Starting phenix.real_space_refine
on Sat Aug 23 11:34:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b8j_15914/08_2025/8b8j_15914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b8j_15914/08_2025/8b8j_15914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b8j_15914/08_2025/8b8j_15914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b8j_15914/08_2025/8b8j_15914.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b8j_15914/08_2025/8b8j_15914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b8j_15914/08_2025/8b8j_15914.map"
  }
  resolution = 2.96
  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=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      76      5.16       5
     C    7686      2.51       5
     N    1884      2.21       5
     O    2034      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11686
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 709, 5840
          Classifications: {'peptide': 709}
          Link IDs: {'PTRANS': 32, 'TRANS': 676}
          Chain breaks: 8
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.10, per 1000 atoms: 0.35
  Number of scatterers: 11686
  At special positions: 0
  Unit cell: (126.294, 83.328, 113.274, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      76     16.00
     O    2034      8.00
     N    1884      7.00
     C    7686      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 352 " - pdb=" SG  CYS A 356 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 338 " - pdb=" SG  CYS B 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 349 " - pdb=" SG  CYS B 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 352 " - pdb=" SG  CYS B 356 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 346.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2696

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 8 sheets defined
      64.7% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 108
    Processing helix  chain 'A' and resid 131 through 142
    Processing helix  chain 'A' and resid 205 through 220
    Processing helix  chain 'A' and resid 234 through 239
    Processing helix  chain 'A' and resid 264 through 273
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 284 through 293
    Processing helix  chain 'A' and resid 293 through 327
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'A' and resid 364 through 375
      removed outlier: 3.513A  pdb=" N   ILE A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 409
    Processing helix  chain 'A' and resid 447 through 473
    Processing helix  chain 'A' and resid 474 through 488
    Processing helix  chain 'A' and resid 504 through 539
      removed outlier: 3.568A  pdb=" N   ALA A 508 " --> pdb=" O   THR A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 573
      removed outlier: 5.505A  pdb=" N   SER A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   CYS A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 638
      removed outlier: 3.880A  pdb=" N   LYS A 616 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA A 617 " --> pdb=" O   MET A 613 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE A 618 " --> pdb=" O   GLY A 614 " (cutoff:3.500A)
      Proline residue:  A 628  - end of helix
      removed outlier: 3.525A  pdb=" N   GLY A 635 " --> pdb=" O   MET A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 662 through 681
      removed outlier: 3.796A  pdb=" N   TYR A 666 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLU A 667 " --> pdb=" O   GLY A 663 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A 671 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 681 " --> pdb=" O   PHE A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 3.953A  pdb=" N   ARG A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 746
      removed outlier: 3.599A  pdb=" N   ILE A 728 " --> pdb=" O   ALA A 724 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A 737 " --> pdb=" O   ALA A 733 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 759
    Processing helix  chain 'A' and resid 762 through 766
    Processing helix  chain 'A' and resid 797 through 802
      removed outlier: 3.769A  pdb=" N   LEU A 801 " --> pdb=" O   PRO A 797 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLY A 802 " --> pdb=" O   TYR A 798 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 797 through 802'
    Processing helix  chain 'A' and resid 825 through 856
    Processing helix  chain 'A' and resid 861 through 875
      removed outlier: 3.601A  pdb=" N   SER A 866 " --> pdb=" O   LYS A 862 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 108
    Processing helix  chain 'B' and resid 131 through 142
    Processing helix  chain 'B' and resid 205 through 220
    Processing helix  chain 'B' and resid 234 through 239
    Processing helix  chain 'B' and resid 264 through 273
    Processing helix  chain 'B' and resid 275 through 279
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 293 through 327
    Processing helix  chain 'B' and resid 331 through 339
    Processing helix  chain 'B' and resid 364 through 375
      removed outlier: 3.512A  pdb=" N   ILE B 373 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 409
    Processing helix  chain 'B' and resid 447 through 473
    Processing helix  chain 'B' and resid 474 through 488
    Processing helix  chain 'B' and resid 504 through 539
      removed outlier: 3.568A  pdb=" N   ALA B 508 " --> pdb=" O   THR B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 573
      removed outlier: 5.504A  pdb=" N   SER B 566 " --> pdb=" O   ASN B 562 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   CYS B 567 " --> pdb=" O   TYR B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 638
      removed outlier: 3.879A  pdb=" N   LYS B 616 " --> pdb=" O   ILE B 612 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA B 617 " --> pdb=" O   MET B 613 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE B 618 " --> pdb=" O   GLY B 614 " (cutoff:3.500A)
      Proline residue:  B 628  - end of helix
      removed outlier: 3.525A  pdb=" N   GLY B 635 " --> pdb=" O   MET B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 655
    Processing helix  chain 'B' and resid 662 through 681
      removed outlier: 3.797A  pdb=" N   TYR B 666 " --> pdb=" O   LEU B 662 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLU B 667 " --> pdb=" O   GLY B 663 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET B 671 " --> pdb=" O   GLU B 667 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE B 681 " --> pdb=" O   PHE B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 709
      removed outlier: 3.953A  pdb=" N   ARG B 701 " --> pdb=" O   ILE B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 746
      removed outlier: 3.599A  pdb=" N   ILE B 728 " --> pdb=" O   ALA B 724 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL B 737 " --> pdb=" O   ALA B 733 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 749 through 759
    Processing helix  chain 'B' and resid 762 through 766
    Processing helix  chain 'B' and resid 797 through 802
      removed outlier: 3.770A  pdb=" N   LEU B 801 " --> pdb=" O   PRO B 797 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLY B 802 " --> pdb=" O   TYR B 798 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 797 through 802'
    Processing helix  chain 'B' and resid 825 through 856
    Processing helix  chain 'B' and resid 861 through 875
      removed outlier: 3.601A  pdb=" N   SER B 866 " --> pdb=" O   LYS B 862 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348
      removed outlier: 3.627A  pdb=" N   TRP A 359 " --> pdb=" O   MET A 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 657 through 658
      removed outlier: 6.940A  pdb=" N   GLN A 657 " --> pdb=" O   ARG A 712 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 785
    Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 116
    Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 348
      removed outlier: 3.628A  pdb=" N   TRP B 359 " --> pdb=" O   MET B 348 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 657 through 658
      removed outlier: 6.942A  pdb=" N   GLN B 657 " --> pdb=" O   ARG B 712 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 785

    720 hydrogen bonds defined for protein.
    2106 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: 1.59

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3544
        1.34 -     1.46: 2910
        1.46 -     1.58: 5430
        1.58 -     1.69: 0
        1.69 -     1.81: 114
  Bond restraints: 11998
  Sorted by residual:
  bond pdb=" C   PRO A 763 "
       pdb=" N   PRO A 764 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.60e-01
  bond pdb=" C   PRO B 763 "
       pdb=" N   PRO B 764 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.32e-01
  bond pdb=" C   GLY B 387 "
       pdb=" O   GLY B 387 "
    ideal  model  delta    sigma   weight residual
    1.234  1.243 -0.010 1.21e-02 6.83e+03 6.18e-01
  bond pdb=" C   VAL B 384 "
       pdb=" O   VAL B 384 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.009 1.13e-02 7.83e+03 5.83e-01
  bond pdb=" C   PHE A 382 "
       pdb=" O   PHE A 382 "
    ideal  model  delta    sigma   weight residual
    1.236  1.227  0.010 1.26e-02 6.30e+03 5.78e-01
  ... (remaining 11993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 16137
        1.99 -     3.97: 111
        3.97 -     5.96: 14
        5.96 -     7.94: 2
        7.94 -     9.93: 2
  Bond angle restraints: 16266
  Sorted by residual:
  angle pdb=" CA  LEU A 662 "
        pdb=" CB  LEU A 662 "
        pdb=" CG  LEU A 662 "
      ideal   model   delta    sigma   weight residual
     116.30  126.23   -9.93 3.50e+00 8.16e-02 8.04e+00
  angle pdb=" CA  LEU B 662 "
        pdb=" CB  LEU B 662 "
        pdb=" CG  LEU B 662 "
      ideal   model   delta    sigma   weight residual
     116.30  126.20   -9.90 3.50e+00 8.16e-02 7.99e+00
  angle pdb=" N   PRO A 763 "
        pdb=" CA  PRO A 763 "
        pdb=" C   PRO A 763 "
      ideal   model   delta    sigma   weight residual
     110.70  114.03   -3.33 1.22e+00 6.72e-01 7.47e+00
  angle pdb=" N   PRO B 763 "
        pdb=" CA  PRO B 763 "
        pdb=" C   PRO B 763 "
      ideal   model   delta    sigma   weight residual
     110.70  114.02   -3.32 1.22e+00 6.72e-01 7.42e+00
  angle pdb=" C   PRO B 541 "
        pdb=" N   ARG B 542 "
        pdb=" CA  ARG B 542 "
      ideal   model   delta    sigma   weight residual
     125.02  129.32   -4.30 1.76e+00 3.23e-01 5.98e+00
  ... (remaining 16261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 6739
       17.49 -    34.97: 290
       34.97 -    52.45: 29
       52.45 -    69.94: 8
       69.94 -    87.42: 2
  Dihedral angle restraints: 7068
    sinusoidal: 2882
      harmonic: 4186
  Sorted by residual:
  dihedral pdb=" CA  LYS A 590 "
           pdb=" C   LYS A 590 "
           pdb=" N   TYR A 591 "
           pdb=" CA  TYR A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.15  -16.85     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  LYS B 590 "
           pdb=" C   LYS B 590 "
           pdb=" N   TYR B 591 "
           pdb=" CA  TYR B 591 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.23  -16.77     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  GLU B 539 "
           pdb=" CB  GLU B 539 "
           pdb=" CG  GLU B 539 "
           pdb=" CD  GLU B 539 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.32  -57.32     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 7065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1077
       0.028 -    0.055: 429
       0.055 -    0.083: 210
       0.083 -    0.110: 54
       0.110 -    0.138: 16
  Chirality restraints: 1786
  Sorted by residual:
  chirality pdb=" CB  ILE A 474 "
            pdb=" CA  ILE A 474 "
            pdb=" CG1 ILE A 474 "
            pdb=" CG2 ILE A 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CB  ILE B 474 "
            pdb=" CA  ILE B 474 "
            pdb=" CG1 ILE B 474 "
            pdb=" CG2 ILE B 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  ARG B 542 "
            pdb=" N   ARG B 542 "
            pdb=" C   ARG B 542 "
            pdb=" CB  ARG B 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 1783 not shown)

  Planarity restraints: 2010
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 762 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO B 763 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 763 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 763 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 762 "   -0.029 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO A 763 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 763 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 763 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 818 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO A 819 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 819 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 819 "    0.020 5.00e-02 4.00e+02
  ... (remaining 2007 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1522
        2.75 -     3.29: 12048
        3.29 -     3.82: 20078
        3.82 -     4.36: 22392
        4.36 -     4.90: 39120
  Nonbonded interactions: 95160
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 365 "
            pdb=" OG  SER B 368 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   CYS A 365 "
            pdb=" OG  SER A 368 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OD1 ASP A 375 "
            pdb=" OG  SER A 748 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASP B 375 "
            pdb=" OG  SER B 748 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASN A 778 "
            pdb=" NH1 ARG A 808 "
     model   vdw
     2.258 3.120
  ... (remaining 95155 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.700
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
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      :  0.003   0.030  12006  Z= 0.136
  Angle     :  0.464   9.926  16282  Z= 0.249
  Chirality :  0.038   0.138   1786
  Planarity :  0.004   0.043   2010
  Dihedral  :  9.830  87.425   4348
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  5.25 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.23), residues: 1382
  helix:  2.62 (0.17), residues: 848
  sheet:  1.10 (0.58), residues: 64
  loop : -0.73 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 813 
 TYR   0.013   0.001   TYR A 580 
 PHE   0.014   0.001   PHE B 560 
 TRP   0.018   0.001   TRP A 397 
 HIS   0.002   0.000   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11998)
  covalent geometry    : angle       0.46378 (16266)
  SS BOND              : bond        0.00177 (    8)
  SS BOND              : angle       0.63597 (   16)
  hydrogen bonds       : bond        0.11598 (  720)
  hydrogen bonds       : angle       5.28926 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  234 ASN cc_start: 0.8677 (m-40) cc_final: 0.8347 (p0)
REVERT: A  326 LEU cc_start: 0.8975 (mt) cc_final: 0.8741 (mt)
REVERT: A  385 PHE cc_start: 0.8610 (t80) cc_final: 0.8405 (t80)
REVERT: A  406 TYR cc_start: 0.8568 (t80) cc_final: 0.8228 (t80)
REVERT: A  409 ASP cc_start: 0.8854 (m-30) cc_final: 0.8369 (t0)
REVERT: A  461 PHE cc_start: 0.8306 (t80) cc_final: 0.7785 (m-10)
REVERT: A  524 LEU cc_start: 0.9711 (mm) cc_final: 0.9280 (tp)
REVERT: A  527 ILE cc_start: 0.9626 (mm) cc_final: 0.9386 (mt)
REVERT: A  544 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7156 (tp40)
REVERT: A  548 GLU cc_start: 0.8978 (tp30) cc_final: 0.8711 (mm-30)
REVERT: A  553 MET cc_start: 0.8156 (tpp) cc_final: 0.7720 (tpp)
REVERT: A  597 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (t70)
REVERT: B  296 ILE cc_start: 0.7948 (mp) cc_final: 0.7609 (mm)
REVERT: B  327 ASP cc_start: 0.7904 (t0) cc_final: 0.7663 (t0)
REVERT: B  409 ASP cc_start: 0.8527 (m-30) cc_final: 0.8112 (t0)
REVERT: B  548 GLU cc_start: 0.9093 (tp30) cc_final: 0.8529 (tp30)
REVERT: B  749 ASP cc_start: 0.7937 (t70) cc_final: 0.7211 (t0)
REVERT: B  855 TYR cc_start: 0.7994 (t80) cc_final: 0.7739 (t80)
  outliers start: 16
  outliers final: 3
  residues processed: 204
  average time/residue: 0.4195
  time to fit residues: 93.8211
Evaluate side-chains
  121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  544 GLN
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  685 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 308 GLN
A 351 GLN
A 401 GLN
A 559 GLN
A 674 GLN
A 695 ASN
A 726 GLN
A 730 GLN
A 820 GLN
B 111 GLN
B 308 GLN
B 401 GLN
B 674 GLN
B 695 ASN
B 726 GLN
B 730 GLN
B 824 HIS
B 830 HIS

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.122183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.086698 restraints weight = 21713.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.94
r_work: 0.3085 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12006  Z= 0.221
  Angle     :  0.656  13.508  16282  Z= 0.342
  Chirality :  0.044   0.189   1786
  Planarity :  0.005   0.045   2010
  Dihedral  :  4.931  53.872   1570
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 11.13 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1382
  helix:  2.04 (0.17), residues: 868
  sheet:  1.48 (0.61), residues: 44
  loop : -0.81 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 219 
 TYR   0.015   0.002   TYR B 580 
 PHE   0.026   0.002   PHE B 462 
 TRP   0.019   0.002   TRP B 829 
 HIS   0.004   0.001   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (11998)
  covalent geometry    : angle       0.65506 (16266)
  SS BOND              : bond        0.00384 (    8)
  SS BOND              : angle       1.50658 (   16)
  hydrogen bonds       : bond        0.05016 (  720)
  hydrogen bonds       : angle       4.44926 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 123
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.7962 (t-90)
REVERT: A  234 ASN cc_start: 0.8758 (m-40) cc_final: 0.8410 (p0)
REVERT: A  242 TYR cc_start: 0.8673 (m-80) cc_final: 0.8427 (m-80)
REVERT: A  282 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6515 (tptm)
REVERT: A  409 ASP cc_start: 0.8701 (m-30) cc_final: 0.8179 (t0)
REVERT: A  524 LEU cc_start: 0.9719 (mm) cc_final: 0.8927 (tp)
REVERT: A  527 ILE cc_start: 0.9715 (mm) cc_final: 0.9483 (mt)
REVERT: A  528 TYR cc_start: 0.9082 (m-10) cc_final: 0.8402 (m-80)
REVERT: A  544 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7322 (tp40)
REVERT: A  548 GLU cc_start: 0.9000 (tp30) cc_final: 0.8650 (mp0)
REVERT: A  553 MET cc_start: 0.8375 (tpp) cc_final: 0.7932 (tpp)
REVERT: A  842 MET cc_start: 0.9032 (ttm) cc_final: 0.8826 (ttm)
REVERT: B  242 TYR cc_start: 0.8685 (m-80) cc_final: 0.8421 (m-80)
REVERT: B  327 ASP cc_start: 0.8030 (t0) cc_final: 0.7801 (t0)
REVERT: B  409 ASP cc_start: 0.8587 (m-30) cc_final: 0.8161 (t0)
REVERT: B  548 GLU cc_start: 0.9156 (tp30) cc_final: 0.8551 (mp0)
REVERT: B  612 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8910 (mp)
REVERT: B  855 TYR cc_start: 0.8064 (t80) cc_final: 0.7855 (t80)
  outliers start: 37
  outliers final: 17
  residues processed: 153
  average time/residue: 0.4754
  time to fit residues: 79.4446
Evaluate side-chains
  121 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  544 GLN
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  859 ASP
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  859 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 135 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0470
   chunk 136 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 138 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 114 optimal weight:    0.8980
   chunk 123 optimal weight:    0.7980
   chunk 122 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 544 GLN
B 730 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.123167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.088088 restraints weight = 22001.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.96
r_work: 0.3111 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12006  Z= 0.137
  Angle     :  0.572  10.939  16282  Z= 0.297
  Chirality :  0.040   0.174   1786
  Planarity :  0.005   0.046   2010
  Dihedral  :  4.700  54.923   1568
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.95 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.22), residues: 1382
  helix:  2.11 (0.17), residues: 870
  sheet:  1.28 (0.57), residues: 44
  loop : -0.91 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 219 
 TYR   0.015   0.001   TYR B 580 
 PHE   0.023   0.002   PHE B 462 
 TRP   0.014   0.001   TRP A 397 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11998)
  covalent geometry    : angle       0.56959 (16266)
  SS BOND              : bond        0.00476 (    8)
  SS BOND              : angle       1.83193 (   16)
  hydrogen bonds       : bond        0.04618 (  720)
  hydrogen bonds       : angle       4.33291 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 VAL cc_start: 0.9412 (t) cc_final: 0.9140 (p)
REVERT: A  108 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8132 (t-90)
REVERT: A  234 ASN cc_start: 0.8727 (m-40) cc_final: 0.8438 (p0)
REVERT: A  409 ASP cc_start: 0.8795 (m-30) cc_final: 0.8290 (t0)
REVERT: A  524 LEU cc_start: 0.9711 (mm) cc_final: 0.9455 (mt)
REVERT: A  548 GLU cc_start: 0.8973 (tp30) cc_final: 0.8261 (tp30)
REVERT: A  553 MET cc_start: 0.8396 (tpp) cc_final: 0.7903 (tpp)
REVERT: A  668 TYR cc_start: 0.9176 (m-80) cc_final: 0.8881 (m-80)
REVERT: B  242 TYR cc_start: 0.8615 (m-80) cc_final: 0.8276 (m-80)
REVERT: B  409 ASP cc_start: 0.8537 (m-30) cc_final: 0.8110 (t0)
REVERT: B  538 PHE cc_start: 0.8493 (t80) cc_final: 0.8169 (t80)
REVERT: B  548 GLU cc_start: 0.9132 (tp30) cc_final: 0.8554 (mp0)
REVERT: B  668 TYR cc_start: 0.9174 (m-80) cc_final: 0.8944 (m-80)
REVERT: B  855 TYR cc_start: 0.8043 (t80) cc_final: 0.7816 (t80)
  outliers start: 31
  outliers final: 10
  residues processed: 142
  average time/residue: 0.4192
  time to fit residues: 65.7166
Evaluate side-chains
  112 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  754 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 122 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 136 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0060
   chunk 45 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
B 730 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.120878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.086016 restraints weight = 22002.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.92
r_work: 0.3074 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  12006  Z= 0.175
  Angle     :  0.606  14.312  16282  Z= 0.311
  Chirality :  0.041   0.190   1786
  Planarity :  0.005   0.047   2010
  Dihedral  :  4.441  52.887   1565
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 14.18 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.22), residues: 1382
  helix:  2.06 (0.17), residues: 870
  sheet:  1.17 (0.56), residues: 44
  loop : -0.90 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 219 
 TYR   0.013   0.001   TYR A 827 
 PHE   0.025   0.002   PHE B 462 
 TRP   0.014   0.001   TRP B 829 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (11998)
  covalent geometry    : angle       0.60351 (16266)
  SS BOND              : bond        0.00535 (    8)
  SS BOND              : angle       1.75266 (   16)
  hydrogen bonds       : bond        0.04734 (  720)
  hydrogen bonds       : angle       4.30896 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 VAL cc_start: 0.9401 (t) cc_final: 0.9141 (p)
REVERT: A  108 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.8299 (t-90)
REVERT: A  234 ASN cc_start: 0.8708 (m-40) cc_final: 0.8487 (p0)
REVERT: A  282 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6416 (tptt)
REVERT: A  348 MET cc_start: 0.9016 (tpp) cc_final: 0.8653 (mmm)
REVERT: A  386 MET cc_start: 0.8235 (tpp) cc_final: 0.7991 (mmm)
REVERT: A  409 ASP cc_start: 0.8729 (m-30) cc_final: 0.8199 (t0)
REVERT: A  548 GLU cc_start: 0.9010 (tp30) cc_final: 0.8292 (tp30)
REVERT: A  553 MET cc_start: 0.8425 (tpp) cc_final: 0.7936 (tpp)
REVERT: A  773 MET cc_start: 0.8576 (mmt) cc_final: 0.8283 (tpp)
REVERT: B  409 ASP cc_start: 0.8541 (m-30) cc_final: 0.8117 (t0)
REVERT: B  458 SER cc_start: 0.8881 (m) cc_final: 0.8556 (p)
REVERT: B  538 PHE cc_start: 0.8500 (t80) cc_final: 0.8189 (t80)
REVERT: B  548 GLU cc_start: 0.9137 (tp30) cc_final: 0.8539 (mp0)
REVERT: B  855 TYR cc_start: 0.8063 (t80) cc_final: 0.7851 (t80)
  outliers start: 35
  outliers final: 20
  residues processed: 139
  average time/residue: 0.4105
  time to fit residues: 63.0261
Evaluate side-chains
  125 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Chi-restraints excluded: chain B residue  863 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 108 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 525 ASN
B 730 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.121911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.086905 restraints weight = 21767.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.92
r_work: 0.3092 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12006  Z= 0.138
  Angle     :  0.576  12.979  16282  Z= 0.295
  Chirality :  0.040   0.152   1786
  Planarity :  0.005   0.049   2010
  Dihedral  :  4.404  55.303   1565
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.44 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.22), residues: 1382
  helix:  2.13 (0.17), residues: 868
  sheet:  1.20 (0.58), residues: 44
  loop : -0.95 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 219 
 TYR   0.014   0.001   TYR B 406 
 PHE   0.026   0.001   PHE B 462 
 TRP   0.013   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (11998)
  covalent geometry    : angle       0.57371 (16266)
  SS BOND              : bond        0.00493 (    8)
  SS BOND              : angle       1.75159 (   16)
  hydrogen bonds       : bond        0.04471 (  720)
  hydrogen bonds       : angle       4.26462 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 VAL cc_start: 0.9392 (t) cc_final: 0.9150 (p)
REVERT: A   94 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8101 (tp40)
REVERT: A  105 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8967 (tt)
REVERT: A  108 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8279 (t-90)
REVERT: A  113 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6913 (pm20)
REVERT: A  142 MET cc_start: 0.8118 (mtp) cc_final: 0.7858 (mtm)
REVERT: A  234 ASN cc_start: 0.8744 (m-40) cc_final: 0.8518 (p0)
REVERT: A  386 MET cc_start: 0.8134 (tpp) cc_final: 0.7933 (mmm)
REVERT: A  409 ASP cc_start: 0.8771 (m-30) cc_final: 0.8243 (t0)
REVERT: A  548 GLU cc_start: 0.9010 (tp30) cc_final: 0.8287 (tp30)
REVERT: A  553 MET cc_start: 0.8404 (tpp) cc_final: 0.7936 (tpp)
REVERT: A  668 TYR cc_start: 0.9166 (m-80) cc_final: 0.8860 (m-80)
REVERT: A  742 MET cc_start: 0.8887 (mtt) cc_final: 0.8567 (mtm)
REVERT: A  773 MET cc_start: 0.8557 (mmt) cc_final: 0.8328 (tpp)
REVERT: B  386 MET cc_start: 0.8471 (tpp) cc_final: 0.8109 (mmm)
REVERT: B  409 ASP cc_start: 0.8616 (m-30) cc_final: 0.8209 (t0)
REVERT: B  458 SER cc_start: 0.8928 (m) cc_final: 0.8634 (p)
REVERT: B  507 MET cc_start: 0.4507 (pmt) cc_final: 0.4156 (pmm)
REVERT: B  538 PHE cc_start: 0.8518 (t80) cc_final: 0.8215 (t80)
REVERT: B  548 GLU cc_start: 0.9105 (tp30) cc_final: 0.8568 (mp0)
REVERT: B  749 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.7945 (t0)
REVERT: B  855 TYR cc_start: 0.8047 (t80) cc_final: 0.7832 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 136
  average time/residue: 0.4948
  time to fit residues: 73.5211
Evaluate side-chains
  127 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 137 optimal weight:    0.5980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 275 HIS
A 559 GLN
A 674 GLN
A 695 ASN
B 275 HIS
B 730 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.120485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.085419 restraints weight = 21846.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.92
r_work: 0.3057 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  12006  Z= 0.171
  Angle     :  0.593  12.806  16282  Z= 0.307
  Chirality :  0.041   0.161   1786
  Planarity :  0.005   0.050   2010
  Dihedral  :  4.161  22.587   1562
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.89 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1382
  helix:  2.08 (0.17), residues: 876
  sheet:  1.13 (0.60), residues: 42
  loop : -0.92 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 219 
 TYR   0.019   0.001   TYR B  77 
 PHE   0.027   0.002   PHE B 462 
 TRP   0.013   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (11998)
  covalent geometry    : angle       0.59050 (16266)
  SS BOND              : bond        0.00321 (    8)
  SS BOND              : angle       1.83985 (   16)
  hydrogen bonds       : bond        0.04643 (  720)
  hydrogen bonds       : angle       4.28472 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 109
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 VAL cc_start: 0.9382 (t) cc_final: 0.9125 (p)
REVERT: A   94 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8101 (tp40)
REVERT: A  105 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8988 (tt)
REVERT: A  108 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.8201 (t-90)
REVERT: A  142 MET cc_start: 0.8108 (mtp) cc_final: 0.7838 (mtm)
REVERT: A  282 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6480 (tptm)
REVERT: A  409 ASP cc_start: 0.8786 (m-30) cc_final: 0.8266 (t0)
REVERT: A  524 LEU cc_start: 0.9719 (mt) cc_final: 0.9376 (pp)
REVERT: A  534 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mtt)
REVERT: A  548 GLU cc_start: 0.9032 (tp30) cc_final: 0.8323 (tp30)
REVERT: A  553 MET cc_start: 0.8426 (tpp) cc_final: 0.7949 (tpp)
REVERT: A  595 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8013 (mt-10)
REVERT: B  409 ASP cc_start: 0.8629 (m-30) cc_final: 0.8215 (t0)
REVERT: B  458 SER cc_start: 0.8973 (m) cc_final: 0.8684 (p)
REVERT: B  529 GLU cc_start: 0.8785 (tt0) cc_final: 0.8186 (pt0)
REVERT: B  538 PHE cc_start: 0.8380 (t80) cc_final: 0.8004 (t80)
REVERT: B  548 GLU cc_start: 0.9110 (tp30) cc_final: 0.8543 (mp0)
REVERT: B  742 MET cc_start: 0.8763 (mpt) cc_final: 0.8404 (mtp)
REVERT: B  749 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.7996 (t0)
REVERT: B  855 TYR cc_start: 0.8077 (t80) cc_final: 0.7868 (t80)
  outliers start: 42
  outliers final: 21
  residues processed: 141
  average time/residue: 0.4740
  time to fit residues: 73.2302
Evaluate side-chains
  130 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Chi-restraints excluded: chain B residue  863 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
A 695 ASN
B 730 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.121337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.086507 restraints weight = 21721.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.92
r_work: 0.3073 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12006  Z= 0.137
  Angle     :  0.581  11.841  16282  Z= 0.296
  Chirality :  0.040   0.147   1786
  Planarity :  0.005   0.056   2010
  Dihedral  :  4.159  22.572   1562
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.99 %
    Favored  : 81.43 %
  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 aren not related in a simple way.
  whole:  1.66 (0.22), residues: 1382
  helix:  2.17 (0.17), residues: 868
  sheet:  1.07 (0.61), residues: 42
  loop : -0.99 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 219 
 TYR   0.014   0.001   TYR B  77 
 PHE   0.027   0.001   PHE B 462 
 TRP   0.014   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (11998)
  covalent geometry    : angle       0.57854 (16266)
  SS BOND              : bond        0.00248 (    8)
  SS BOND              : angle       1.77025 (   16)
  hydrogen bonds       : bond        0.04430 (  720)
  hydrogen bonds       : angle       4.25733 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 114
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.5930 (m-80)
REVERT: A   76 VAL cc_start: 0.9381 (t) cc_final: 0.9125 (p)
REVERT: A  105 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8976 (tt)
REVERT: A  108 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8298 (t-90)
REVERT: A  142 MET cc_start: 0.8096 (mtp) cc_final: 0.7803 (mtm)
REVERT: A  386 MET cc_start: 0.8448 (tpp) cc_final: 0.8064 (mmm)
REVERT: A  409 ASP cc_start: 0.8770 (m-30) cc_final: 0.8245 (t0)
REVERT: A  524 LEU cc_start: 0.9719 (mt) cc_final: 0.9456 (pp)
REVERT: A  548 GLU cc_start: 0.9017 (tp30) cc_final: 0.8300 (tp30)
REVERT: A  553 MET cc_start: 0.8436 (tpp) cc_final: 0.7970 (tpp)
REVERT: A  595 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8047 (mt-10)
REVERT: A  668 TYR cc_start: 0.9179 (m-80) cc_final: 0.8876 (m-80)
REVERT: A  742 MET cc_start: 0.8974 (mtt) cc_final: 0.8610 (mtm)
REVERT: B  386 MET cc_start: 0.8504 (tpp) cc_final: 0.8075 (mmm)
REVERT: B  409 ASP cc_start: 0.8613 (m-30) cc_final: 0.8204 (t0)
REVERT: B  458 SER cc_start: 0.8905 (m) cc_final: 0.8662 (p)
REVERT: B  524 LEU cc_start: 0.9706 (mt) cc_final: 0.9427 (pp)
REVERT: B  538 PHE cc_start: 0.8388 (t80) cc_final: 0.8012 (t80)
REVERT: B  548 GLU cc_start: 0.9079 (tp30) cc_final: 0.8556 (mp0)
REVERT: B  742 MET cc_start: 0.8828 (mpt) cc_final: 0.8445 (mtp)
REVERT: B  749 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.7967 (t0)
  outliers start: 33
  outliers final: 21
  residues processed: 139
  average time/residue: 0.4444
  time to fit residues: 68.2109
Evaluate side-chains
  130 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 PHE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 131 optimal weight:    0.3980
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 121 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 730 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.121090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.086316 restraints weight = 21757.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.96
r_work: 0.3078 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  12006  Z= 0.148
  Angle     :  0.602  11.845  16282  Z= 0.307
  Chirality :  0.040   0.157   1786
  Planarity :  0.005   0.059   2010
  Dihedral  :  4.151  22.626   1562
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.44 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.22), residues: 1382
  helix:  2.18 (0.17), residues: 868
  sheet:  1.10 (0.63), residues: 42
  loop : -0.97 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B 219 
 TYR   0.015   0.001   TYR B 406 
 PHE   0.027   0.001   PHE B 462 
 TRP   0.013   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (11998)
  covalent geometry    : angle       0.59939 (16266)
  SS BOND              : bond        0.00253 (    8)
  SS BOND              : angle       1.79975 (   16)
  hydrogen bonds       : bond        0.04502 (  720)
  hydrogen bonds       : angle       4.26268 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 113
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A   76 VAL cc_start: 0.9376 (t) cc_final: 0.9134 (p)
REVERT: A  105 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.9002 (tp)
REVERT: A  108 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8257 (t-90)
REVERT: A  142 MET cc_start: 0.8125 (mtp) cc_final: 0.7838 (mtm)
REVERT: A  282 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6444 (tptm)
REVERT: A  386 MET cc_start: 0.8379 (tpp) cc_final: 0.8044 (mmm)
REVERT: A  409 ASP cc_start: 0.8775 (m-30) cc_final: 0.8250 (t0)
REVERT: A  524 LEU cc_start: 0.9694 (mt) cc_final: 0.9389 (pp)
REVERT: A  525 ASN cc_start: 0.9215 (m-40) cc_final: 0.8887 (m-40)
REVERT: A  529 GLU cc_start: 0.8841 (tt0) cc_final: 0.8355 (pt0)
REVERT: A  534 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8175 (mtt)
REVERT: A  548 GLU cc_start: 0.9029 (tp30) cc_final: 0.8341 (tp30)
REVERT: A  553 MET cc_start: 0.8445 (tpp) cc_final: 0.7989 (tpp)
REVERT: A  595 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7938 (mt-10)
REVERT: A  742 MET cc_start: 0.8972 (mtt) cc_final: 0.8599 (mtm)
REVERT: A  773 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8231 (mmm)
REVERT: B  386 MET cc_start: 0.8475 (tpp) cc_final: 0.8179 (mmm)
REVERT: B  409 ASP cc_start: 0.8617 (m-30) cc_final: 0.8203 (t0)
REVERT: B  458 SER cc_start: 0.8891 (m) cc_final: 0.8659 (p)
REVERT: B  524 LEU cc_start: 0.9687 (mt) cc_final: 0.9354 (pp)
REVERT: B  529 GLU cc_start: 0.8783 (tt0) cc_final: 0.8211 (pt0)
REVERT: B  538 PHE cc_start: 0.8392 (t80) cc_final: 0.7983 (t80)
REVERT: B  548 GLU cc_start: 0.9090 (tp30) cc_final: 0.8554 (mp0)
REVERT: B  742 MET cc_start: 0.8781 (mpt) cc_final: 0.8429 (mtp)
REVERT: B  749 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8029 (t0)
  outliers start: 42
  outliers final: 27
  residues processed: 144
  average time/residue: 0.4389
  time to fit residues: 69.5429
Evaluate side-chains
  143 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  773 MET
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  637 TYR
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 114 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 134 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
A 695 ASN
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 GLN
B 695 ASN
B 730 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.119366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.084446 restraints weight = 21641.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.95
r_work: 0.3048 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  12006  Z= 0.213
  Angle     :  0.636  12.172  16282  Z= 0.328
  Chirality :  0.042   0.164   1786
  Planarity :  0.006   0.141   2010
  Dihedral  :  4.236  22.422   1562
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.22 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.22), residues: 1382
  helix:  2.07 (0.17), residues: 878
  sheet:  0.97 (0.62), residues: 42
  loop : -0.98 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 219 
 TYR   0.024   0.001   TYR B 637 
 PHE   0.028   0.002   PHE B 462 
 TRP   0.013   0.002   TRP A 273 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (11998)
  covalent geometry    : angle       0.63362 (16266)
  SS BOND              : bond        0.00346 (    8)
  SS BOND              : angle       1.93652 (   16)
  hydrogen bonds       : bond        0.04762 (  720)
  hydrogen bonds       : angle       4.35237 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 112
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   51 GLU cc_start: 0.7731 (mp0) cc_final: 0.7258 (mp0)
REVERT: A   76 VAL cc_start: 0.9378 (t) cc_final: 0.9149 (p)
REVERT: A   94 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8070 (tp40)
REVERT: A   96 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8059 (ptp-110)
REVERT: A  108 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8241 (t-90)
REVERT: A  142 MET cc_start: 0.8128 (mtp) cc_final: 0.7793 (mtm)
REVERT: A  282 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6408 (tptt)
REVERT: A  409 ASP cc_start: 0.8777 (m-30) cc_final: 0.8263 (t0)
REVERT: A  525 ASN cc_start: 0.9230 (m-40) cc_final: 0.8999 (m-40)
REVERT: A  529 GLU cc_start: 0.8814 (tt0) cc_final: 0.8341 (pt0)
REVERT: A  548 GLU cc_start: 0.9072 (tp30) cc_final: 0.8353 (tp30)
REVERT: A  553 MET cc_start: 0.8448 (tpp) cc_final: 0.7988 (tpp)
REVERT: A  595 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7977 (mt-10)
REVERT: A  742 MET cc_start: 0.8919 (mtt) cc_final: 0.8565 (mtm)
REVERT: B  409 ASP cc_start: 0.8629 (m-30) cc_final: 0.8223 (t0)
REVERT: B  458 SER cc_start: 0.8758 (m) cc_final: 0.8508 (p)
REVERT: B  524 LEU cc_start: 0.9694 (mt) cc_final: 0.9350 (pp)
REVERT: B  529 GLU cc_start: 0.8824 (tt0) cc_final: 0.8219 (pt0)
REVERT: B  538 PHE cc_start: 0.8440 (t80) cc_final: 0.7956 (t80)
REVERT: B  548 GLU cc_start: 0.9094 (tp30) cc_final: 0.8509 (mp0)
REVERT: B  742 MET cc_start: 0.8743 (mpt) cc_final: 0.8434 (mtp)
REVERT: B  749 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8044 (t0)
  outliers start: 36
  outliers final: 24
  residues processed: 140
  average time/residue: 0.4397
  time to fit residues: 67.4227
Evaluate side-chains
  135 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 134 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0970
   chunk 79 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
A 695 ASN
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 GLN
B 695 ASN
B 730 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.121129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.086301 restraints weight = 21873.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.91
r_work: 0.3081 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  12006  Z= 0.140
  Angle     :  0.614  12.104  16282  Z= 0.312
  Chirality :  0.040   0.155   1786
  Planarity :  0.005   0.113   2010
  Dihedral  :  4.213  22.438   1562
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.22 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1382
  helix:  2.16 (0.17), residues: 868
  sheet:  1.01 (0.62), residues: 42
  loop : -1.01 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 452 
 TYR   0.014   0.001   TYR B 406 
 PHE   0.029   0.001   PHE B 462 
 TRP   0.014   0.001   TRP A 397 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11998)
  covalent geometry    : angle       0.61159 (16266)
  SS BOND              : bond        0.00249 (    8)
  SS BOND              : angle       1.80596 (   16)
  hydrogen bonds       : bond        0.04484 (  720)
  hydrogen bonds       : angle       4.31288 ( 2106)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 117
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   76 VAL cc_start: 0.9348 (t) cc_final: 0.9142 (p)
REVERT: A  108 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8168 (t-90)
REVERT: A  142 MET cc_start: 0.8127 (mtp) cc_final: 0.7766 (mtm)
REVERT: A  282 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6498 (tptm)
REVERT: A  386 MET cc_start: 0.8361 (tpp) cc_final: 0.7922 (mmm)
REVERT: A  409 ASP cc_start: 0.8773 (m-30) cc_final: 0.8255 (t0)
REVERT: A  525 ASN cc_start: 0.9224 (m-40) cc_final: 0.8988 (m-40)
REVERT: A  529 GLU cc_start: 0.8811 (tt0) cc_final: 0.8344 (pt0)
REVERT: A  538 PHE cc_start: 0.8162 (t80) cc_final: 0.7263 (t80)
REVERT: A  548 GLU cc_start: 0.9050 (tp30) cc_final: 0.8318 (tp30)
REVERT: A  553 MET cc_start: 0.8424 (tpp) cc_final: 0.7963 (tpp)
REVERT: A  595 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8078 (mt-10)
REVERT: A  668 TYR cc_start: 0.9174 (m-80) cc_final: 0.8912 (m-80)
REVERT: A  742 MET cc_start: 0.8973 (mtt) cc_final: 0.8594 (mtm)
REVERT: A  773 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7818 (mmm)
REVERT: B  386 MET cc_start: 0.8507 (tpp) cc_final: 0.8106 (mmm)
REVERT: B  409 ASP cc_start: 0.8743 (m-30) cc_final: 0.8317 (t0)
REVERT: B  458 SER cc_start: 0.8983 (m) cc_final: 0.8761 (p)
REVERT: B  503 LEU cc_start: 0.1521 (OUTLIER) cc_final: 0.0568 (tt)
REVERT: B  524 LEU cc_start: 0.9688 (mt) cc_final: 0.9343 (pp)
REVERT: B  529 GLU cc_start: 0.8773 (tt0) cc_final: 0.8208 (pt0)
REVERT: B  538 PHE cc_start: 0.8448 (t80) cc_final: 0.8028 (t80)
REVERT: B  548 GLU cc_start: 0.9075 (tp30) cc_final: 0.8535 (mp0)
REVERT: B  742 MET cc_start: 0.8795 (mpt) cc_final: 0.8461 (mtp)
REVERT: B  749 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8027 (t0)
  outliers start: 35
  outliers final: 23
  residues processed: 143
  average time/residue: 0.4236
  time to fit residues: 66.9097
Evaluate side-chains
  141 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 HIS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  282 LYS
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  480 SER
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  625 VAL
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  773 MET
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  625 VAL
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  685 PHE
Chi-restraints excluded: chain B residue  734 ILE
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  754 LEU
Chi-restraints excluded: chain B residue  762 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 111 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 120 optimal weight:    0.7980
   chunk 99 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0470
   chunk 117 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 730 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.121755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.087000 restraints weight = 21915.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.93
r_work: 0.3094 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  12006  Z= 0.133
  Angle     :  0.608  12.131  16282  Z= 0.307
  Chirality :  0.040   0.154   1786
  Planarity :  0.005   0.098   2010
  Dihedral  :  4.162  22.587   1562
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.54 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.22), residues: 1382
  helix:  2.16 (0.17), residues: 876
  sheet:  1.08 (0.62), residues: 42
  loop : -1.02 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG B 219 
 TYR   0.014   0.001   TYR B 406 
 PHE   0.029   0.001   PHE B 462 
 TRP   0.015   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11998)
  covalent geometry    : angle       0.60556 (16266)
  SS BOND              : bond        0.00268 (    8)
  SS BOND              : angle       1.75649 (   16)
  hydrogen bonds       : bond        0.04393 (  720)
  hydrogen bonds       : angle       4.28520 ( 2106)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2965.81 seconds
wall clock time: 51 minutes 24.83 seconds (3084.83 seconds total)