Starting phenix.real_space_refine
on Wed Aug  5 19:22:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vji_65114/08_2026/9vji_65114_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vji_65114/08_2026/9vji_65114.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vji_65114/08_2026/9vji_65114_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vji_65114/08_2026/9vji_65114_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vji_65114/08_2026/9vji_65114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vji_65114/08_2026/9vji_65114.map"
  }
  resolution = 4.2
  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=   0.002
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      82      5.16       5
     C    7150      2.51       5
     N    1978      2.21       5
     O    2016      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11226
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 716, 5613
          Classifications: {'peptide': 716}
          Link IDs: {'PTRANS': 37, 'TRANS': 678}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 5613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 716, 5613
          Classifications: {'peptide': 716}
          Link IDs: {'PTRANS': 37, 'TRANS': 678}
          Chain breaks: 5
  Time building chain proxies: 2.21, per 1000 atoms: 0.20
  Number of scatterers: 11226
  At special positions: 0
  Unit cell: (105.78, 117.26, 92.66, 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      82     16.00
     O    2016      8.00
     N    1978      7.00
     C    7150      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: 0.64
  Conformation dependent library (CDL) restraints added in 434.6 milliseconds
  

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2672

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 10 sheets defined
      54.5% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 38
      removed outlier: 3.728A  pdb=" N   GLU A  23 " --> pdb=" O   ILE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 50
      Proline residue:  A  47  - end of helix
    Processing helix  chain 'A' and resid 86 through 99
    Processing helix  chain 'A' and resid 112 through 126
    Processing helix  chain 'A' and resid 175 through 182
    Processing helix  chain 'A' and resid 183 through 185
      No H-bonds generated for 'chain 'A' and resid 183 through 185'
    Processing helix  chain 'A' and resid 190 through 205
    Processing helix  chain 'A' and resid 216 through 227
      removed outlier: 3.720A  pdb=" N   VAL A 220 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 285 through 296
      removed outlier: 3.530A  pdb=" N   GLU A 289 " --> pdb=" O   THR A 285 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 319
      removed outlier: 3.820A  pdb=" N   GLN A 319 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 341
      removed outlier: 4.042A  pdb=" N   GLN A 341 " --> pdb=" O   THR A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 353
      removed outlier: 4.248A  pdb=" N   VAL A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 386
    Processing helix  chain 'A' and resid 412 through 422
    Processing helix  chain 'A' and resid 459 through 475
      removed outlier: 4.553A  pdb=" N   TYR A 466 " --> pdb=" O   ASN A 462 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   LYS A 467 " --> pdb=" O   LYS A 463 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   HIS A 468 " --> pdb=" O   PHE A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 491
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 4.546A  pdb=" N   ARG A 529 " --> pdb=" O   GLN A 525 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   GLU A 530 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 546
      removed outlier: 3.760A  pdb=" N   GLU A 546 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 557
    Processing helix  chain 'A' and resid 563 through 575
    Processing helix  chain 'A' and resid 576 through 595
    Processing helix  chain 'A' and resid 595 through 601
      removed outlier: 3.883A  pdb=" N   THR A 599 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ARG A 600 " --> pdb=" O   PRO A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 613
    Processing helix  chain 'A' and resid 637 through 654
    Processing helix  chain 'A' and resid 668 through 677
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 702 through 714
      removed outlier: 3.757A  pdb=" N   SER A 714 " --> pdb=" O   ALA A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 739
    Processing helix  chain 'A' and resid 806 through 812
      removed outlier: 3.628A  pdb=" N   CYS A 811 " --> pdb=" O   TRP A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 834
    Processing helix  chain 'B' and resid 20 through 38
    Processing helix  chain 'B' and resid 41 through 50
      Proline residue:  B  47  - end of helix
    Processing helix  chain 'B' and resid 86 through 99
    Processing helix  chain 'B' and resid 112 through 126
    Processing helix  chain 'B' and resid 175 through 182
    Processing helix  chain 'B' and resid 190 through 205
    Processing helix  chain 'B' and resid 216 through 227
      removed outlier: 3.599A  pdb=" N   VAL B 220 " --> pdb=" O   ASN B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 256 through 264
    Processing helix  chain 'B' and resid 285 through 296
      removed outlier: 3.699A  pdb=" N   GLY B 296 " --> pdb=" O   ALA B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 319
      removed outlier: 3.795A  pdb=" N   GLN B 319 " --> pdb=" O   ARG B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 341
      removed outlier: 3.548A  pdb=" N   GLY B 340 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLN B 341 " --> pdb=" O   THR B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 4.272A  pdb=" N   VAL B 353 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 386
    Processing helix  chain 'B' and resid 412 through 422
      removed outlier: 3.543A  pdb=" N   LEU B 416 " --> pdb=" O   THR B 412 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN B 417 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 464 through 475
      removed outlier: 4.081A  pdb=" N   HIS B 468 " --> pdb=" O   PHE B 464 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU B 475 " --> pdb=" O   GLU B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 491
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.623A  pdb=" N   ARG B 526 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP B 527 " --> pdb=" O   ARG B 523 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   ARG B 529 " --> pdb=" O   GLN B 525 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLU B 530 " --> pdb=" O   ARG B 526 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B 531 " --> pdb=" O   ASP B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 546
      removed outlier: 3.892A  pdb=" N   GLU B 546 " --> pdb=" O   ALA B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 557
    Processing helix  chain 'B' and resid 563 through 575
    Processing helix  chain 'B' and resid 576 through 595
    Processing helix  chain 'B' and resid 595 through 601
      removed outlier: 3.872A  pdb=" N   THR B 599 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG B 600 " --> pdb=" O   PRO B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 613
    Processing helix  chain 'B' and resid 637 through 654
      removed outlier: 3.521A  pdb=" N   LEU B 654 " --> pdb=" O   MET B 650 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 677
    Processing helix  chain 'B' and resid 679 through 693
    Processing helix  chain 'B' and resid 702 through 714
      removed outlier: 3.748A  pdb=" N   SER B 714 " --> pdb=" O   ALA B 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 725 through 739
    Processing helix  chain 'B' and resid 806 through 812
      removed outlier: 3.642A  pdb=" N   CYS B 811 " --> pdb=" O   TRP B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 822 through 834
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58
      removed outlier: 6.034A  pdb=" N   THR A  77 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   ASP A 212 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 171 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   LEU A 107 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ASP A 174 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   VAL A 109 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 326
      removed outlier: 3.689A  pdb=" N   VAL A 345 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER A 304 " --> pdb=" O   TYR A 347 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   ARG A 248 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE A 398 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   LEU A 250 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   MET A 400 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   CYS A 249 " --> pdb=" O   ARG A 497 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 620
      removed outlier: 4.039A  pdb=" N   GLY A 615 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 656 through 657
    Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 745
    Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 58
      removed outlier: 6.029A  pdb=" N   THR B  77 " --> pdb=" O   ALA B 210 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   ASP B 212 " --> pdb=" O   THR B  77 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   VAL B  79 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU B 171 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   LEU B 107 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ASP B 174 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 5.611A  pdb=" N   VAL B 109 " --> pdb=" O   ASP B 174 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   VAL B 152 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   VAL B 108 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 326
      removed outlier: 3.835A  pdb=" N   VAL B 345 " --> pdb=" O   ILE B 300 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER B 304 " --> pdb=" O   TYR B 347 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 396 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE B 398 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   LEU B 250 " --> pdb=" O   ILE B 398 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   MET B 400 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   CYS B 249 " --> pdb=" O   ARG B 497 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 615 through 620
      removed outlier: 3.993A  pdb=" N   GLY B 615 " --> pdb=" O   LEU B 631 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 656 through 657
    Processing sheet with id=AB1, first strand: chain 'B' and resid 744 through 745

    551 hydrogen bonds defined for protein.
    1623 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3687
        1.34 -     1.46: 1899
        1.46 -     1.58: 5764
        1.58 -     1.70: 0
        1.70 -     1.82: 124
  Bond restraints: 11474
  Sorted by residual:
  bond pdb=" N   GLU A 408 "
       pdb=" CA  GLU A 408 "
    ideal  model  delta    sigma   weight residual
    1.451  1.489 -0.039 1.60e-02 3.91e+03 5.81e+00
  bond pdb=" C   GLU A 408 "
       pdb=" N   PRO A 409 "
    ideal  model  delta    sigma   weight residual
    1.331  1.351 -0.021 1.31e-02 5.83e+03 2.55e+00
  bond pdb=" C   PRO A 409 "
       pdb=" O   PRO A 409 "
    ideal  model  delta    sigma   weight residual
    1.234  1.217  0.016 1.14e-02 7.69e+03 1.99e+00
  bond pdb=" CA  PRO A 409 "
       pdb=" C   PRO A 409 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 1.31e-02 5.83e+03 1.38e+00
  bond pdb=" CB  MET A 842 "
       pdb=" CG  MET A 842 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.35e+00
  ... (remaining 11469 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 15477
        2.61 -     5.23: 91
        5.23 -     7.84: 9
        7.84 -    10.45: 3
       10.45 -    13.07: 2
  Bond angle restraints: 15582
  Sorted by residual:
  angle pdb=" CB  MET B 842 "
        pdb=" CG  MET B 842 "
        pdb=" SD  MET B 842 "
      ideal   model   delta    sigma   weight residual
     112.70  125.77  -13.07 3.00e+00 1.11e-01 1.90e+01
  angle pdb=" CB  MET A 842 "
        pdb=" CG  MET A 842 "
        pdb=" SD  MET A 842 "
      ideal   model   delta    sigma   weight residual
     112.70  124.30  -11.60 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" CA  MET B 842 "
        pdb=" CB  MET B 842 "
        pdb=" CG  MET B 842 "
      ideal   model   delta    sigma   weight residual
     114.10  121.12   -7.02 2.00e+00 2.50e-01 1.23e+01
  angle pdb=" CB  MET A 241 "
        pdb=" CG  MET A 241 "
        pdb=" SD  MET A 241 "
      ideal   model   delta    sigma   weight residual
     112.70  122.47   -9.77 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" N   PRO A 409 "
        pdb=" CA  PRO A 409 "
        pdb=" C   PRO A 409 "
      ideal   model   delta    sigma   weight residual
     111.38  116.44   -5.06 1.59e+00 3.96e-01 1.01e+01
  ... (remaining 15577 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.58: 5627
       14.58 -    29.17: 836
       29.17 -    43.75: 300
       43.75 -    58.34: 74
       58.34 -    72.92: 23
  Dihedral angle restraints: 6860
    sinusoidal: 2726
      harmonic: 4134
  Sorted by residual:
  dihedral pdb=" CA  ASN A 299 "
           pdb=" CB  ASN A 299 "
           pdb=" CG  ASN A 299 "
           pdb=" OD1 ASN A 299 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -167.08  -72.92     2      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CA  ASN B 299 "
           pdb=" CB  ASN B 299 "
           pdb=" CG  ASN B 299 "
           pdb=" OD1 ASN B 299 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -167.84  -72.16     2      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  MET A 744 "
           pdb=" C   MET A 744 "
           pdb=" N   ALA A 745 "
           pdb=" CA  ALA A 745 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.53   16.47     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 6857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1189
       0.028 -    0.056: 371
       0.056 -    0.084: 120
       0.084 -    0.112: 90
       0.112 -    0.140: 14
  Chirality restraints: 1784
  Sorted by residual:
  chirality pdb=" CA  VAL B  46 "
            pdb=" N   VAL B  46 "
            pdb=" C   VAL B  46 "
            pdb=" CB  VAL B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.30    0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  MET B 842 "
            pdb=" N   MET B 842 "
            pdb=" C   MET B 842 "
            pdb=" CB  MET B 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CA  MET A 842 "
            pdb=" N   MET A 842 "
            pdb=" C   MET A 842 "
            pdb=" CB  MET A 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1781 not shown)

  Planarity restraints: 1994
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 408 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.05e+00
        pdb=" N   PRO B 409 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 409 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 409 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 842 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   MET B 842 "    0.029 2.00e-02 2.50e+03
        pdb=" O   MET B 842 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN B 843 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 842 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   MET A 842 "    0.029 2.00e-02 2.50e+03
        pdb=" O   MET A 842 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN A 843 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1991 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1128
        2.75 -     3.28: 11050
        3.28 -     3.82: 19073
        3.82 -     4.36: 20844
        4.36 -     4.90: 36542
  Nonbonded interactions: 88637
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 349 "
            pdb=" OG  SER B 384 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG1 THR A 349 "
            pdb=" OG  SER A 384 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   ASP B 610 "
            pdb=" OG1 THR B 614 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OH  TYR B 609 "
            pdb=" OG1 THR B 634 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   ASP A 610 "
            pdb=" OG1 THR A 614 "
     model   vdw
     2.226 3.040
  ... (remaining 88632 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     8.920
  Find NCS groups from input model:        0.170
  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:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5043
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      :  0.002   0.039  11474  Z= 0.101
  Angle     :  0.526  13.069  15582  Z= 0.253
  Chirality :  0.037   0.140   1784
  Planarity :  0.003   0.044   1994
  Dihedral  : 16.537  72.921   4188
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 28.77 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.23), residues: 1408
  helix:  1.81 (0.19), residues: 706
  sheet:  1.74 (0.39), residues: 180
  loop : -0.46 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 472 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.019   0.001   PHE A 309 
 TRP   0.006   0.001   TRP A 339 
 HIS   0.001   0.000   HIS A 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00213 /  0.10 (11474)
  covalent geometry    : angle       0.52576 /  0.25 (15582)
  hydrogen bonds       : bond        0.19260 / 12.85 (  551)
  hydrogen bonds       : angle       6.34970 /  4.50 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 396
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.6376 (mtp) cc_final: 0.6079 (mtp)
REVERT: A  177 MET cc_start: 0.4988 (mmt) cc_final: 0.4441 (mmm)
REVERT: A  188 MET cc_start: 0.7189 (ppp) cc_final: 0.6519 (ppp)
REVERT: A  255 LEU cc_start: 0.6845 (tp) cc_final: 0.6448 (tp)
REVERT: A  472 ARG cc_start: 0.6114 (mmm160) cc_final: 0.5493 (mmt-90)
REVERT: A  842 MET cc_start: 0.4793 (ppp) cc_final: 0.3390 (ppp)
REVERT: B   36 MET cc_start: 0.6584 (mtp) cc_final: 0.6124 (mtp)
REVERT: B  177 MET cc_start: 0.4792 (mmt) cc_final: 0.4590 (mmm)
REVERT: B  188 MET cc_start: 0.7463 (ppp) cc_final: 0.6500 (ppp)
REVERT: B  255 LEU cc_start: 0.6725 (tp) cc_final: 0.6191 (tt)
REVERT: B  379 VAL cc_start: 0.8612 (t) cc_final: 0.8023 (t)
REVERT: B  485 LEU cc_start: 0.7390 (mt) cc_final: 0.7074 (tt)
REVERT: B  558 LEU cc_start: 0.8622 (mt) cc_final: 0.7370 (mt)
REVERT: B  842 MET cc_start: 0.5042 (ppp) cc_final: 0.1940 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 396
  average time/residue: 0.1079
  time to fit residues: 57.5189
Evaluate side-chains
  188 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 ASN
A 328 HIS
A 383 GLN
A 483 ASN
A 727 HIS
B  50 HIS
** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 ASN
B 483 ASN
B 727 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.225419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.194466 restraints weight = 21041.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.197796 restraints weight = 16380.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.199791 restraints weight = 12805.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.200275 restraints weight = 9677.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.200726 restraints weight = 9418.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.4533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5793
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11474  Z= 0.147
  Angle     :  0.647   8.583  15582  Z= 0.323
  Chirality :  0.042   0.159   1784
  Planarity :  0.005   0.038   1994
  Dihedral  :  3.593  15.606   1578
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.93 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.22), residues: 1408
  helix:  1.41 (0.19), residues: 712
  sheet:  1.23 (0.36), residues: 214
  loop : -0.67 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  74 
 TYR   0.016   0.002   TYR B 184 
 PHE   0.042   0.002   PHE B 123 
 TRP   0.014   0.002   TRP A 426 
 HIS   0.006   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 (11474)
  covalent geometry    : angle       0.64745 /  0.32 (15582)
  hydrogen bonds       : bond        0.04038 /  2.78 (  551)
  hydrogen bonds       : angle       4.59957 /  3.20 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 259
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.5262 (tmm) cc_final: 0.5048 (tmm)
REVERT: A  506 THR cc_start: 0.6811 (p) cc_final: 0.6296 (p)
REVERT: A  531 LEU cc_start: 0.7236 (tp) cc_final: 0.6975 (tp)
REVERT: B   21 ASP cc_start: 0.6688 (p0) cc_final: 0.6339 (p0)
REVERT: B   96 ARG cc_start: 0.4411 (mmt180) cc_final: 0.4154 (mmp80)
REVERT: B  188 MET cc_start: 0.7506 (ppp) cc_final: 0.7153 (ppp)
REVERT: B  506 THR cc_start: 0.7216 (p) cc_final: 0.5961 (p)
REVERT: B  546 GLU cc_start: 0.6779 (pp20) cc_final: 0.6218 (pm20)
REVERT: B  558 LEU cc_start: 0.8414 (mt) cc_final: 0.7899 (mt)
REVERT: B  628 LEU cc_start: 0.6175 (mt) cc_final: 0.5721 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 260
  average time/residue: 0.0847
  time to fit residues: 31.7692
Evaluate side-chains
  180 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 102 optimal weight:   10.0000
   chunk 101 optimal weight:    0.0040
   chunk 33 optimal weight:    0.3980
   chunk 125 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 138 optimal weight:    5.9990
   chunk 11 optimal weight:    0.2980
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.4594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
A 483 ASN
A 575 ASN
A 621 ASN
B  50 HIS
B 216 ASN
B 483 ASN
B 575 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.224150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.193098 restraints weight = 21013.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.195431 restraints weight = 17333.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.197377 restraints weight = 14951.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.198151 restraints weight = 10877.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.198771 restraints weight = 10427.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5924
moved from start:          0.5014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11474  Z= 0.124
  Angle     :  0.615   7.618  15582  Z= 0.302
  Chirality :  0.042   0.178   1784
  Planarity :  0.004   0.052   1994
  Dihedral  :  3.553  14.469   1578
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.34 %
    Favored  : 95.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.22), residues: 1408
  helix:  1.34 (0.19), residues: 716
  sheet:  0.94 (0.35), residues: 214
  loop : -0.66 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  96 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.011   0.001   PHE B 732 
 TRP   0.015   0.001   TRP A 426 
 HIS   0.012   0.001   HIS A 501 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 (11474)
  covalent geometry    : angle       0.61540 /  0.30 (15582)
  hydrogen bonds       : bond        0.03591 /  2.44 (  551)
  hydrogen bonds       : angle       4.35934 /  3.04 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LEU cc_start: 0.7462 (mm) cc_final: 0.7233 (mm)
REVERT: A  558 LEU cc_start: 0.8353 (mp) cc_final: 0.8132 (mp)
REVERT: A  570 LEU cc_start: 0.7786 (tp) cc_final: 0.7467 (mm)
REVERT: A  842 MET cc_start: 0.4085 (ppp) cc_final: 0.3836 (ppp)
REVERT: B   21 ASP cc_start: 0.6696 (p0) cc_final: 0.6181 (p0)
REVERT: B  177 MET cc_start: 0.6743 (mmm) cc_final: 0.5835 (mmm)
REVERT: B  188 MET cc_start: 0.7707 (ppp) cc_final: 0.7224 (ppp)
REVERT: B  385 LEU cc_start: 0.8713 (mm) cc_final: 0.8309 (mm)
REVERT: B  462 ASN cc_start: 0.7568 (p0) cc_final: 0.7336 (p0)
REVERT: B  531 LEU cc_start: 0.7397 (tp) cc_final: 0.7129 (tp)
REVERT: B  628 LEU cc_start: 0.6598 (mt) cc_final: 0.6065 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.0852
  time to fit residues: 28.5130
Evaluate side-chains
  166 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 137 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0770
   chunk 57 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   overall best weight:    0.6140

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 HIS
A 483 ASN
B  50 HIS
B 483 ASN
B 575 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.227847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.194992 restraints weight = 20795.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.198785 restraints weight = 14724.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.200780 restraints weight = 11224.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.201367 restraints weight = 8749.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.202043 restraints weight = 8595.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6026
moved from start:          0.5421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11474  Z= 0.119
  Angle     :  0.606   8.354  15582  Z= 0.295
  Chirality :  0.042   0.190   1784
  Planarity :  0.004   0.047   1994
  Dihedral  :  3.589  17.466   1578
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.70 %
    Favored  : 97.21 %
  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 are not related in a simple way.
  whole:  0.87 (0.23), residues: 1408
  helix:  1.37 (0.19), residues: 712
  sheet:  0.67 (0.35), residues: 214
  loop : -0.61 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 122 
 TYR   0.015   0.001   TYR A  38 
 PHE   0.019   0.001   PHE B 123 
 TRP   0.014   0.001   TRP A 426 
 HIS   0.003   0.001   HIS A 501 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (11474)
  covalent geometry    : angle       0.60591 /  0.30 (15582)
  hydrogen bonds       : bond        0.03302 /  2.24 (  551)
  hydrogen bonds       : angle       4.19994 /  2.93 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASP cc_start: 0.6536 (t0) cc_final: 0.6290 (t70)
REVERT: B   21 ASP cc_start: 0.6767 (p0) cc_final: 0.6243 (p0)
REVERT: B   36 MET cc_start: 0.6041 (ttt) cc_final: 0.5460 (ttp)
REVERT: B  173 LEU cc_start: 0.7876 (mt) cc_final: 0.7589 (mt)
REVERT: B  177 MET cc_start: 0.6895 (mmm) cc_final: 0.6140 (mmm)
REVERT: B  188 MET cc_start: 0.7827 (ppp) cc_final: 0.7250 (ppp)
REVERT: B  241 MET cc_start: 0.3438 (mmp) cc_final: 0.3153 (ttp)
REVERT: B  374 TYR cc_start: 0.6362 (m-80) cc_final: 0.5916 (m-80)
REVERT: B  531 LEU cc_start: 0.7313 (tp) cc_final: 0.7090 (tp)
REVERT: B  558 LEU cc_start: 0.8672 (mt) cc_final: 0.8332 (mt)
REVERT: B  628 LEU cc_start: 0.6802 (mt) cc_final: 0.6411 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 224
  average time/residue: 0.0837
  time to fit residues: 27.5496
Evaluate side-chains
  169 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 119 optimal weight:    0.8980
   chunk 86 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0270
   chunk 98 optimal weight:    0.0170
   chunk 40 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 118 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.4876

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 HIS
A 483 ASN
A 575 ASN
B  50 HIS
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.220740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.187241 restraints weight = 20719.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.189765 restraints weight = 19325.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.191712 restraints weight = 16042.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.192641 restraints weight = 11542.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.193306 restraints weight = 11260.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6154
moved from start:          0.5740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11474  Z= 0.111
  Angle     :  0.601   7.456  15582  Z= 0.289
  Chirality :  0.041   0.190   1784
  Planarity :  0.004   0.041   1994
  Dihedral  :  3.525  15.303   1578
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.22), residues: 1408
  helix:  1.39 (0.19), residues: 716
  sheet:  0.72 (0.37), residues: 194
  loop : -0.62 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  96 
 TYR   0.010   0.001   TYR A  38 
 PHE   0.010   0.001   PHE A 131 
 TRP   0.010   0.001   TRP A 641 
 HIS   0.003   0.000   HIS A 727 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 (11474)
  covalent geometry    : angle       0.60086 /  0.29 (15582)
  hydrogen bonds       : bond        0.03128 /  2.13 (  551)
  hydrogen bonds       : angle       4.10878 /  2.85 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASP cc_start: 0.6731 (t0) cc_final: 0.6450 (t70)
REVERT: A  474 THR cc_start: 0.9111 (p) cc_final: 0.8860 (t)
REVERT: A  506 THR cc_start: 0.7530 (p) cc_final: 0.7109 (p)
REVERT: B   21 ASP cc_start: 0.6844 (p0) cc_final: 0.6313 (p0)
REVERT: B   36 MET cc_start: 0.6122 (ttt) cc_final: 0.5652 (ttp)
REVERT: B   83 MET cc_start: 0.5241 (tmm) cc_final: 0.4187 (tmm)
REVERT: B  173 LEU cc_start: 0.7829 (mt) cc_final: 0.7454 (mt)
REVERT: B  177 MET cc_start: 0.7120 (mmm) cc_final: 0.6310 (mmm)
REVERT: B  188 MET cc_start: 0.7801 (ppp) cc_final: 0.7231 (ppp)
REVERT: B  241 MET cc_start: 0.3856 (mmp) cc_final: 0.3089 (ttm)
REVERT: B  385 LEU cc_start: 0.8773 (mm) cc_final: 0.8230 (mm)
REVERT: B  487 MET cc_start: 0.7713 (tmm) cc_final: 0.7206 (mtt)
REVERT: B  508 LYS cc_start: 0.8683 (pptt) cc_final: 0.7847 (tptt)
REVERT: B  531 LEU cc_start: 0.7192 (tp) cc_final: 0.6877 (tp)
REVERT: B  558 LEU cc_start: 0.8534 (mt) cc_final: 0.8052 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0872
  time to fit residues: 27.5643
Evaluate side-chains
  170 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 138 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    2.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 ASN
** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
B  50 HIS
B 383 GLN
B 575 ASN
B 621 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.203707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.170437 restraints weight = 21174.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.171923 restraints weight = 18573.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.173426 restraints weight = 15701.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.173675 restraints weight = 11356.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.174201 restraints weight = 11299.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6635
moved from start:          0.7037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11474  Z= 0.202
  Angle     :  0.760   7.911  15582  Z= 0.377
  Chirality :  0.046   0.203   1784
  Planarity :  0.005   0.045   1994
  Dihedral  :  4.379  22.657   1578
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.54 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.22), residues: 1408
  helix:  0.86 (0.19), residues: 726
  sheet: -0.13 (0.35), residues: 222
  loop : -0.74 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  80 
 TYR   0.026   0.002   TYR B 342 
 PHE   0.022   0.003   PHE A 498 
 TRP   0.025   0.003   TRP A 426 
 HIS   0.004   0.001   HIS A 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.20 (11474)
  covalent geometry    : angle       0.76043 /  0.38 (15582)
  hydrogen bonds       : bond        0.04350 /  2.93 (  551)
  hydrogen bonds       : angle       4.64396 /  3.30 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 253
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASP cc_start: 0.6781 (t0) cc_final: 0.6492 (t70)
REVERT: A  188 MET cc_start: 0.8079 (ppp) cc_final: 0.7775 (ppp)
REVERT: A  290 LEU cc_start: 0.8029 (tp) cc_final: 0.7797 (tp)
REVERT: A  385 LEU cc_start: 0.9003 (mm) cc_final: 0.8742 (mm)
REVERT: A  396 LEU cc_start: 0.8522 (tp) cc_final: 0.8315 (tp)
REVERT: A  487 MET cc_start: 0.7790 (tmm) cc_final: 0.7509 (mtt)
REVERT: A  508 LYS cc_start: 0.8699 (pptt) cc_final: 0.7985 (tptt)
REVERT: A  566 GLU cc_start: 0.7520 (mp0) cc_final: 0.6819 (mm-30)
REVERT: A  570 LEU cc_start: 0.8265 (tp) cc_final: 0.7943 (tt)
REVERT: A  833 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6645 (tt0)
REVERT: B   36 MET cc_start: 0.6578 (ttt) cc_final: 0.6323 (mtp)
REVERT: B  188 MET cc_start: 0.8212 (ppp) cc_final: 0.7380 (ppp)
REVERT: B  290 LEU cc_start: 0.8001 (tp) cc_final: 0.7698 (tp)
REVERT: B  472 ARG cc_start: 0.8023 (mmp-170) cc_final: 0.7435 (mmt180)
REVERT: B  566 GLU cc_start: 0.7725 (mp0) cc_final: 0.7032 (mm-30)
REVERT: B  649 THR cc_start: 0.8838 (p) cc_final: 0.8592 (t)
REVERT: B  833 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6580 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 254
  average time/residue: 0.0795
  time to fit residues: 29.5827
Evaluate side-chains
  183 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 52 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 94 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 120 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 115 optimal weight:    7.9990
   chunk 99 optimal weight:   30.0000
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 483 ASN
A 575 ASN
A 820 ASN
B 383 GLN
B 518 HIS
B 575 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.208957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.175604 restraints weight = 20809.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.175738 restraints weight = 18798.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.178000 restraints weight = 15244.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.178679 restraints weight = 11319.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.179152 restraints weight = 10909.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.7161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11474  Z= 0.121
  Angle     :  0.645   8.062  15582  Z= 0.311
  Chirality :  0.042   0.181   1784
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.848  16.334   1578
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.23 %
    Favored  : 98.69 %
  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 are not related in a simple way.
  whole:  0.43 (0.22), residues: 1408
  helix:  1.15 (0.19), residues: 736
  sheet: -0.13 (0.36), residues: 218
  loop : -0.83 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 523 
 TYR   0.016   0.002   TYR B 382 
 PHE   0.031   0.002   PHE B 123 
 TRP   0.017   0.001   TRP A 426 
 HIS   0.003   0.001   HIS A 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 (11474)
  covalent geometry    : angle       0.64531 /  0.31 (15582)
  hydrogen bonds       : bond        0.03342 /  2.28 (  551)
  hydrogen bonds       : angle       4.20160 /  2.96 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 244
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASP cc_start: 0.6898 (t0) cc_final: 0.6627 (t70)
REVERT: A  123 PHE cc_start: 0.6110 (m-10) cc_final: 0.5732 (m-80)
REVERT: A  290 LEU cc_start: 0.8106 (tp) cc_final: 0.7695 (tp)
REVERT: A  385 LEU cc_start: 0.9098 (mm) cc_final: 0.8678 (mm)
REVERT: A  396 LEU cc_start: 0.8440 (tp) cc_final: 0.8239 (tp)
REVERT: A  408 GLU cc_start: 0.8245 (tp30) cc_final: 0.7988 (tm-30)
REVERT: A  487 MET cc_start: 0.7606 (tmm) cc_final: 0.7275 (mtt)
REVERT: A  508 LYS cc_start: 0.8690 (pptt) cc_final: 0.7939 (tptt)
REVERT: A  566 GLU cc_start: 0.7408 (mp0) cc_final: 0.6959 (mm-30)
REVERT: B   21 ASP cc_start: 0.6884 (p0) cc_final: 0.6280 (p0)
REVERT: B   36 MET cc_start: 0.6497 (ttt) cc_final: 0.6242 (mtp)
REVERT: B  188 MET cc_start: 0.8023 (ppp) cc_final: 0.7308 (ppp)
REVERT: B  290 LEU cc_start: 0.8227 (tp) cc_final: 0.7982 (tp)
REVERT: B  385 LEU cc_start: 0.9028 (mm) cc_final: 0.8402 (mm)
REVERT: B  472 ARG cc_start: 0.7985 (mmp-170) cc_final: 0.7059 (mmt180)
REVERT: B  529 ARG cc_start: 0.7269 (ptp90) cc_final: 0.6980 (ptt-90)
REVERT: B  566 GLU cc_start: 0.7565 (mp0) cc_final: 0.6810 (mm-30)
REVERT: B  649 THR cc_start: 0.8821 (p) cc_final: 0.8606 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 245
  average time/residue: 0.0734
  time to fit residues: 26.7986
Evaluate side-chains
  192 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 108 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 ASN
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.201488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.168397 restraints weight = 20859.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.168208 restraints weight = 19576.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.170332 restraints weight = 17536.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.170868 restraints weight = 12217.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.171538 restraints weight = 11652.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.7850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11474  Z= 0.177
  Angle     :  0.713   8.136  15582  Z= 0.349
  Chirality :  0.045   0.221   1784
  Planarity :  0.005   0.051   1994
  Dihedral  :  4.165  18.859   1578
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.39 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.22), residues: 1408
  helix:  0.95 (0.19), residues: 726
  sheet: -0.34 (0.35), residues: 222
  loop : -0.97 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 813 
 TYR   0.028   0.002   TYR A 374 
 PHE   0.023   0.002   PHE B 464 
 TRP   0.018   0.002   TRP A 426 
 HIS   0.004   0.001   HIS B 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.18 (11474)
  covalent geometry    : angle       0.71310 /  0.35 (15582)
  hydrogen bonds       : bond        0.03903 /  2.67 (  551)
  hydrogen bonds       : angle       4.46936 /  3.16 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.7972 (ppp) cc_final: 0.7540 (ppp)
REVERT: A  189 GLN cc_start: 0.7142 (pm20) cc_final: 0.6507 (mm110)
REVERT: A  487 MET cc_start: 0.7750 (tmm) cc_final: 0.7282 (mtt)
REVERT: A  508 LYS cc_start: 0.8692 (pptt) cc_final: 0.8043 (tptt)
REVERT: A  566 GLU cc_start: 0.7471 (mp0) cc_final: 0.6817 (mm-30)
REVERT: A  570 LEU cc_start: 0.8355 (tp) cc_final: 0.8123 (tp)
REVERT: A  842 MET cc_start: 0.4996 (ppp) cc_final: 0.4668 (ppp)
REVERT: B  188 MET cc_start: 0.8098 (ppp) cc_final: 0.7292 (ppp)
REVERT: B  189 GLN cc_start: 0.6931 (pm20) cc_final: 0.6402 (mm110)
REVERT: B  385 LEU cc_start: 0.9001 (mm) cc_final: 0.8467 (mm)
REVERT: B  508 LYS cc_start: 0.8787 (pptt) cc_final: 0.8508 (mmtt)
REVERT: B  566 GLU cc_start: 0.7654 (mp0) cc_final: 0.6820 (mm-30)
REVERT: B  649 THR cc_start: 0.8807 (p) cc_final: 0.8562 (t)
REVERT: B  744 MET cc_start: 0.7182 (tpp) cc_final: 0.6964 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0765
  time to fit residues: 26.6223
Evaluate side-chains
  178 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 101 optimal weight:    0.5980
   chunk 100 optimal weight:    0.3980
   chunk 125 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   chunk 71 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 38 optimal weight:    0.3980
   chunk 88 optimal weight:    5.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 148 HIS
A 483 ASN
A 575 ASN
B 148 HIS
B 573 ASN
B 575 ASN
B 685 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.198583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.165128 restraints weight = 20907.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.165681 restraints weight = 19782.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.167737 restraints weight = 17436.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.168107 restraints weight = 12223.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.168756 restraints weight = 11631.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.8294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  11474  Z= 0.171
  Angle     :  0.707   7.466  15582  Z= 0.346
  Chirality :  0.044   0.199   1784
  Planarity :  0.005   0.050   1994
  Dihedral  :  4.206  18.334   1578
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.57 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.22), residues: 1408
  helix:  0.86 (0.19), residues: 728
  sheet: -0.45 (0.38), residues: 198
  loop : -0.96 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 529 
 TYR   0.017   0.002   TYR B 683 
 PHE   0.022   0.002   PHE B 309 
 TRP   0.023   0.002   TRP A 426 
 HIS   0.003   0.001   HIS A 486 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.17 (11474)
  covalent geometry    : angle       0.70713 /  0.35 (15582)
  hydrogen bonds       : bond        0.03863 /  2.63 (  551)
  hydrogen bonds       : angle       4.52877 /  3.19 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 233
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7494 (mtp) cc_final: 0.7285 (mtp)
REVERT: A  188 MET cc_start: 0.8065 (ppp) cc_final: 0.7632 (ppp)
REVERT: A  189 GLN cc_start: 0.7218 (pm20) cc_final: 0.6500 (mm110)
REVERT: A  260 LEU cc_start: 0.8624 (tp) cc_final: 0.8385 (tp)
REVERT: A  326 LEU cc_start: 0.6406 (tt) cc_final: 0.6026 (pp)
REVERT: A  385 LEU cc_start: 0.9022 (mm) cc_final: 0.8531 (mm)
REVERT: A  566 GLU cc_start: 0.7351 (mp0) cc_final: 0.6894 (mm-30)
REVERT: B   21 ASP cc_start: 0.6650 (p0) cc_final: 0.6337 (p0)
REVERT: B  188 MET cc_start: 0.8172 (ppp) cc_final: 0.7717 (ppp)
REVERT: B  385 LEU cc_start: 0.9029 (mm) cc_final: 0.8444 (mm)
REVERT: B  472 ARG cc_start: 0.8533 (mmm160) cc_final: 0.8278 (mmm160)
REVERT: B  508 LYS cc_start: 0.8776 (pptt) cc_final: 0.8517 (mmtt)
REVERT: B  566 GLU cc_start: 0.7894 (mp0) cc_final: 0.6951 (mm-30)
REVERT: B  649 THR cc_start: 0.8742 (p) cc_final: 0.8528 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 233
  average time/residue: 0.0736
  time to fit residues: 25.5206
Evaluate side-chains
  194 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 94 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0370
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.8660

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 148 HIS
A 483 ASN
A 575 ASN
B 148 HIS
B 483 ASN
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.201872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.168328 restraints weight = 21042.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.169204 restraints weight = 20645.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.171441 restraints weight = 16632.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.171783 restraints weight = 11921.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.172451 restraints weight = 11759.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.8404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11474  Z= 0.134
  Angle     :  0.676   7.804  15582  Z= 0.328
  Chirality :  0.044   0.184   1784
  Planarity :  0.004   0.040   1994
  Dihedral  :  4.007  16.903   1578
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.33 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.22), residues: 1408
  helix:  0.97 (0.19), residues: 728
  sheet: -0.39 (0.38), residues: 198
  loop : -0.96 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 529 
 TYR   0.020   0.002   TYR A 342 
 PHE   0.016   0.002   PHE B 309 
 TRP   0.030   0.002   TRP A 641 
 HIS   0.004   0.001   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 (11474)
  covalent geometry    : angle       0.67591 /  0.33 (15582)
  hydrogen bonds       : bond        0.03478 /  2.41 (  551)
  hydrogen bonds       : angle       4.30760 /  3.04 ( 1623)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7504 (mtp) cc_final: 0.7254 (mtp)
REVERT: A  177 MET cc_start: 0.7848 (mmt) cc_final: 0.7492 (mmm)
REVERT: A  188 MET cc_start: 0.7960 (ppp) cc_final: 0.7731 (ppp)
REVERT: A  385 LEU cc_start: 0.9007 (mm) cc_final: 0.8369 (mm)
REVERT: A  485 LEU cc_start: 0.8349 (tp) cc_final: 0.8101 (tt)
REVERT: A  487 MET cc_start: 0.7784 (tmm) cc_final: 0.7337 (mtt)
REVERT: A  508 LYS cc_start: 0.8639 (pptt) cc_final: 0.7905 (tptt)
REVERT: A  566 GLU cc_start: 0.7368 (mp0) cc_final: 0.6686 (mm-30)
REVERT: A  744 MET cc_start: 0.7211 (tpp) cc_final: 0.6989 (tpp)
REVERT: B   21 ASP cc_start: 0.6535 (p0) cc_final: 0.6198 (p0)
REVERT: B   64 THR cc_start: 0.8439 (m) cc_final: 0.7912 (t)
REVERT: B   83 MET cc_start: 0.8339 (tpt) cc_final: 0.7755 (tpt)
REVERT: B  188 MET cc_start: 0.8184 (ppp) cc_final: 0.7630 (ppp)
REVERT: B  291 GLU cc_start: 0.7660 (pp20) cc_final: 0.7439 (pp20)
REVERT: B  385 LEU cc_start: 0.9067 (mm) cc_final: 0.8466 (mm)
REVERT: B  508 LYS cc_start: 0.8787 (pptt) cc_final: 0.8546 (mmtt)
REVERT: B  531 LEU cc_start: 0.6032 (pt) cc_final: 0.4930 (tp)
REVERT: B  566 GLU cc_start: 0.7712 (mp0) cc_final: 0.6892 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.0761
  time to fit residues: 25.5840
Evaluate side-chains
  184 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 107 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 130 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9990
   chunk 112 optimal weight:    0.4980
   chunk 83 optimal weight:    0.0670
   chunk 89 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0000
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.4722

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 483 ASN
A 575 ASN
B 483 ASN
B 575 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.203990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.172699 restraints weight = 21153.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.173070 restraints weight = 18202.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.175222 restraints weight = 15168.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.175875 restraints weight = 10873.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.176407 restraints weight = 10563.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6558
moved from start:          0.8513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11474  Z= 0.124
  Angle     :  0.677   8.587  15582  Z= 0.326
  Chirality :  0.043   0.196   1784
  Planarity :  0.004   0.040   1994
  Dihedral  :  3.911  16.307   1578
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.41 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.22), residues: 1408
  helix:  1.02 (0.19), residues: 726
  sheet: -0.37 (0.38), residues: 200
  loop : -0.90 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 529 
 TYR   0.018   0.001   TYR A 342 
 PHE   0.023   0.001   PHE B 115 
 TRP   0.021   0.001   TRP A 426 
 HIS   0.004   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.12 (11474)
  covalent geometry    : angle       0.67705 /  0.33 (15582)
  hydrogen bonds       : bond        0.03331 /  2.28 (  551)
  hydrogen bonds       : angle       4.22415 /  2.97 ( 1623)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1419.88 seconds
wall clock time: 25 minutes 16.29 seconds (1516.29 seconds total)