
  outliers final: 9
  residues processed: 179
  average time/residue: 0.2266
  time to fit residues: 59.9935
Evaluate side-chains
  151 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
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  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 17 optimal weight:    1.9990
   chunk 130 optimal weight:    0.2980
   chunk 143 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   chunk 117 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0370
   chunk 88 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 142 optimal weight:    0.7980
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.140144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.112520 restraints weight = 17343.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.113609 restraints weight = 13816.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115332 restraints weight = 10569.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  12494  Z= 0.118
  Angle     :  0.547   9.694  16940  Z= 0.286
  Chirality :  0.040   0.170   1834
  Planarity :  0.005   0.069   2100
  Dihedral  :  7.826 135.064   1676
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.52 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.21), residues: 1434
  helix:  1.36 (0.16), residues: 874
  sheet: -0.33 (0.61), residues: 64
  loop : -1.43 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 333 
 HIS   0.004   0.001   HIS B 830 
 PHE   0.017   0.001   PHE A 558 
 TYR   0.015   0.001   TYR B 855 
 ARG   0.002   0.000   ARG B  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04742 (  720)
  hydrogen bonds       : angle       4.33985 ( 2130)
  SS BOND              : bond        0.00497 (    6)
  SS BOND              : angle       3.58460 (   12)
  covalent geometry    : bond        0.00245 (12488)
  covalent geometry    : angle       0.53843 (16928)

*********************** 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
  174 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  553 MET cc_start: 0.8252 (tpp) cc_final: 0.8023 (tpp)
REVERT: A  773 MET cc_start: 0.9385 (mmm) cc_final: 0.9078 (tpp)
REVERT: A  811 ASP cc_start: 0.8035 (t0) cc_final: 0.7433 (m-30)
REVERT: A  851 PHE cc_start: 0.7654 (m-80) cc_final: 0.7439 (m-10)
REVERT: B   47 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7123 (t80)
REVERT: B  520 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8843 (mt)
REVERT: B  536 THR cc_start: 0.7841 (t) cc_final: 0.7399 (t)
REVERT: B  773 MET cc_start: 0.9385 (mmm) cc_final: 0.9060 (tpp)
REVERT: B  851 PHE cc_start: 0.7722 (m-80) cc_final: 0.7453 (m-10)
  outliers start: 19
  outliers final: 6
  residues processed: 169
  average time/residue: 0.2569
  time to fit residues: 64.3241
Evaluate side-chains
  149 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  349 CYS
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  667 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 67 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3613 r_free = 0.3613 target = 0.138501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111016 restraints weight = 17138.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.111149 restraints weight = 12910.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112465 restraints weight = 10178.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12494  Z= 0.132
  Angle     :  0.550  10.026  16940  Z= 0.288
  Chirality :  0.041   0.189   1834
  Planarity :  0.005   0.068   2100
  Dihedral  :  7.667 132.176   1676
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.96 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.22), residues: 1434
  helix:  1.68 (0.17), residues: 868
  sheet: -0.25 (0.66), residues: 62
  loop : -1.22 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 333 
 HIS   0.004   0.001   HIS B 830 
 PHE   0.016   0.001   PHE A 558 
 TYR   0.015   0.001   TYR B 855 
 ARG   0.002   0.000   ARG A 810 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04858 (  720)
  hydrogen bonds       : angle       4.20704 ( 2130)
  SS BOND              : bond        0.00556 (    6)
  SS BOND              : angle       3.50160 (   12)
  covalent geometry    : bond        0.00290 (12488)
  covalent geometry    : angle       0.54191 (16928)

*********************** 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
  166 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7236 (t80)
REVERT: A  524 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8596 (mp)
REVERT: A  773 MET cc_start: 0.9287 (mmm) cc_final: 0.8634 (tpp)
REVERT: A  851 PHE cc_start: 0.7627 (m-80) cc_final: 0.7396 (m-10)
REVERT: B  520 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8868 (mt)
REVERT: B  773 MET cc_start: 0.9266 (mmm) cc_final: 0.8582 (tpp)
REVERT: B  851 PHE cc_start: 0.7706 (m-80) cc_final: 0.7452 (m-10)
  outliers start: 26
  outliers final: 16
  residues processed: 159
  average time/residue: 0.2095
  time to fit residues: 50.1692
Evaluate side-chains
  153 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
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  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  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  520 ILE
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  729 MET
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 124 optimal weight:    7.9990
   chunk 111 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 121 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.9990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.134663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.107597 restraints weight = 17311.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.107982 restraints weight = 13805.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.109192 restraints weight = 11549.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12494  Z= 0.173
  Angle     :  0.587   9.841  16940  Z= 0.305
  Chirality :  0.043   0.195   1834
  Planarity :  0.005   0.065   2100
  Dihedral  :  7.763 130.395   1676
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.01 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.22), residues: 1434
  helix:  1.66 (0.17), residues: 868
  sheet: -0.34 (0.63), residues: 64
  loop : -1.14 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 333 
 HIS   0.006   0.001   HIS B 830 
 PHE   0.014   0.001   PHE A 558 
 TYR   0.016   0.001   TYR B 855 
 ARG   0.002   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05214 (  720)
  hydrogen bonds       : angle       4.28810 ( 2130)
  SS BOND              : bond        0.00540 (    6)
  SS BOND              : angle       3.76852 (   12)
  covalent geometry    : bond        0.00399 (12488)
  covalent geometry    : angle       0.57848 (16928)

*********************** 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
  169 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8653 (mp)
REVERT: A  773 MET cc_start: 0.9173 (mmm) cc_final: 0.8645 (tpp)
REVERT: B  773 MET cc_start: 0.9188 (mmm) cc_final: 0.8621 (tpp)
REVERT: B  851 PHE cc_start: 0.7799 (m-80) cc_final: 0.7583 (m-10)
  outliers start: 30
  outliers final: 16
  residues processed: 162
  average time/residue: 0.2833
  time to fit residues: 70.0309
Evaluate side-chains
  149 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  349 CYS
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  630 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  349 CYS
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  630 VAL
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  734 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 135 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   overall best weight:    1.5384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.135610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108320 restraints weight = 17453.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.108881 restraints weight = 13589.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.110559 restraints weight = 10763.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12494  Z= 0.148
  Angle     :  0.557  10.241  16940  Z= 0.291
  Chirality :  0.041   0.187   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.797 129.487   1676
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.39 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.22), residues: 1434
  helix:  1.81 (0.17), residues: 856
  sheet: -0.38 (0.61), residues: 64
  loop : -1.08 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 650 
 HIS   0.005   0.001   HIS B 830 
 PHE   0.014   0.001   PHE B 558 
 TYR   0.016   0.001   TYR B 855 
 ARG   0.002   0.000   ARG B  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04963 (  720)
  hydrogen bonds       : angle       4.22494 ( 2130)
  SS BOND              : bond        0.00528 (    6)
  SS BOND              : angle       3.61869 (   12)
  covalent geometry    : bond        0.00335 (12488)
  covalent geometry    : angle       0.54851 (16928)

*********************** 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
  181 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 1.209 
Fit side-chains
REVERT: A  520 ILE cc_start: 0.9145 (mm) cc_final: 0.8878 (mt)
REVERT: A  773 MET cc_start: 0.9180 (mmm) cc_final: 0.8664 (tpp)
REVERT: A  842 MET cc_start: 0.7977 (ttt) cc_final: 0.7761 (ttp)
REVERT: B  138 TYR cc_start: 0.7891 (m-80) cc_final: 0.7665 (m-80)
REVERT: B  773 MET cc_start: 0.9195 (mmm) cc_final: 0.8668 (tpp)
REVERT: B  851 PHE cc_start: 0.7768 (m-80) cc_final: 0.7540 (m-10)
  outliers start: 40
  outliers final: 23
  residues processed: 168
  average time/residue: 0.2172
  time to fit residues: 54.6665
Evaluate side-chains
  160 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 PHE
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  630 VAL
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  770 TYR
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  696 ASN
Chi-restraints excluded: chain B residue  729 MET
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 128 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 120 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0970
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0060
   overall best weight:    0.4794

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.140127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.112498 restraints weight = 17305.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.113960 restraints weight = 12513.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.114384 restraints weight = 10494.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12494  Z= 0.113
  Angle     :  0.532  10.983  16940  Z= 0.272
  Chirality :  0.040   0.168   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.590 128.380   1676
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.75 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.22), residues: 1434
  helix:  2.12 (0.17), residues: 860
  sheet: -0.27 (0.60), residues: 64
  loop : -0.91 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 333 
 HIS   0.003   0.000   HIS B 830 
 PHE   0.015   0.001   PHE B  73 
 TYR   0.016   0.001   TYR B 855 
 ARG   0.002   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04407 (  720)
  hydrogen bonds       : angle       4.08894 ( 2130)
  SS BOND              : bond        0.00467 (    6)
  SS BOND              : angle       3.14268 (   12)
  covalent geometry    : bond        0.00225 (12488)
  covalent geometry    : angle       0.52512 (16928)

*********************** 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
  181 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 ILE cc_start: 0.9113 (mm) cc_final: 0.8875 (mt)
REVERT: A  773 MET cc_start: 0.9277 (mmm) cc_final: 0.8660 (tpp)
REVERT: A  842 MET cc_start: 0.7901 (ttt) cc_final: 0.7667 (ttp)
REVERT: B  520 ILE cc_start: 0.9102 (mm) cc_final: 0.8856 (mt)
REVERT: B  553 MET cc_start: 0.8175 (tpp) cc_final: 0.7974 (tpp)
REVERT: B  773 MET cc_start: 0.9276 (mmm) cc_final: 0.8648 (tpp)
REVERT: B  851 PHE cc_start: 0.7671 (m-80) cc_final: 0.7430 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 175
  average time/residue: 0.2283
  time to fit residues: 59.4438
Evaluate side-chains
  157 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 PHE
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  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain B residue   73 PHE
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  557 LEU
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  696 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 104 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0370
   chunk 20 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 49 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7058

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.139956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.112257 restraints weight = 17342.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.112530 restraints weight = 14963.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.114110 restraints weight = 12018.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12494  Z= 0.114
  Angle     :  0.527  10.957  16940  Z= 0.272
  Chirality :  0.040   0.170   1834
  Planarity :  0.005   0.066   2100
  Dihedral  :  7.537 127.857   1676
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.91 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.22), residues: 1434
  helix:  2.12 (0.17), residues: 866
  sheet: -0.25 (0.58), residues: 64
  loop : -0.94 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 650 
 HIS   0.003   0.001   HIS B 830 
 PHE   0.014   0.001   PHE B 558 
 TYR   0.019   0.001   TYR A 306 
 ARG   0.001   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04459 (  720)
  hydrogen bonds       : angle       4.07144 ( 2130)
  SS BOND              : bond        0.00444 (    6)
  SS BOND              : angle       3.17392 (   12)
  covalent geometry    : bond        0.00238 (12488)
  covalent geometry    : angle       0.52018 (16928)

*********************** 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: 24
    poor density    : 147
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 ILE cc_start: 0.9105 (mm) cc_final: 0.8872 (mt)
REVERT: A  842 MET cc_start: 0.7924 (ttt) cc_final: 0.7690 (ttp)
REVERT: B  773 MET cc_start: 0.9233 (mmm) cc_final: 0.8999 (tpp)
REVERT: B  851 PHE cc_start: 0.7676 (m-80) cc_final: 0.7436 (m-10)
  outliers start: 24
  outliers final: 18
  residues processed: 164
  average time/residue: 0.2312
  time to fit residues: 57.3486
Evaluate side-chains
  153 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 1.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 PHE
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  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain B residue   73 PHE
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  557 LEU
Chi-restraints excluded: chain B residue  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  696 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 136 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 134 optimal weight:    1.9990
   chunk 135 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   chunk 118 optimal weight:    6.9990
   overall best weight:    2.1388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.105991 restraints weight = 17372.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.108025 restraints weight = 13119.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.108452 restraints weight = 10770.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12494  Z= 0.182
  Angle     :  0.596  10.070  16940  Z= 0.311
  Chirality :  0.043   0.183   1834
  Planarity :  0.005   0.065   2100
  Dihedral  :  7.808 128.215   1676
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.22), residues: 1434
  helix:  1.91 (0.17), residues: 854
  sheet: -0.45 (0.58), residues: 64
  loop : -0.98 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 273 
 HIS   0.006   0.001   HIS A 830 
 PHE   0.013   0.002   PHE B 558 
 TYR   0.023   0.002   TYR A 138 
 ARG   0.002   0.000   ARG B 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05181 (  720)
  hydrogen bonds       : angle       4.26930 ( 2130)
  SS BOND              : bond        0.00468 (    6)
  SS BOND              : angle       3.69287 (   12)
  covalent geometry    : bond        0.00424 (12488)
  covalent geometry    : angle       0.58855 (16928)

*********************** 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
  161 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.267 
Fit side-chains
REVERT: A  773 MET cc_start: 0.9139 (mmm) cc_final: 0.8717 (tpp)
REVERT: A  842 MET cc_start: 0.7959 (ttt) cc_final: 0.7755 (ttt)
REVERT: B  773 MET cc_start: 0.9250 (mmm) cc_final: 0.8821 (tpp)
  outliers start: 28
  outliers final: 17
  residues processed: 150
  average time/residue: 0.2238
  time to fit residues: 50.6270
Evaluate side-chains
  144 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 PHE
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  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  696 ASN
Chi-restraints excluded: chain A residue  729 MET
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  520 ILE
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  696 ASN
Chi-restraints excluded: chain B residue  734 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 139 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.0184

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.109030 restraints weight = 17229.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.108971 restraints weight = 12241.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109762 restraints weight = 10360.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12494  Z= 0.129
  Angle     :  0.546  10.638  16940  Z= 0.284
  Chirality :  0.041   0.173   1834
  Planarity :  0.005   0.065   2100
  Dihedral  :  7.611 127.697   1676
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 19.50 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.22), residues: 1434
  helix:  2.08 (0.17), residues: 854
  sheet: -0.43 (0.57), residues: 64
  loop : -0.90 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 650 
 HIS   0.004   0.001   HIS B 830 
 PHE   0.014   0.001   PHE B 558 
 TYR   0.017   0.001   TYR A 855 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04756 (  720)
  hydrogen bonds       : angle       4.17145 ( 2130)
  SS BOND              : bond        0.00478 (    6)
  SS BOND              : angle       3.37618 (   12)
  covalent geometry    : bond        0.00279 (12488)
  covalent geometry    : angle       0.53904 (16928)

********************** 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
  149 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 1.134 
Fit side-chains
REVERT: A  219 ARG cc_start: 0.7974 (mpt180) cc_final: 0.7581 (mpt180)
REVERT: A  773 MET cc_start: 0.9246 (mmm) cc_final: 0.8773 (tpp)
REVERT: B  219 ARG cc_start: 0.7922 (mpt180) cc_final: 0.7654 (mpt180)
REVERT: B  553 MET cc_start: 0.8272 (tpp) cc_final: 0.8001 (tpp)
REVERT: B  773 MET cc_start: 0.9292 (mmm) cc_final: 0.9046 (tpp)
  outliers start: 16
  outliers final: 14
  residues processed: 143
  average time/residue: 0.2665
  time to fit residues: 59.7362
Evaluate side-chains
  144 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 PHE
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  613 MET
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  696 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  613 MET
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  696 ASN
Chi-restraints excluded: chain B residue  729 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0370
   chunk 74 optimal weight:    0.7980
   chunk 131 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0980
   chunk 17 optimal weight:    0.3980
   chunk 99 optimal weight:    2.9990
   chunk 144 optimal weight:    3.9990
   overall best weight:    0.4658

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113559 restraints weight = 17198.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.113724 restraints weight = 13683.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115287 restraints weight = 11605.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12494  Z= 0.112
  Angle     :  0.534  11.315  16940  Z= 0.273
  Chirality :  0.040   0.164   1834
  Planarity :  0.005   0.065   2100
  Dihedral  :  7.462 126.561   1676
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 19.65 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.22), residues: 1434
  helix:  2.26 (0.17), residues: 854
  sheet: -0.28 (0.59), residues: 64
  loop : -0.87 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 333 
 HIS   0.003   0.000   HIS B 830 
 PHE   0.014   0.001   PHE B 558 
 TYR   0.016   0.001   TYR B 855 
 ARG   0.003   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  720)
  hydrogen bonds       : angle       4.07956 ( 2130)
  SS BOND              : bond        0.00419 (    6)
  SS BOND              : angle       3.06510 (   12)
  covalent geometry    : bond        0.00229 (12488)
  covalent geometry    : angle       0.52746 (16928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3381.67 seconds
wall clock time: 60 minutes 50.17 seconds (3650.17 seconds total)