Starting phenix.real_space_refine
on Sun Aug 24 07:56:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qa6_18300/08_2025/8qa6_18300_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qa6_18300/08_2025/8qa6_18300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qa6_18300/08_2025/8qa6_18300_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qa6_18300/08_2025/8qa6_18300_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qa6_18300/08_2025/8qa6_18300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qa6_18300/08_2025/8qa6_18300.map"
  }
  resolution = 2.91
  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=  -0.000 sd=   0.047
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      44      5.16       5
     C    5826      2.51       5
     N    1518      2.21       5
     O    1696      1.98       5
     H    8720      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17808
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 553, 8797
          Classifications: {'peptide': 553}
          Link IDs: {'PTRANS': 31, 'TRANS': 521}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 8797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 553, 8797
          Classifications: {'peptide': 553}
          Link IDs: {'PTRANS': 31, 'TRANS': 521}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 107
          Unusual residues: {'FAD': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 107
          Unusual residues: {'FAD': 1}
          Classifications: {'peptide': 2, 'undetermined': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 2.86, per 1000 atoms: 0.16
  Number of scatterers: 17808
  At special positions: 0
  Unit cell: (106.19, 116.522, 78.638, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P       4     15.00
     O    1696      8.00
     N    1518      7.00
     C    5826      6.00
     H    8720      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 437.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 6 sheets defined
      51.1% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 54
    Processing helix  chain 'A' and resid 69 through 85
      removed outlier: 3.971A  pdb=" N   ALA A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 100
      removed outlier: 3.626A  pdb=" N   ASP A 100 " --> pdb=" O   PRO A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 119
    Processing helix  chain 'A' and resid 134 through 149
    Processing helix  chain 'A' and resid 174 through 187
      removed outlier: 3.811A  pdb=" N   LEU A 178 " --> pdb=" O   TYR A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 221
    Processing helix  chain 'A' and resid 232 through 247
      removed outlier: 3.834A  pdb=" N   PHE A 236 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 271
      removed outlier: 3.652A  pdb=" N   LEU A 265 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LYS A 270 " --> pdb=" O   ARG A 266 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LEU A 271 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
      removed outlier: 3.746A  pdb=" N   LYS A 281 " --> pdb=" O   PRO A 277 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 290 through 313
      removed outlier: 3.891A  pdb=" N   SER A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 337
      removed outlier: 4.524A  pdb=" N   THR A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 407
      removed outlier: 5.626A  pdb=" N   TYR A 404 " --> pdb=" O   LYS A 401 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   LEU A 405 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR A 407 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 421
    Processing helix  chain 'A' and resid 427 through 441
      removed outlier: 3.990A  pdb=" N   VAL A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 466
    Processing helix  chain 'A' and resid 467 through 477
    Processing helix  chain 'A' and resid 518 through 530
      removed outlier: 3.767A  pdb=" N   LYS A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 533
      No H-bonds generated for 'chain 'A' and resid 531 through 533'
    Processing helix  chain 'A' and resid 576 through 595
      removed outlier: 3.531A  pdb=" N   PHE A 582 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ASP A 585 " --> pdb=" O   MET A 581 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   GLU A 586 " --> pdb=" O   PHE A 582 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TRP A 591 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ILE A 592 " --> pdb=" O   PHE A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 599
    Processing helix  chain 'A' and resid 603 through 616
    Processing helix  chain 'A' and resid 631 through 644
    Processing helix  chain 'B' and resid 45 through 54
    Processing helix  chain 'B' and resid 69 through 85
      removed outlier: 3.970A  pdb=" N   ALA B  85 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 100
      removed outlier: 3.625A  pdb=" N   ASP B 100 " --> pdb=" O   PRO B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 119
    Processing helix  chain 'B' and resid 134 through 149
    Processing helix  chain 'B' and resid 174 through 187
      removed outlier: 3.906A  pdb=" N   LEU B 178 " --> pdb=" O   TYR B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 221
    Processing helix  chain 'B' and resid 232 through 247
      removed outlier: 3.836A  pdb=" N   PHE B 236 " --> pdb=" O   GLU B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 271
      removed outlier: 3.649A  pdb=" N   LEU B 265 " --> pdb=" O   GLY B 261 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS B 270 " --> pdb=" O   ARG B 266 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU B 271 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 288
      removed outlier: 3.768A  pdb=" N   LYS B 281 " --> pdb=" O   PRO B 277 " (cutoff:3.500A)
      Proline residue:  B 286  - end of helix
    Processing helix  chain 'B' and resid 290 through 313
      removed outlier: 3.870A  pdb=" N   SER B 312 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY B 313 " --> pdb=" O   LEU B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 337
      removed outlier: 4.515A  pdb=" N   THR B 329 " --> pdb=" O   ARG B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 407
      removed outlier: 5.626A  pdb=" N   TYR B 404 " --> pdb=" O   LYS B 401 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   LEU B 405 " --> pdb=" O   ASP B 402 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR B 407 " --> pdb=" O   TYR B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 421
    Processing helix  chain 'B' and resid 427 through 441
      removed outlier: 3.943A  pdb=" N   VAL B 431 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU B 439 " --> pdb=" O   PHE B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 466
    Processing helix  chain 'B' and resid 467 through 477
    Processing helix  chain 'B' and resid 518 through 530
      removed outlier: 3.762A  pdb=" N   LYS B 530 " --> pdb=" O   LEU B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 533
      No H-bonds generated for 'chain 'B' and resid 531 through 533'
    Processing helix  chain 'B' and resid 576 through 595
      removed outlier: 3.534A  pdb=" N   PHE B 582 " --> pdb=" O   VAL B 578 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ASP B 585 " --> pdb=" O   MET B 581 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLU B 586 " --> pdb=" O   PHE B 582 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TRP B 591 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE B 592 " --> pdb=" O   PHE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 599
    Processing helix  chain 'B' and resid 603 through 616
    Processing helix  chain 'B' and resid 631 through 644
    Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 64
      removed outlier: 3.585A  pdb=" N   HIS A 127 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   THR A 124 " --> pdb=" O   ASN A 152 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   MET A 154 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   LEU A 126 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   CYS A 193 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA A 195 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE A 224 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE A 225 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   GLY A 255 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   THR A 227 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   GLY A 317 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TRP A  59 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   PHE A 320 " --> pdb=" O   TRP A  59 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   SER A  61 " --> pdb=" O   PHE A 320 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 485
      removed outlier: 6.505A  pdb=" N   GLU A 514 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   SER A 484 " --> pdb=" O   TYR A 512 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   TYR A 512 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.614A  pdb=" N   THR A 573 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TRP A 561 " --> pdb=" O   GLN A 571 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   GLN A 571 " --> pdb=" O   TRP A 561 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 64
      removed outlier: 3.585A  pdb=" N   HIS B 127 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   THR B 124 " --> pdb=" O   ASN B 152 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   MET B 154 " --> pdb=" O   THR B 124 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 154 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   CYS B 193 " --> pdb=" O   ILE B 153 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ALA B 195 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE B 224 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ILE B 225 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   GLY B 255 " --> pdb=" O   ILE B 225 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   THR B 227 " --> pdb=" O   GLY B 255 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   GLY B 317 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TRP B  59 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   PHE B 320 " --> pdb=" O   TRP B  59 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   SER B  61 " --> pdb=" O   PHE B 320 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 480 through 485
      removed outlier: 6.504A  pdb=" N   GLU B 514 " --> pdb=" O   ILE B 482 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   SER B 484 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   TYR B 512 " --> pdb=" O   SER B 484 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 506 through 509
      removed outlier: 6.614A  pdb=" N   THR B 573 " --> pdb=" O   VAL B 559 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TRP B 561 " --> pdb=" O   GLN B 571 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLN B 571 " --> pdb=" O   TRP B 561 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1179 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: 3.54

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 8702
        1.03 -     1.22: 18
        1.22 -     1.42: 3990
        1.42 -     1.62: 5266
        1.62 -     1.81: 80
  Bond restraints: 18056
  Sorted by residual:
  bond pdb=" C2' SAM B 701 "
       pdb=" C3' SAM B 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.247  0.285 2.00e-02 2.50e+03 2.03e+02
  bond pdb=" C2' SAM A 701 "
       pdb=" C3' SAM A 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.247  0.285 2.00e-02 2.50e+03 2.03e+02
  bond pdb=" C2' SAM B 703 "
       pdb=" C3' SAM B 703 "
    ideal  model  delta    sigma   weight residual
    1.532  1.251  0.281 2.00e-02 2.50e+03 1.98e+02
  bond pdb=" C2' SAM A 703 "
       pdb=" C3' SAM A 703 "
    ideal  model  delta    sigma   weight residual
    1.532  1.251  0.281 2.00e-02 2.50e+03 1.98e+02
  bond pdb=" C6  SAM A 703 "
       pdb=" N6  SAM A 703 "
    ideal  model  delta    sigma   weight residual
    1.333  1.456 -0.123 2.00e-02 2.50e+03 3.76e+01
  ... (remaining 18051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.49: 32521
        5.49 -    10.98: 49
       10.98 -    16.46: 10
       16.46 -    21.95: 0
       21.95 -    27.44: 8
  Bond angle restraints: 32588
  Sorted by residual:
  angle pdb=" C1' SAM B 703 "
        pdb=" N9  SAM B 703 "
        pdb=" C8  SAM B 703 "
      ideal   model   delta    sigma   weight residual
     123.85   96.41   27.44 3.00e+00 1.11e-01 8.37e+01
  angle pdb=" C1' SAM A 703 "
        pdb=" N9  SAM A 703 "
        pdb=" C8  SAM A 703 "
      ideal   model   delta    sigma   weight residual
     123.85   96.45   27.40 3.00e+00 1.11e-01 8.34e+01
  angle pdb=" C1' SAM B 703 "
        pdb=" N9  SAM B 703 "
        pdb=" C4  SAM B 703 "
      ideal   model   delta    sigma   weight residual
     130.15  156.71  -26.56 3.00e+00 1.11e-01 7.84e+01
  angle pdb=" C1' SAM A 703 "
        pdb=" N9  SAM A 703 "
        pdb=" C4  SAM A 703 "
      ideal   model   delta    sigma   weight residual
     130.15  156.60  -26.45 3.00e+00 1.11e-01 7.78e+01
  angle pdb=" C1' SAM B 701 "
        pdb=" N9  SAM B 701 "
        pdb=" C8  SAM B 701 "
      ideal   model   delta    sigma   weight residual
     123.85   98.83   25.02 3.00e+00 1.11e-01 6.96e+01
  ... (remaining 32583 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.91: 8233
       34.91 -    69.81: 373
       69.81 -   104.72: 34
      104.72 -   139.62: 0
      139.62 -   174.53: 2
  Dihedral angle restraints: 8642
    sinusoidal: 4752
      harmonic: 3890
  Sorted by residual:
  dihedral pdb=" O5' FAD A 702 "
           pdb=" O3P FAD A 702 "
           pdb=" P   FAD A 702 "
           pdb=" PA  FAD A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.77  112.76 -174.53     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O5' FAD B 702 "
           pdb=" O3P FAD B 702 "
           pdb=" P   FAD B 702 "
           pdb=" PA  FAD B 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.77  112.71 -174.48     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CA  ILE B 192 "
           pdb=" C   ILE B 192 "
           pdb=" N   CYS B 193 "
           pdb=" CA  CYS B 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 8639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.323: 1360
       0.323 -    0.646: 4
       0.646 -    0.969: 0
       0.969 -    1.292: 0
       1.292 -    1.616: 4
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" SD  SAM B 701 "
            pdb=" CG  SAM B 701 "
            pdb=" CE  SAM B 701 "
            pdb=" C5' SAM B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      5.50    3.89    1.62 2.00e-01 2.50e+01 6.52e+01
  chirality pdb=" SD  SAM A 701 "
            pdb=" CG  SAM A 701 "
            pdb=" CE  SAM A 701 "
            pdb=" C5' SAM A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      5.50    3.89    1.61 2.00e-01 2.50e+01 6.49e+01
  chirality pdb=" SD  SAM A 703 "
            pdb=" CG  SAM A 703 "
            pdb=" CE  SAM A 703 "
            pdb=" C5' SAM A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      5.50    3.94    1.57 2.00e-01 2.50e+01 6.14e+01
  ... (remaining 1365 not shown)

  Planarity restraints: 2646
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 152 "    0.056 2.00e-02 2.50e+03   6.90e-02 7.14e+01
        pdb=" CG  ASN B 152 "   -0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 152 "    0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 152 "   -0.108 2.00e-02 2.50e+03
        pdb="HD21 ASN B 152 "   -0.006 2.00e-02 2.50e+03
        pdb="HD22 ASN B 152 "    0.107 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 152 "   -0.055 2.00e-02 2.50e+03   6.87e-02 7.08e+01
        pdb=" CG  ASN A 152 "    0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 152 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 152 "    0.108 2.00e-02 2.50e+03
        pdb="HD21 ASN A 152 "    0.006 2.00e-02 2.50e+03
        pdb="HD22 ASN A 152 "   -0.106 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 118 "   -0.038 2.00e-02 2.50e+03   4.61e-02 3.19e+01
        pdb=" CG  ASN A 118 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 118 "    0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 118 "    0.073 2.00e-02 2.50e+03
        pdb="HD21 ASN A 118 "    0.002 2.00e-02 2.50e+03
        pdb="HD22 ASN A 118 "   -0.071 2.00e-02 2.50e+03
  ... (remaining 2643 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 912
        2.17 -     2.78: 34656
        2.78 -     3.39: 51387
        3.39 -     3.99: 66352
        3.99 -     4.60: 103216
  Nonbonded interactions: 256523
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 568 "
            pdb="HE22 GLN B 571 "
     model   vdw
     1.565 2.450
  nonbonded pdb="HE22 GLN A 571 "
            pdb=" OE1 GLU B 568 "
     model   vdw
     1.566 2.450
  nonbonded pdb="HE21 GLN A 555 "
            pdb=" H   GLU B 568 "
     model   vdw
     1.605 2.100
  nonbonded pdb=" HZ3 LYS B 584 "
            pdb=" OD1 ASP B 585 "
     model   vdw
     1.669 2.450
  nonbonded pdb=" O   VAL B 240 "
            pdb=" HG1 THR B 244 "
     model   vdw
     1.670 2.450
  ... (remaining 256518 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.260
  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:             0.060
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.620
  Find NCS groups from input model:        0.120
  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:7.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
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      :  0.010   0.285   9336  Z= 0.500
  Angle     :  1.084  27.438  12696  Z= 0.428
  Chirality :  0.098   1.616   1368
  Planarity :  0.006   0.094   1608
  Dihedral  : 17.507 174.526   3576
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 18.92 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.25), residues: 1094
  helix: -0.01 (0.23), residues: 470
  sheet: -0.08 (0.37), residues: 176
  loop : -0.69 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  82 
 TYR   0.017   0.002   TYR B  90 
 PHE   0.021   0.001   PHE A 582 
 TRP   0.024   0.002   TRP A  95 
 HIS   0.006   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.01013 ( 9336)
  covalent geometry    : angle       1.08352 (12696)
  hydrogen bonds       : bond        0.14595 (  413)
  hydrogen bonds       : angle       7.21031 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.7861 (mmt) cc_final: 0.7466 (mmt)
  outliers start: 5
  outliers final: 2
  residues processed: 106
  average time/residue: 0.8032
  time to fit residues: 93.3867
Evaluate side-chains
  105 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 TYR
Chi-restraints excluded: chain B residue  119 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 477 GLN
B 477 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.156877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.127575 restraints weight = 32114.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.13
r_work: 0.3419 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9336  Z= 0.146
  Angle     :  0.583   4.724  12696  Z= 0.295
  Chirality :  0.042   0.154   1368
  Planarity :  0.005   0.039   1608
  Dihedral  : 11.040 178.888   1418
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 18.30 %
    Favored  : 80.35 %
  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 aren not related in a simple way.
  whole:  0.80 (0.26), residues: 1094
  helix:  1.43 (0.24), residues: 476
  sheet: -0.10 (0.38), residues: 178
  loop : -0.06 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  51 
 TYR   0.012   0.001   TYR A 197 
 PHE   0.023   0.002   PHE B 582 
 TRP   0.014   0.001   TRP B  95 
 HIS   0.004   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9336)
  covalent geometry    : angle       0.58296 (12696)
  hydrogen bonds       : bond        0.03877 (  413)
  hydrogen bonds       : angle       5.14946 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7325 (mp0)
REVERT: A  445 ARG cc_start: 0.7350 (ptp90) cc_final: 0.7145 (ptp90)
REVERT: B  137 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6494 (mm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 119
  average time/residue: 0.8276
  time to fit residues: 107.4220
Evaluate side-chains
  111 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  637 GLU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  533 GLU
Chi-restraints excluded: chain B residue  637 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 90 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 477 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.153045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.123365 restraints weight = 32252.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.15
r_work: 0.3365 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9336  Z= 0.186
  Angle     :  0.582   4.521  12696  Z= 0.297
  Chirality :  0.042   0.148   1368
  Planarity :  0.004   0.038   1608
  Dihedral  : 10.983 168.775   1414
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.78 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.26), residues: 1094
  helix:  1.60 (0.24), residues: 476
  sheet: -0.18 (0.38), residues: 178
  loop :  0.02 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  51 
 TYR   0.013   0.002   TYR B 512 
 PHE   0.021   0.002   PHE B 582 
 TRP   0.011   0.001   TRP A  95 
 HIS   0.003   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 9336)
  covalent geometry    : angle       0.58175 (12696)
  hydrogen bonds       : bond        0.03885 (  413)
  hydrogen bonds       : angle       4.84650 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7389 (mp0)
REVERT: B  106 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (mp0)
REVERT: B  137 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6571 (mm-30)
REVERT: B  327 MET cc_start: 0.7691 (tmt) cc_final: 0.7355 (tmt)
REVERT: B  399 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7408 (mp0)
  outliers start: 15
  outliers final: 9
  residues processed: 115
  average time/residue: 0.8982
  time to fit residues: 112.0688
Evaluate side-chains
  111 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  637 GLU
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  533 GLU
Chi-restraints excluded: chain B residue  637 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0060
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0020
   chunk 27 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7806

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
B 477 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.155317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.126143 restraints weight = 32173.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.12
r_work: 0.3409 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9336  Z= 0.104
  Angle     :  0.511   4.280  12696  Z= 0.258
  Chirality :  0.040   0.143   1368
  Planarity :  0.004   0.039   1608
  Dihedral  : 10.556 171.486   1414
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 18.61 %
    Favored  : 80.25 %
  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 aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1094
  helix:  1.86 (0.24), residues: 476
  sheet: -0.05 (0.39), residues: 178
  loop :  0.20 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  51 
 TYR   0.010   0.001   TYR B 512 
 PHE   0.017   0.001   PHE A 582 
 TRP   0.008   0.001   TRP B  95 
 HIS   0.003   0.000   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9336)
  covalent geometry    : angle       0.51126 (12696)
  hydrogen bonds       : bond        0.03179 (  413)
  hydrogen bonds       : angle       4.54410 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7366 (mp0)
REVERT: B  137 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6546 (mm-30)
REVERT: B  399 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7377 (mp0)
  outliers start: 11
  outliers final: 4
  residues processed: 118
  average time/residue: 0.9164
  time to fit residues: 117.7784
Evaluate side-chains
  106 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  637 GLU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  452 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0970
   chunk 64 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    0.3980
   chunk 48 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.0580

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.154314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.124711 restraints weight = 32174.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.17
r_work: 0.3334 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9336  Z= 0.123
  Angle     :  0.517   4.389  12696  Z= 0.260
  Chirality :  0.040   0.141   1368
  Planarity :  0.004   0.038   1608
  Dihedral  : 10.505 168.996   1414
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.40 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.26), residues: 1094
  helix:  1.92 (0.24), residues: 476
  sheet:  0.02 (0.40), residues: 174
  loop :  0.32 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  51 
 TYR   0.011   0.001   TYR A 512 
 PHE   0.017   0.001   PHE A 582 
 TRP   0.008   0.001   TRP B  95 
 HIS   0.004   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9336)
  covalent geometry    : angle       0.51678 (12696)
  hydrogen bonds       : bond        0.03193 (  413)
  hydrogen bonds       : angle       4.46543 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7353 (mp0)
REVERT: A  460 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7994 (mp)
REVERT: A  473 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7134 (tmm160)
REVERT: A  594 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8283 (mm110)
REVERT: B  137 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6560 (mm-30)
REVERT: B  399 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7359 (mp0)
REVERT: B  460 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7996 (mp)
REVERT: B  473 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6769 (tmm160)
REVERT: B  594 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8295 (mm110)
  outliers start: 15
  outliers final: 5
  residues processed: 124
  average time/residue: 0.9540
  time to fit residues: 127.8704
Evaluate side-chains
  115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  473 ARG
Chi-restraints excluded: chain B residue  637 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0770
   chunk 73 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 555 GLN
B 487 ASN
B 555 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.154868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.125654 restraints weight = 32103.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.13
r_work: 0.3399 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9336  Z= 0.109
  Angle     :  0.503   4.275  12696  Z= 0.253
  Chirality :  0.039   0.139   1368
  Planarity :  0.004   0.037   1608
  Dihedral  : 10.446 170.165   1414
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.71 %
    Favored  : 79.63 %
  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 aren not related in a simple way.
  whole:  1.49 (0.26), residues: 1094
  helix:  2.03 (0.24), residues: 476
  sheet:  0.04 (0.40), residues: 174
  loop :  0.36 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.011   0.001   TYR B 512 
 PHE   0.016   0.001   PHE A 582 
 TRP   0.007   0.001   TRP A  95 
 HIS   0.003   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9336)
  covalent geometry    : angle       0.50314 (12696)
  hydrogen bonds       : bond        0.03055 (  413)
  hydrogen bonds       : angle       4.39275 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7399 (mp0)
REVERT: A  460 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8030 (mp)
REVERT: A  473 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7215 (tmm160)
REVERT: B  137 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6546 (mm-30)
REVERT: B  399 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7412 (mp0)
REVERT: B  460 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8035 (mp)
REVERT: B  473 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6843 (tmm160)
  outliers start: 16
  outliers final: 5
  residues processed: 115
  average time/residue: 0.9622
  time to fit residues: 119.7362
Evaluate side-chains
  114 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  473 ARG
Chi-restraints excluded: chain B residue  533 GLU
Chi-restraints excluded: chain B residue  637 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0980
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
B 555 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.156438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.127128 restraints weight = 32206.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.15
r_work: 0.3418 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9336  Z= 0.094
  Angle     :  0.484   4.218  12696  Z= 0.243
  Chirality :  0.039   0.138   1368
  Planarity :  0.004   0.037   1608
  Dihedral  : 10.301 171.425   1414
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 18.92 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.27), residues: 1094
  helix:  2.23 (0.24), residues: 476
  sheet:  0.31 (0.42), residues: 170
  loop :  0.53 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.009   0.001   TYR A 512 
 PHE   0.015   0.001   PHE B 582 
 TRP   0.007   0.001   TRP B  95 
 HIS   0.004   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9336)
  covalent geometry    : angle       0.48445 (12696)
  hydrogen bonds       : bond        0.02839 (  413)
  hydrogen bonds       : angle       4.25988 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7416 (mp0)
REVERT: A  473 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7223 (tmm160)
REVERT: A  623 ASP cc_start: 0.8597 (t0) cc_final: 0.8341 (t0)
REVERT: B  137 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6550 (mm-30)
REVERT: B  399 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7407 (mp0)
REVERT: B  473 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7182 (tmm160)
  outliers start: 13
  outliers final: 4
  residues processed: 118
  average time/residue: 0.9087
  time to fit residues: 116.7302
Evaluate side-chains
  114 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  473 ARG
Chi-restraints excluded: chain B residue  637 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.154680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.125332 restraints weight = 32180.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.14
r_work: 0.3401 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9336  Z= 0.123
  Angle     :  0.505   4.376  12696  Z= 0.253
  Chirality :  0.039   0.137   1368
  Planarity :  0.004   0.038   1608
  Dihedral  : 10.366 169.675   1414
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 19.44 %
    Favored  : 79.11 %
  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 aren not related in a simple way.
  whole:  1.77 (0.26), residues: 1094
  helix:  2.25 (0.24), residues: 476
  sheet:  0.27 (0.42), residues: 170
  loop :  0.49 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 473 
 TYR   0.012   0.001   TYR A 512 
 PHE   0.016   0.001   PHE B 582 
 TRP   0.007   0.001   TRP B  95 
 HIS   0.003   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9336)
  covalent geometry    : angle       0.50516 (12696)
  hydrogen bonds       : bond        0.02980 (  413)
  hydrogen bonds       : angle       4.28217 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7441 (mp0)
REVERT: B  137 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6561 (mm-30)
REVERT: B  399 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7424 (mp0)
REVERT: B  473 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7174 (tmm160)
  outliers start: 14
  outliers final: 4
  residues processed: 114
  average time/residue: 0.8659
  time to fit residues: 107.4235
Evaluate side-chains
  109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  473 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 91 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 555 GLN
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.127366 restraints weight = 32122.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.10
r_work: 0.3382 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9336  Z= 0.094
  Angle     :  0.486   4.352  12696  Z= 0.243
  Chirality :  0.039   0.138   1368
  Planarity :  0.004   0.038   1608
  Dihedral  : 10.272 171.501   1414
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 19.65 %
    Favored  : 79.21 %
  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 aren not related in a simple way.
  whole:  1.96 (0.27), residues: 1094
  helix:  2.38 (0.24), residues: 476
  sheet:  0.38 (0.42), residues: 170
  loop :  0.61 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.009   0.001   TYR A 197 
 PHE   0.015   0.001   PHE B 582 
 TRP   0.009   0.001   TRP A  59 
 HIS   0.003   0.000   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9336)
  covalent geometry    : angle       0.48567 (12696)
  hydrogen bonds       : bond        0.02786 (  413)
  hydrogen bonds       : angle       4.17990 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  399 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7395 (mp0)
REVERT: A  473 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7190 (tmm160)
REVERT: A  623 ASP cc_start: 0.8569 (t0) cc_final: 0.8329 (t0)
REVERT: B  137 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6539 (mm-30)
REVERT: B  399 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7378 (mp0)
REVERT: B  473 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7149 (tmm160)
  outliers start: 11
  outliers final: 4
  residues processed: 117
  average time/residue: 0.9206
  time to fit residues: 116.9790
Evaluate side-chains
  110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  473 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 95 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 67 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 555 GLN
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.156955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.127940 restraints weight = 31907.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.13
r_work: 0.3386 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9336  Z= 0.092
  Angle     :  0.490   5.654  12696  Z= 0.243
  Chirality :  0.039   0.157   1368
  Planarity :  0.004   0.038   1608
  Dihedral  : 10.224 171.472   1414
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 19.65 %
    Favored  : 79.21 %
  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 aren not related in a simple way.
  whole:  2.07 (0.27), residues: 1094
  helix:  2.48 (0.24), residues: 476
  sheet:  0.45 (0.43), residues: 170
  loop :  0.65 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.009   0.001   TYR A 512 
 PHE   0.014   0.001   PHE B 582 
 TRP   0.009   0.001   TRP B  59 
 HIS   0.002   0.000   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9336)
  covalent geometry    : angle       0.49050 (12696)
  hydrogen bonds       : bond        0.02739 (  413)
  hydrogen bonds       : angle       4.13601 ( 1179)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 ILE cc_start: 0.7433 (mt) cc_final: 0.7194 (mm)
REVERT: A  327 MET cc_start: 0.7531 (tmt) cc_final: 0.7016 (tmt)
REVERT: A  399 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7402 (mp0)
REVERT: A  473 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7188 (tmm160)
REVERT: A  623 ASP cc_start: 0.8556 (t0) cc_final: 0.8324 (t0)
REVERT: B  137 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6537 (mm-30)
REVERT: B  287 ILE cc_start: 0.7435 (mt) cc_final: 0.7196 (mm)
REVERT: B  327 MET cc_start: 0.7533 (tmt) cc_final: 0.7023 (tmt)
REVERT: B  399 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7388 (mp0)
REVERT: B  473 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7148 (tmm160)
  outliers start: 11
  outliers final: 5
  residues processed: 110
  average time/residue: 0.9373
  time to fit residues: 111.1378
Evaluate side-chains
  109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 CYS
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain B residue  452 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  473 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0030
   chunk 109 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0970
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0060
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.3204

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 555 GLN
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.158362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.129699 restraints weight = 32139.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.12
r_work: 0.3433 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9336  Z= 0.081
  Angle     :  0.472   4.427  12696  Z= 0.234
  Chirality :  0.039   0.136   1368
  Planarity :  0.004   0.040   1608
  Dihedral  : 10.126 173.595   1414
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 20.27 %
    Favored  : 78.69 %
  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 aren not related in a simple way.
  whole:  2.23 (0.27), residues: 1094
  helix:  2.60 (0.24), residues: 476
  sheet:  0.68 (0.43), residues: 168
  loop :  0.69 (0.32), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.008   0.001   TYR A 197 
 PHE   0.013   0.001   PHE B 582 
 TRP   0.006   0.001   TRP A  59 
 HIS   0.003   0.000   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 9336)
  covalent geometry    : angle       0.47229 (12696)
  hydrogen bonds       : bond        0.02540 (  413)
  hydrogen bonds       : angle       4.04503 ( 1179)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5034.00 seconds
wall clock time: 85 minutes 48.66 seconds (5148.66 seconds total)