Starting phenix.real_space_refine
on Wed Feb  4 02:27:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w3i_65602/02_2026/9w3i_65602.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w3i_65602/02_2026/9w3i_65602.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w3i_65602/02_2026/9w3i_65602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w3i_65602/02_2026/9w3i_65602.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w3i_65602/02_2026/9w3i_65602.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w3i_65602/02_2026/9w3i_65602.cif"
  }
  resolution = 3.16
  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=   0.087
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5384      2.51       5
     N    1370      2.21       5
     O    1476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8284
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 4142
          Classifications: {'peptide': 552}
          Link IDs: {'PTRANS': 23, 'TRANS': 528}
          Chain breaks: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.65, per 1000 atoms: 0.32
  Number of scatterers: 8284
  At special positions: 0
  Unit cell: (104.384, 115.568, 89.472, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1476      8.00
     N    1370      7.00
     C    5384      6.00
    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: 0.76
  Conformation dependent library (CDL) restraints added in 282.5 milliseconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 2 sheets defined
      49.1% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 104
      removed outlier: 4.136A  pdb=" N   TRP A 103 " --> pdb=" O   PRO A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 107
      No H-bonds generated for 'chain 'A' and resid 105 through 107'
    Processing helix  chain 'A' and resid 108 through 115
      removed outlier: 3.630A  pdb=" N   SER A 114 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 122
      removed outlier: 3.715A  pdb=" N   THR A 121 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 125
      No H-bonds generated for 'chain 'A' and resid 123 through 125'
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 142 through 147
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.660A  pdb=" N   LEU A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 180
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 213
      removed outlier: 3.572A  pdb=" N   LEU A 211 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY A 212 " --> pdb=" O   GLN A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
    Processing helix  chain 'A' and resid 237 through 243
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.747A  pdb=" N   LEU A 279 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 275 through 279'
    Processing helix  chain 'A' and resid 285 through 294
      removed outlier: 4.344A  pdb=" N   THR A 291 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ARG A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 4.225A  pdb=" N   SER A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 319
      removed outlier: 3.760A  pdb=" N   VAL A 313 " --> pdb=" O   PRO A 309 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE A 315 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A 318 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 366
      removed outlier: 4.283A  pdb=" N   GLY A 360 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 401
      removed outlier: 3.568A  pdb=" N   ALA A 394 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ILE A 395 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A 396 " --> pdb=" O   MET A 392 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   MET A 400 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 442
      removed outlier: 4.058A  pdb=" N   THR A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 452
      removed outlier: 3.955A  pdb=" N   TYR A 451 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 467
      removed outlier: 3.864A  pdb=" N   ALA A 464 " --> pdb=" O   ILE A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 477
      removed outlier: 3.913A  pdb=" N   LEU A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 4.076A  pdb=" N   LEU A 493 " --> pdb=" O   MET A 489 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 495 " --> pdb=" O   ALA A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 509
      removed outlier: 3.573A  pdb=" N   LEU A 504 " --> pdb=" O   VAL A 500 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 506 " --> pdb=" O   MET A 502 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA A 507 " --> pdb=" O   GLY A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 520
      removed outlier: 3.899A  pdb=" N   LYS A 514 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 582
      removed outlier: 3.554A  pdb=" N   LEU A 568 " --> pdb=" O   ASN A 564 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU A 570 " --> pdb=" O   MET A 566 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET A 573 " --> pdb=" O   GLY A 569 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ARG A 574 " --> pdb=" O   GLU A 570 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG A 577 " --> pdb=" O   MET A 573 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 581 " --> pdb=" O   ARG A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 612
      removed outlier: 3.587A  pdb=" N   ALA A 611 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 621
      removed outlier: 3.968A  pdb=" N   VAL A 618 " --> pdb=" O   GLU A 614 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LYS A 621 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 640
    Processing helix  chain 'A' and resid 656 through 664
    Processing helix  chain 'B' and resid 99 through 104
      removed outlier: 4.137A  pdb=" N   TRP B 103 " --> pdb=" O   PRO B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 108 through 115
      removed outlier: 3.629A  pdb=" N   SER B 114 " --> pdb=" O   ARG B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 122
      removed outlier: 3.715A  pdb=" N   THR B 121 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 125
      No H-bonds generated for 'chain 'B' and resid 123 through 125'
    Processing helix  chain 'B' and resid 132 through 137
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 149 through 159
      removed outlier: 3.661A  pdb=" N   LEU B 157 " --> pdb=" O   LEU B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 180
    Processing helix  chain 'B' and resid 189 through 194
    Processing helix  chain 'B' and resid 198 through 204
    Processing helix  chain 'B' and resid 205 through 213
      removed outlier: 3.572A  pdb=" N   LEU B 211 " --> pdb=" O   PHE B 207 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY B 212 " --> pdb=" O   GLN B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 232
    Processing helix  chain 'B' and resid 237 through 243
    Processing helix  chain 'B' and resid 275 through 279
      removed outlier: 3.747A  pdb=" N   LEU B 279 " --> pdb=" O   TRP B 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 275 through 279'
    Processing helix  chain 'B' and resid 285 through 294
      removed outlier: 4.344A  pdb=" N   THR B 291 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   ARG B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 4.226A  pdb=" N   SER B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 319
      removed outlier: 3.760A  pdb=" N   VAL B 313 " --> pdb=" O   PRO B 309 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE B 315 " --> pdb=" O   THR B 311 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE B 318 " --> pdb=" O   ILE B 314 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE B 319 " --> pdb=" O   ILE B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 366
      removed outlier: 4.284A  pdb=" N   GLY B 360 " --> pdb=" O   ALA B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 401
      removed outlier: 3.569A  pdb=" N   ALA B 394 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ILE B 395 " --> pdb=" O   GLU B 391 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY B 396 " --> pdb=" O   MET B 392 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   MET B 400 " --> pdb=" O   GLY B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 442
      removed outlier: 4.058A  pdb=" N   THR B 441 " --> pdb=" O   ALA B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 452
      removed outlier: 3.955A  pdb=" N   TYR B 451 " --> pdb=" O   LEU B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 467
      removed outlier: 3.864A  pdb=" N   ALA B 464 " --> pdb=" O   ILE B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 477
      removed outlier: 3.913A  pdb=" N   LEU B 477 " --> pdb=" O   GLY B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 496
      removed outlier: 4.076A  pdb=" N   LEU B 493 " --> pdb=" O   MET B 489 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL B 495 " --> pdb=" O   ALA B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 509
      removed outlier: 3.574A  pdb=" N   LEU B 504 " --> pdb=" O   VAL B 500 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE B 506 " --> pdb=" O   MET B 502 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA B 507 " --> pdb=" O   GLY B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 520
      removed outlier: 3.898A  pdb=" N   LYS B 514 " --> pdb=" O   ILE B 510 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE B 515 " --> pdb=" O   SER B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 582
      removed outlier: 3.554A  pdb=" N   LEU B 568 " --> pdb=" O   ASN B 564 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY B 569 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU B 570 " --> pdb=" O   MET B 566 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET B 573 " --> pdb=" O   GLY B 569 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ARG B 574 " --> pdb=" O   GLU B 570 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG B 577 " --> pdb=" O   MET B 573 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU B 581 " --> pdb=" O   ARG B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 612
      removed outlier: 3.588A  pdb=" N   ALA B 611 " --> pdb=" O   SER B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 621
      removed outlier: 3.967A  pdb=" N   VAL B 618 " --> pdb=" O   GLU B 614 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS B 621 " --> pdb=" O   LYS B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 640
    Processing helix  chain 'B' and resid 656 through 664
    Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 538
      removed outlier: 4.348A  pdb=" N   ASN A 523 " --> pdb=" O   GLU A 557 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   VAL A 553 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A 552 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   ASP A 597 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   VAL A 554 " --> pdb=" O   ASP A 597 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   LEU A 628 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 536 through 538
      removed outlier: 4.348A  pdb=" N   ASN B 523 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   VAL B 553 " --> pdb=" O   LYS B 527 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU B 552 " --> pdb=" O   ILE B 595 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   ASP B 597 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   VAL B 554 " --> pdb=" O   ASP B 597 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   LEU B 628 " --> pdb=" O   PHE B 654 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    666 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: 0.81

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2259
        1.33 -     1.45: 1382
        1.45 -     1.57: 4701
        1.57 -     1.69: 0
        1.69 -     1.80: 94
  Bond restraints: 8436
  Sorted by residual:
  bond pdb=" C   SER A 160 "
       pdb=" N   SER A 161 "
    ideal  model  delta    sigma   weight residual
    1.329  1.248  0.081 1.37e-02 5.33e+03 3.46e+01
  bond pdb=" C   SER B 160 "
       pdb=" N   SER B 161 "
    ideal  model  delta    sigma   weight residual
    1.329  1.249  0.080 1.37e-02 5.33e+03 3.42e+01
  bond pdb=" CA  THR A 347 "
       pdb=" CB  THR A 347 "
    ideal  model  delta    sigma   weight residual
    1.526  1.560 -0.034 1.76e-02 3.23e+03 3.75e+00
  bond pdb=" CA  THR B 347 "
       pdb=" CB  THR B 347 "
    ideal  model  delta    sigma   weight residual
    1.526  1.560 -0.034 1.76e-02 3.23e+03 3.73e+00
  bond pdb=" CB  THR A 410 "
       pdb=" CG2 THR A 410 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.51e+00
  ... (remaining 8431 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 10848
        2.22 -     4.44: 508
        4.44 -     6.67: 76
        6.67 -     8.89: 15
        8.89 -    11.11: 5
  Bond angle restraints: 11452
  Sorted by residual:
  angle pdb=" N   VAL B 353 "
        pdb=" CA  VAL B 353 "
        pdb=" C   VAL B 353 "
      ideal   model   delta    sigma   weight residual
     112.96  108.22    4.74 1.00e+00 1.00e+00 2.25e+01
  angle pdb=" N   VAL A 353 "
        pdb=" CA  VAL A 353 "
        pdb=" C   VAL A 353 "
      ideal   model   delta    sigma   weight residual
     112.96  108.23    4.73 1.00e+00 1.00e+00 2.23e+01
  angle pdb=" O   LEU A 145 "
        pdb=" C   LEU A 145 "
        pdb=" N   TYR A 146 "
      ideal   model   delta    sigma   weight residual
     122.28  115.40    6.88 1.47e+00 4.63e-01 2.19e+01
  angle pdb=" O   LEU B 145 "
        pdb=" C   LEU B 145 "
        pdb=" N   TYR B 146 "
      ideal   model   delta    sigma   weight residual
     122.28  115.41    6.87 1.47e+00 4.63e-01 2.19e+01
  angle pdb=" N   THR A 427 "
        pdb=" CA  THR A 427 "
        pdb=" C   THR A 427 "
      ideal   model   delta    sigma   weight residual
     108.45  114.02   -5.57 1.26e+00 6.30e-01 1.95e+01
  ... (remaining 11447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4485
       17.89 -    35.79: 452
       35.79 -    53.68: 85
       53.68 -    71.57: 8
       71.57 -    89.47: 6
  Dihedral angle restraints: 5036
    sinusoidal: 1866
      harmonic: 3170
  Sorted by residual:
  dihedral pdb=" CA  ILE B 122 "
           pdb=" C   ILE B 122 "
           pdb=" N   ALA B 123 "
           pdb=" CA  ALA B 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.45   26.55     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  ILE A 122 "
           pdb=" C   ILE A 122 "
           pdb=" N   ALA A 123 "
           pdb=" CA  ALA A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.45   26.55     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  PHE B 284 "
           pdb=" C   PHE B 284 "
           pdb=" N   LEU B 285 "
           pdb=" CA  LEU B 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.51   26.49     0      5.00e+00 4.00e-02 2.81e+01
  ... (remaining 5033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 782
       0.043 -    0.086: 453
       0.086 -    0.129: 127
       0.129 -    0.172: 28
       0.172 -    0.215: 12
  Chirality restraints: 1402
  Sorted by residual:
  chirality pdb=" CB  VAL A 374 "
            pdb=" CA  VAL A 374 "
            pdb=" CG1 VAL A 374 "
            pdb=" CG2 VAL A 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  VAL B 374 "
            pdb=" CA  VAL B 374 "
            pdb=" CG1 VAL B 374 "
            pdb=" CG2 VAL B 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  THR A 520 "
            pdb=" CA  THR A 520 "
            pdb=" OG1 THR A 520 "
            pdb=" CG2 THR A 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1399 not shown)

  Planarity restraints: 1414
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 145 "   -0.018 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   LEU B 145 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LEU B 145 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR B 146 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 145 "    0.018 2.00e-02 2.50e+03   3.34e-02 1.12e+01
        pdb=" C   LEU A 145 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   LEU A 145 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 146 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 308 "    0.054 5.00e-02 4.00e+02   8.14e-02 1.06e+01
        pdb=" N   PRO B 309 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO B 309 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 309 "    0.046 5.00e-02 4.00e+02
  ... (remaining 1411 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 835
        2.73 -     3.27: 7902
        3.27 -     3.82: 13570
        3.82 -     4.36: 17530
        4.36 -     4.90: 28573
  Nonbonded interactions: 68410
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 367 "
            pdb=" OG1 THR A 411 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG  SER B 367 "
            pdb=" OG1 THR B 411 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   SER B 413 "
            pdb=" OG  SER B 417 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   SER A 413 "
            pdb=" OG  SER A 417 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   SER A 367 "
            pdb=" OG1 THR A 411 "
     model   vdw
     2.285 3.040
  ... (remaining 68405 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.780
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.600
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
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      :  0.009   0.081   8436  Z= 0.389
  Angle     :  1.103  11.110  11452  Z= 0.608
  Chirality :  0.057   0.215   1402
  Planarity :  0.008   0.081   1414
  Dihedral  : 14.844  89.467   2992
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  9.33 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.58 (0.16), residues: 1084
  helix: -4.76 (0.08), residues: 672
  sheet: -2.39 (0.85), residues: 34
  loop : -3.31 (0.26), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 181 
 TYR   0.014   0.003   TYR B 408 
 PHE   0.013   0.002   PHE A 449 
 TRP   0.009   0.001   TRP B 478 
 HIS   0.003   0.001   HIS A 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00867 ( 8436)
  covalent geometry    : angle       1.10264 (11452)
  hydrogen bonds       : bond        0.30603 (  230)
  hydrogen bonds       : angle      12.82833 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8746 (mtp) cc_final: 0.8506 (mtp)
REVERT: A  219 ILE cc_start: 0.8650 (pt) cc_final: 0.8447 (mt)
REVERT: A  546 MET cc_start: 0.6640 (mmp) cc_final: 0.6352 (mmp)
REVERT: B  370 GLU cc_start: 0.6253 (tt0) cc_final: 0.6017 (tt0)
REVERT: B  489 MET cc_start: 0.6935 (mmm) cc_final: 0.6511 (mmm)
REVERT: B  566 MET cc_start: 0.7909 (mmm) cc_final: 0.7520 (mtm)
  outliers start: 2
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1032
  time to fit residues: 22.1813
Evaluate side-chains
  119 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    6.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 182 GLN
A 242 GLN
A 344 ASN
A 389 ASN
A 666 HIS
B 344 ASN
B 389 ASN
B 541 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.218427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.195004 restraints weight = 10716.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 1.73
r_work: 0.4043 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3926 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8436  Z= 0.128
  Angle     :  0.635   6.529  11452  Z= 0.342
  Chirality :  0.042   0.253   1402
  Planarity :  0.006   0.055   1414
  Dihedral  :  6.891  22.263   1172
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.33 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.74 (0.18), residues: 1084
  helix: -4.11 (0.11), residues: 678
  sheet: -2.60 (0.73), residues: 44
  loop : -2.83 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.020   0.001   TYR B 421 
 PHE   0.021   0.001   PHE A 302 
 TRP   0.004   0.001   TRP A 303 
 HIS   0.001   0.001   HIS B 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8436)
  covalent geometry    : angle       0.63549 (11452)
  hydrogen bonds       : bond        0.04062 (  230)
  hydrogen bonds       : angle       6.74623 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  377 THR cc_start: 0.8446 (t) cc_final: 0.8110 (m)
REVERT: A  546 MET cc_start: 0.7558 (mmp) cc_final: 0.7342 (mmp)
REVERT: A  592 ARG cc_start: 0.6002 (ttt90) cc_final: 0.5540 (mtt90)
REVERT: B  370 GLU cc_start: 0.6617 (tt0) cc_final: 0.6414 (tt0)
REVERT: B  592 ARG cc_start: 0.6691 (ttt90) cc_final: 0.5847 (tpt90)
  outliers start: 13
  outliers final: 12
  residues processed: 139
  average time/residue: 0.0799
  time to fit residues: 15.7174
Evaluate side-chains
  131 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  336 LYS
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  471 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0040
   chunk 88 optimal weight:    0.0870
   chunk 107 optimal weight:    0.0870
   chunk 100 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 21 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   overall best weight:    0.3348

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 382 ASN
B  50 HIS
B 382 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.221833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.198911 restraints weight = 10546.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 1.68
r_work: 0.4090 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3970 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8436  Z= 0.105
  Angle     :  0.569   9.517  11452  Z= 0.299
  Chirality :  0.040   0.260   1402
  Planarity :  0.004   0.047   1414
  Dihedral  :  5.985  25.794   1172
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.44 %
    Favored  : 81.67 %
  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 are not related in a simple way.
  whole: -4.93 (0.21), residues: 1084
  helix: -3.48 (0.14), residues: 692
  sheet: -2.68 (0.67), residues: 48
  loop : -2.34 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 416 
 TYR   0.019   0.001   TYR B 421 
 PHE   0.025   0.001   PHE A 302 
 TRP   0.004   0.000   TRP B 303 
 HIS   0.001   0.000   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8436)
  covalent geometry    : angle       0.56868 (11452)
  hydrogen bonds       : bond        0.03071 (  230)
  hydrogen bonds       : angle       5.67293 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  156 SER cc_start: 0.8216 (t) cc_final: 0.7702 (m)
REVERT: A  377 THR cc_start: 0.8460 (t) cc_final: 0.8059 (m)
REVERT: A  421 TYR cc_start: 0.7729 (t80) cc_final: 0.7351 (t80)
REVERT: A  434 MET cc_start: 0.6013 (ttm) cc_final: 0.5755 (ttt)
REVERT: A  592 ARG cc_start: 0.6128 (ttt90) cc_final: 0.5711 (mtt90)
REVERT: B  280 MET cc_start: 0.4762 (tmm) cc_final: 0.4485 (tmm)
REVERT: B  336 LYS cc_start: 0.5558 (OUTLIER) cc_final: 0.5041 (mptt)
REVERT: B  357 LEU cc_start: 0.7841 (tp) cc_final: 0.7548 (mt)
REVERT: B  370 GLU cc_start: 0.6443 (tt0) cc_final: 0.6176 (tt0)
REVERT: B  592 ARG cc_start: 0.6501 (ttt90) cc_final: 0.5722 (tpt90)
  outliers start: 17
  outliers final: 9
  residues processed: 141
  average time/residue: 0.0727
  time to fit residues: 14.5447
Evaluate side-chains
  125 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 LYS
Chi-restraints excluded: chain B residue  347 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 182 GLN
A 242 GLN
A 541 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.213934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.189895 restraints weight = 10766.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 1.72
r_work: 0.3995 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3877 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   8436  Z= 0.203
  Angle     :  0.662   6.833  11452  Z= 0.344
  Chirality :  0.044   0.252   1402
  Planarity :  0.005   0.054   1414
  Dihedral  :  6.303  22.640   1172
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 17.67 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.22), residues: 1084
  helix: -3.18 (0.16), residues: 678
  sheet: -2.35 (0.77), residues: 44
  loop : -2.23 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 574 
 TYR   0.016   0.002   TYR B 408 
 PHE   0.026   0.002   PHE A 302 
 TRP   0.006   0.001   TRP B 103 
 HIS   0.002   0.000   HIS B 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 8436)
  covalent geometry    : angle       0.66178 (11452)
  hydrogen bonds       : bond        0.04058 (  230)
  hydrogen bonds       : angle       5.69331 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  377 THR cc_start: 0.8604 (t) cc_final: 0.8196 (m)
REVERT: A  592 ARG cc_start: 0.6331 (ttt90) cc_final: 0.5900 (mtt90)
REVERT: B  280 MET cc_start: 0.4911 (tmm) cc_final: 0.4673 (tmm)
REVERT: B  496 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7910 (mp)
REVERT: B  592 ARG cc_start: 0.6637 (ttt90) cc_final: 0.6103 (mtt90)
  outliers start: 39
  outliers final: 27
  residues processed: 148
  average time/residue: 0.0598
  time to fit residues: 13.1029
Evaluate side-chains
  138 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 LYS
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  415 SER
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  525 VAL
Chi-restraints excluded: chain B residue  627 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 72 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 100 optimal weight:    0.5980
   chunk 87 optimal weight:    0.3980
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   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  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.218588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.195049 restraints weight = 10595.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.4118 rms_B_bonded: 1.69
r_work: 0.4027 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3910 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8436  Z= 0.118
  Angle     :  0.581   8.401  11452  Z= 0.301
  Chirality :  0.041   0.258   1402
  Planarity :  0.004   0.049   1414
  Dihedral  :  5.727  24.885   1172
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.11 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.08 (0.23), residues: 1084
  helix: -2.89 (0.17), residues: 684
  sheet: -2.31 (0.77), residues: 44
  loop : -1.89 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.027   0.001   PHE A 302 
 TRP   0.003   0.001   TRP B 478 
 HIS   0.001   0.000   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8436)
  covalent geometry    : angle       0.58138 (11452)
  hydrogen bonds       : bond        0.02983 (  230)
  hydrogen bonds       : angle       5.20576 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  377 THR cc_start: 0.8478 (t) cc_final: 0.8053 (m)
REVERT: A  592 ARG cc_start: 0.6270 (ttt90) cc_final: 0.5781 (mtt90)
REVERT: B  357 LEU cc_start: 0.8259 (tp) cc_final: 0.7946 (mt)
REVERT: B  496 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7937 (mp)
REVERT: B  592 ARG cc_start: 0.6503 (ttt90) cc_final: 0.6023 (mtt90)
  outliers start: 22
  outliers final: 14
  residues processed: 129
  average time/residue: 0.0729
  time to fit residues: 13.4933
Evaluate side-chains
  124 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  471 VAL
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0030
   chunk 2 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0970
   chunk 93 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 182 GLN
A 339 ASN
B 382 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.219704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.197104 restraints weight = 10623.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 1.62
r_work: 0.4053 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3939 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8436  Z= 0.106
  Angle     :  0.553   7.431  11452  Z= 0.288
  Chirality :  0.040   0.250   1402
  Planarity :  0.004   0.048   1414
  Dihedral  :  5.302  20.473   1172
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.78 %
    Favored  : 77.56 %
  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 are not related in a simple way.
  whole: -3.72 (0.23), residues: 1084
  helix: -2.61 (0.18), residues: 688
  sheet: -2.11 (0.79), residues: 44
  loop : -1.72 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.013   0.001   TYR A 408 
 PHE   0.030   0.001   PHE A 302 
 TRP   0.003   0.000   TRP B 303 
 HIS   0.001   0.000   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8436)
  covalent geometry    : angle       0.55328 (11452)
  hydrogen bonds       : bond        0.02738 (  230)
  hydrogen bonds       : angle       4.90334 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  156 SER cc_start: 0.8223 (t) cc_final: 0.7910 (m)
REVERT: A  377 THR cc_start: 0.8405 (t) cc_final: 0.7983 (m)
REVERT: A  421 TYR cc_start: 0.7789 (t80) cc_final: 0.7485 (t80)
REVERT: A  592 ARG cc_start: 0.6344 (ttt90) cc_final: 0.5878 (mtt90)
REVERT: B  292 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6919 (ttt-90)
REVERT: B  357 LEU cc_start: 0.8143 (tp) cc_final: 0.7842 (mt)
REVERT: B  592 ARG cc_start: 0.6506 (ttt90) cc_final: 0.5990 (mtt90)
  outliers start: 33
  outliers final: 20
  residues processed: 146
  average time/residue: 0.0801
  time to fit residues: 16.7479
Evaluate side-chains
  135 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  339 ASN
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  525 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0570
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0470
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.221080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.198475 restraints weight = 10645.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 1.64
r_work: 0.4050 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3938 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8436  Z= 0.110
  Angle     :  0.555   7.064  11452  Z= 0.288
  Chirality :  0.041   0.250   1402
  Planarity :  0.004   0.048   1414
  Dihedral  :  5.219  21.698   1172
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.78 %
    Favored  : 77.56 %
  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 are not related in a simple way.
  whole: -3.55 (0.24), residues: 1084
  helix: -2.48 (0.18), residues: 690
  sheet: -2.03 (0.80), residues: 44
  loop : -1.63 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.022   0.001   TYR B 421 
 PHE   0.029   0.001   PHE A 302 
 TRP   0.003   0.000   TRP B 303 
 HIS   0.001   0.000   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8436)
  covalent geometry    : angle       0.55525 (11452)
  hydrogen bonds       : bond        0.02825 (  230)
  hydrogen bonds       : angle       4.82667 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  377 THR cc_start: 0.8417 (t) cc_final: 0.7993 (m)
REVERT: A  421 TYR cc_start: 0.7655 (t80) cc_final: 0.7384 (t80)
REVERT: A  592 ARG cc_start: 0.6375 (ttt90) cc_final: 0.5880 (mtt90)
REVERT: B  292 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6955 (ttt-90)
REVERT: B  357 LEU cc_start: 0.8171 (tp) cc_final: 0.7881 (mt)
REVERT: B  592 ARG cc_start: 0.6520 (ttt90) cc_final: 0.5974 (mtt90)
  outliers start: 24
  outliers final: 20
  residues processed: 130
  average time/residue: 0.0750
  time to fit residues: 13.7890
Evaluate side-chains
  136 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  339 ASN
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  525 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0030
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0010
   chunk 68 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 57 optimal weight:    8.9990
   chunk 27 optimal weight:    0.1980
   chunk 60 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.2596

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 339 ASN
A 541 GLN
B 188 GLN
B 382 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.222989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.200719 restraints weight = 10558.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.4163 rms_B_bonded: 1.63
r_work: 0.4073 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3959 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8436  Z= 0.095
  Angle     :  0.541   6.758  11452  Z= 0.281
  Chirality :  0.040   0.245   1402
  Planarity :  0.004   0.047   1414
  Dihedral  :  5.033  20.243   1172
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.33 %
    Favored  : 77.56 %
  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 are not related in a simple way.
  whole: -3.41 (0.24), residues: 1084
  helix: -2.37 (0.18), residues: 690
  sheet: -1.87 (0.81), residues: 44
  loop : -1.60 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.022   0.001   TYR B 421 
 PHE   0.032   0.001   PHE A 302 
 TRP   0.003   0.000   TRP B 303 
 HIS   0.001   0.000   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8436)
  covalent geometry    : angle       0.54062 (11452)
  hydrogen bonds       : bond        0.02681 (  230)
  hydrogen bonds       : angle       4.72700 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  357 LEU cc_start: 0.8292 (tp) cc_final: 0.7967 (mt)
REVERT: A  421 TYR cc_start: 0.7670 (t80) cc_final: 0.7417 (t80)
REVERT: A  592 ARG cc_start: 0.6369 (ttt90) cc_final: 0.5825 (mtt90)
REVERT: B  292 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7004 (ttt-90)
REVERT: B  357 LEU cc_start: 0.8151 (tp) cc_final: 0.7901 (mt)
REVERT: B  592 ARG cc_start: 0.6445 (ttt90) cc_final: 0.5899 (mtt90)
  outliers start: 19
  outliers final: 17
  residues processed: 130
  average time/residue: 0.0696
  time to fit residues: 12.9547
Evaluate side-chains
  133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  556 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 77 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.219360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.196417 restraints weight = 10627.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.4121 rms_B_bonded: 1.63
r_work: 0.4030 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3917 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8436  Z= 0.142
  Angle     :  0.583   7.211  11452  Z= 0.302
  Chirality :  0.042   0.255   1402
  Planarity :  0.004   0.049   1414
  Dihedral  :  5.240  21.916   1172
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.67 %
    Favored  : 76.56 %
  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 are not related in a simple way.
  whole: -3.35 (0.24), residues: 1084
  helix: -2.32 (0.19), residues: 688
  sheet: -1.88 (0.80), residues: 44
  loop : -1.57 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.014   0.001   TYR B 421 
 PHE   0.047   0.001   PHE B 302 
 TRP   0.006   0.001   TRP B 103 
 HIS   0.002   0.000   HIS B 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8436)
  covalent geometry    : angle       0.58303 (11452)
  hydrogen bonds       : bond        0.03088 (  230)
  hydrogen bonds       : angle       4.84900 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  357 LEU cc_start: 0.8465 (tp) cc_final: 0.8120 (mt)
REVERT: A  421 TYR cc_start: 0.7742 (t80) cc_final: 0.7449 (t80)
REVERT: A  592 ARG cc_start: 0.6378 (ttt90) cc_final: 0.5875 (mtt90)
REVERT: A  598 MET cc_start: 0.8811 (mtp) cc_final: 0.8475 (mmm)
REVERT: B  292 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6977 (ttt-90)
REVERT: B  357 LEU cc_start: 0.8406 (tp) cc_final: 0.8164 (mt)
REVERT: B  592 ARG cc_start: 0.6521 (ttt90) cc_final: 0.5958 (mtt90)
  outliers start: 25
  outliers final: 21
  residues processed: 128
  average time/residue: 0.0748
  time to fit residues: 13.7348
Evaluate side-chains
  137 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 LYS
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  525 VAL
Chi-restraints excluded: chain B residue  556 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 73 optimal weight:    0.4980
   chunk 63 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0070
   chunk 42 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 95 optimal weight:    0.5980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.221629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.199212 restraints weight = 10586.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 1.62
r_work: 0.4055 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3940 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8436  Z= 0.111
  Angle     :  0.554   7.166  11452  Z= 0.288
  Chirality :  0.041   0.248   1402
  Planarity :  0.004   0.048   1414
  Dihedral  :  5.054  21.406   1172
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.56 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.24), residues: 1084
  helix: -2.26 (0.19), residues: 690
  sheet: -1.77 (0.81), residues: 44
  loop : -1.51 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.043   0.001   PHE B 302 
 TRP   0.002   0.000   TRP B 303 
 HIS   0.001   0.000   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8436)
  covalent geometry    : angle       0.55406 (11452)
  hydrogen bonds       : bond        0.02795 (  230)
  hydrogen bonds       : angle       4.71921 (  666)

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  421 TYR cc_start: 0.7708 (t80) cc_final: 0.7446 (t80)
REVERT: A  592 ARG cc_start: 0.6393 (ttt90) cc_final: 0.5835 (mtt90)
REVERT: A  598 MET cc_start: 0.8806 (mtp) cc_final: 0.8476 (mmm)
REVERT: B  292 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6999 (ttt-90)
REVERT: B  357 LEU cc_start: 0.8331 (tp) cc_final: 0.8080 (mt)
REVERT: B  592 ARG cc_start: 0.6464 (ttt90) cc_final: 0.5889 (mtt90)
  outliers start: 20
  outliers final: 18
  residues processed: 127
  average time/residue: 0.0748
  time to fit residues: 13.3675
Evaluate side-chains
  133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  498 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  336 LYS
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  525 VAL
Chi-restraints excluded: chain B residue  556 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0170
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6820

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.219444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.196548 restraints weight = 10753.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 1.63
r_work: 0.4038 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3924 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8436  Z= 0.125
  Angle     :  0.568   7.152  11452  Z= 0.294
  Chirality :  0.042   0.252   1402
  Planarity :  0.004   0.049   1414
  Dihedral  :  5.089  21.519   1172
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.56 %
    Favored  : 76.11 %
  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 are not related in a simple way.
  whole: -3.13 (0.24), residues: 1084
  helix: -2.17 (0.19), residues: 690
  sheet: -1.74 (0.81), residues: 44
  loop : -1.45 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 574 
 TYR   0.022   0.001   TYR B 421 
 PHE   0.042   0.001   PHE B 302 
 TRP   0.004   0.000   TRP A 103 
 HIS   0.001   0.000   HIS B 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8436)
  covalent geometry    : angle       0.56800 (11452)
  hydrogen bonds       : bond        0.02868 (  230)
  hydrogen bonds       : angle       4.73096 (  666)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1917.73 seconds
wall clock time: 33 minutes 27.91 seconds (2007.91 seconds total)