Starting phenix.real_space_refine
on Thu Oct 22 17:57:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oek_70400/10_2026/9oek_70400.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oek_70400/10_2026/9oek_70400.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oek_70400/10_2026/9oek_70400.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oek_70400/10_2026/9oek_70400.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oek_70400/10_2026/9oek_70400.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oek_70400/10_2026/9oek_70400.cif"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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: 3
    Type Number    sf(0)   Gaussians
     C    1950      2.51       5
     N     540      2.21       5
     O     580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3070
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 307
          Classifications: {'peptide': 41}
          Link IDs: {'TRANS': 40}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.54, per 1000 atoms: 0.18
  Number of scatterers: 3070
  At special positions: 0
  Unit cell: (67.89, 116.07, 39.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     580      8.00
     N     540      7.00
     C    1950      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.20
  Conformation dependent library (CDL) restraints added in 119.4 milliseconds
  

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  720

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 65.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 572
      removed outlier: 6.242A  pdb=" N   TYR A 571 " --> pdb=" O   HIS B 572 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   TYR B 571 " --> pdb=" O   HIS C 572 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   TYR C 571 " --> pdb=" O   HIS D 572 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   TYR D 571 " --> pdb=" O   HIS E 572 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 576 through 579
      removed outlier: 6.327A  pdb=" N   ILE A 577 " --> pdb=" O   LEU B 578 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE B 577 " --> pdb=" O   LEU C 578 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILE C 577 " --> pdb=" O   LEU D 578 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILE D 577 " --> pdb=" O   LEU E 578 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 583 through 584
    Processing sheet with id=AA4, first strand: chain 'A' and resid 587 through 608
      removed outlier: 6.972A  pdb=" N   SER B 591 " --> pdb=" O   LYS A 590 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU A 592 " --> pdb=" O   SER B 591 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   GLN B 593 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   GLY A 594 " --> pdb=" O   GLN B 593 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   ASN B 603 " --> pdb=" O   LYS A 602 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ASN A 604 " --> pdb=" O   ASN B 603 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   VAL B 605 " --> pdb=" O   ASN A 604 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   VAL A 606 " --> pdb=" O   VAL B 605 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   SER B 607 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL A 608 " --> pdb=" O   SER B 607 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER C 591 " --> pdb=" O   LYS B 590 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU B 592 " --> pdb=" O   SER C 591 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   GLN C 593 " --> pdb=" O   LEU B 592 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY B 594 " --> pdb=" O   GLN C 593 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN C 603 " --> pdb=" O   LYS B 602 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN B 604 " --> pdb=" O   ASN C 603 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL C 605 " --> pdb=" O   ASN B 604 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL B 606 " --> pdb=" O   VAL C 605 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   SER C 607 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL B 608 " --> pdb=" O   SER C 607 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER D 591 " --> pdb=" O   LYS C 590 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU C 592 " --> pdb=" O   SER D 591 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   GLN D 593 " --> pdb=" O   LEU C 592 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY C 594 " --> pdb=" O   GLN D 593 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN D 603 " --> pdb=" O   LYS C 602 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN C 604 " --> pdb=" O   ASN D 603 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL D 605 " --> pdb=" O   ASN C 604 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL C 606 " --> pdb=" O   VAL D 605 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   SER D 607 " --> pdb=" O   VAL C 606 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL C 608 " --> pdb=" O   SER D 607 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER E 591 " --> pdb=" O   LYS D 590 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU D 592 " --> pdb=" O   SER E 591 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLN E 593 " --> pdb=" O   LEU D 592 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY D 594 " --> pdb=" O   GLN E 593 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN E 603 " --> pdb=" O   LYS D 602 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN D 604 " --> pdb=" O   ASN E 603 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL E 605 " --> pdb=" O   ASN D 604 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL D 606 " --> pdb=" O   VAL E 605 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   SER E 607 " --> pdb=" O   VAL D 606 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL D 608 " --> pdb=" O   SER E 607 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 570 through 572
      removed outlier: 6.256A  pdb=" N   TYR F 571 " --> pdb=" O   HIS G 572 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   TYR G 571 " --> pdb=" O   HIS H 572 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   TYR H 571 " --> pdb=" O   HIS I 572 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   TYR I 571 " --> pdb=" O   HIS J 572 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'F' and resid 576 through 579
      removed outlier: 6.320A  pdb=" N   ILE F 577 " --> pdb=" O   LEU G 578 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ILE G 577 " --> pdb=" O   LEU H 578 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE H 577 " --> pdb=" O   LEU I 578 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ILE I 577 " --> pdb=" O   LEU J 578 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'F' and resid 583 through 584
    Processing sheet with id=AA8, first strand: chain 'F' and resid 587 through 608
      removed outlier: 6.813A  pdb=" N   SER G 591 " --> pdb=" O   LYS F 590 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU F 592 " --> pdb=" O   SER G 591 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLN G 593 " --> pdb=" O   LEU F 592 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY F 594 " --> pdb=" O   GLN G 593 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN G 603 " --> pdb=" O   LYS F 602 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN F 604 " --> pdb=" O   ASN G 603 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL G 605 " --> pdb=" O   ASN F 604 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL F 606 " --> pdb=" O   VAL G 605 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   SER G 607 " --> pdb=" O   VAL F 606 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL F 608 " --> pdb=" O   SER G 607 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER H 591 " --> pdb=" O   LYS G 590 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU G 592 " --> pdb=" O   SER H 591 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLN H 593 " --> pdb=" O   LEU G 592 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLY G 594 " --> pdb=" O   GLN H 593 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN H 603 " --> pdb=" O   LYS G 602 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN G 604 " --> pdb=" O   ASN H 603 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL H 605 " --> pdb=" O   ASN G 604 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL G 606 " --> pdb=" O   VAL H 605 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   SER H 607 " --> pdb=" O   VAL G 606 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL G 608 " --> pdb=" O   SER H 607 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER I 591 " --> pdb=" O   LYS H 590 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU H 592 " --> pdb=" O   SER I 591 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLN I 593 " --> pdb=" O   LEU H 592 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY H 594 " --> pdb=" O   GLN I 593 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN I 603 " --> pdb=" O   LYS H 602 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN H 604 " --> pdb=" O   ASN I 603 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL I 605 " --> pdb=" O   ASN H 604 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL H 606 " --> pdb=" O   VAL I 605 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   SER I 607 " --> pdb=" O   VAL H 606 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL H 608 " --> pdb=" O   SER I 607 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER J 591 " --> pdb=" O   LYS I 590 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU I 592 " --> pdb=" O   SER J 591 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLN J 593 " --> pdb=" O   LEU I 592 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY I 594 " --> pdb=" O   GLN J 593 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN J 603 " --> pdb=" O   LYS I 602 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN I 604 " --> pdb=" O   ASN J 603 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL J 605 " --> pdb=" O   ASN I 604 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL I 606 " --> pdb=" O   VAL J 605 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   SER J 607 " --> pdb=" O   VAL I 606 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL I 608 " --> pdb=" O   SER J 607 " (cutoff:3.500A)

    96 hydrogen bonds defined for protein.
    288 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.39

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 530
        1.29 -     1.35: 500
        1.35 -     1.42: 130
        1.42 -     1.48: 420
        1.48 -     1.55: 1500
  Bond restraints: 3080
  Sorted by residual:
  bond pdb=" C   ASN C 603 "
       pdb=" N   ASN C 604 "
    ideal  model  delta    sigma   weight residual
    1.331  1.324  0.007 1.38e-02 5.25e+03 2.49e-01
  bond pdb=" C   ASN H 603 "
       pdb=" N   ASN H 604 "
    ideal  model  delta    sigma   weight residual
    1.331  1.324  0.007 1.38e-02 5.25e+03 2.46e-01
  bond pdb=" C   ASN I 603 "
       pdb=" N   ASN I 604 "
    ideal  model  delta    sigma   weight residual
    1.331  1.325  0.007 1.38e-02 5.25e+03 2.33e-01
  bond pdb=" CA  ASN C 603 "
       pdb=" CB  ASN C 603 "
    ideal  model  delta    sigma   weight residual
    1.526  1.518  0.008 1.70e-02 3.46e+03 2.31e-01
  bond pdb=" C   ASN F 603 "
       pdb=" N   ASN F 604 "
    ideal  model  delta    sigma   weight residual
    1.331  1.325  0.006 1.38e-02 5.25e+03 2.06e-01
  ... (remaining 3075 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.86: 3701
        0.86 -     1.73: 317
        1.73 -     2.59: 62
        2.59 -     3.46: 30
        3.46 -     4.32: 20
  Bond angle restraints: 4130
  Sorted by residual:
  angle pdb=" N   GLY F 581 "
        pdb=" CA  GLY F 581 "
        pdb=" C   GLY F 581 "
      ideal   model   delta    sigma   weight residual
     113.18  117.50   -4.32 2.37e+00 1.78e-01 3.32e+00
  angle pdb=" N   GLY E 581 "
        pdb=" CA  GLY E 581 "
        pdb=" C   GLY E 581 "
      ideal   model   delta    sigma   weight residual
     113.18  117.48   -4.30 2.37e+00 1.78e-01 3.29e+00
  angle pdb=" N   GLY H 581 "
        pdb=" CA  GLY H 581 "
        pdb=" C   GLY H 581 "
      ideal   model   delta    sigma   weight residual
     113.18  117.48   -4.30 2.37e+00 1.78e-01 3.29e+00
  angle pdb=" N   GLY I 581 "
        pdb=" CA  GLY I 581 "
        pdb=" C   GLY I 581 "
      ideal   model   delta    sigma   weight residual
     113.18  117.47   -4.29 2.37e+00 1.78e-01 3.28e+00
  angle pdb=" N   GLY A 581 "
        pdb=" CA  GLY A 581 "
        pdb=" C   GLY A 581 "
      ideal   model   delta    sigma   weight residual
     113.18  117.46   -4.28 2.37e+00 1.78e-01 3.26e+00
  ... (remaining 4125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.18: 1580
       11.18 -    22.35: 200
       22.35 -    33.53: 50
       33.53 -    44.71: 20
       44.71 -    55.88: 20
  Dihedral angle restraints: 1870
    sinusoidal: 740
      harmonic: 1130
  Sorted by residual:
  dihedral pdb=" CA  ASP B 575 "
           pdb=" CB  ASP B 575 "
           pdb=" CG  ASP B 575 "
           pdb=" OD1 ASP B 575 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.88   55.88     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  ASP F 575 "
           pdb=" CB  ASP F 575 "
           pdb=" CG  ASP F 575 "
           pdb=" OD1 ASP F 575 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.88   55.88     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  ASP J 575 "
           pdb=" CB  ASP J 575 "
           pdb=" CG  ASP J 575 "
           pdb=" OD1 ASP J 575 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.87   55.87     1      2.00e+01 2.50e-03 1.05e+01
  ... (remaining 1867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 225
       0.022 -    0.045: 145
       0.045 -    0.067: 50
       0.067 -    0.089: 49
       0.089 -    0.111: 51
  Chirality restraints: 520
  Sorted by residual:
  chirality pdb=" CA  VAL B 599 "
            pdb=" N   VAL B 599 "
            pdb=" C   VAL B 599 "
            pdb=" CB  VAL B 599 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.09e-01
  chirality pdb=" CA  VAL I 599 "
            pdb=" N   VAL I 599 "
            pdb=" C   VAL I 599 "
            pdb=" CB  VAL I 599 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.09e-01
  chirality pdb=" CA  VAL A 605 "
            pdb=" N   VAL A 605 "
            pdb=" C   VAL A 605 "
            pdb=" CB  VAL A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.09e-01
  ... (remaining 517 not shown)

  Planarity restraints: 510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS H 590 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.88e+00
        pdb=" C   LYS H 590 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   LYS H 590 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER H 591 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F 590 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.83e+00
        pdb=" C   LYS F 590 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   LYS F 590 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER F 591 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 590 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   LYS C 590 "    0.023 2.00e-02 2.50e+03
        pdb=" O   LYS C 590 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   SER C 591 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 507 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 1432
        2.94 -     3.43: 2523
        3.43 -     3.92: 4803
        3.92 -     4.41: 4968
        4.41 -     4.90: 9977
  Nonbonded interactions: 23703
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 603 "
            pdb=" OD2 ASP B 575 "
     model   vdw
     2.454 3.120
  nonbonded pdb=" O   ASN A 603 "
            pdb=" O   LYS B 602 "
     model   vdw
     2.474 3.040
  nonbonded pdb=" ND2 ASN D 603 "
            pdb=" OD2 ASP E 575 "
     model   vdw
     2.494 3.120
  nonbonded pdb=" ND2 ASN I 603 "
            pdb=" OD2 ASP J 575 "
     model   vdw
     2.494 3.120
  nonbonded pdb=" ND2 ASN H 603 "
            pdb=" OD2 ASP I 575 "
     model   vdw
     2.495 3.120
  ... (remaining 23698 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.150
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
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   0.014   3080  Z= 0.158
  Angle     :  0.637   4.320   4130  Z= 0.336
  Chirality :  0.047   0.111    520
  Planarity :  0.004   0.014    510
  Dihedral  : 13.008  55.884   1150
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 11.43 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.31), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 588 
 TYR   0.005   0.001   TYR D 571 
 HIS   0.001   0.001   HIS D 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 ( 3080)
  covalent geometry    : angle       0.63651 /  0.34 ( 4130)
  hydrogen bonds       : bond        0.17474 / 11.39 (   96)
  hydrogen bonds       : angle      11.25488 /  7.49 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7273 (m-30) cc_final: 0.7044 (m-30)
REVERT: A  583 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8364 (mp)
REVERT: A  590 LYS cc_start: 0.6658 (ttmt) cc_final: 0.5767 (tmmt)
REVERT: B  596 LYS cc_start: 0.8694 (tptp) cc_final: 0.8399 (tptm)
REVERT: C  598 GLU cc_start: 0.7935 (tt0) cc_final: 0.7674 (tt0)
REVERT: D  587 VAL cc_start: 0.8913 (p) cc_final: 0.8697 (p)
REVERT: E  592 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8033 (mt)
REVERT: F  575 ASP cc_start: 0.7041 (m-30) cc_final: 0.6792 (m-30)
REVERT: F  590 LYS cc_start: 0.6503 (ttmt) cc_final: 0.5827 (tmmt)
REVERT: G  596 LYS cc_start: 0.8699 (tptp) cc_final: 0.8405 (tptm)
REVERT: H  598 GLU cc_start: 0.7920 (tt0) cc_final: 0.7663 (tt0)
REVERT: I  587 VAL cc_start: 0.8894 (p) cc_final: 0.8689 (p)
REVERT: J  592 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8038 (mt)
  outliers start: 20
  outliers final: 9
  residues processed: 89
  average time/residue: 0.1089
  time to fit residues: 10.8579
Evaluate side-chains
  99 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain E residue  592 LEU
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  583 ILE
Chi-restraints excluded: chain J residue  592 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37]
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 593 GLN
B 593 GLN
D 572 HIS
D 593 GLN
E 572 HIS
E 593 GLN
F 572 HIS
G 593 GLN
I 572 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.177770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.164487 restraints weight = 4058.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 3.08
r_work: 0.4318 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3080  Z= 0.225
  Angle     :  0.729   6.203   4130  Z= 0.378
  Chirality :  0.048   0.130    520
  Planarity :  0.005   0.036    510
  Dihedral  :  7.854  28.732    444
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.57 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.35), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.26), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.003   ARG F 588 
 TYR   0.010   0.002   TYR A 571 
 HIS   0.002   0.001   HIS D 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00487 /  0.22 ( 3080)
  covalent geometry    : angle       0.72925 /  0.38 ( 4130)
  hydrogen bonds       : bond        0.06336 /  4.08 (   96)
  hydrogen bonds       : angle       7.99647 /  5.31 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.6737 (m-30) cc_final: 0.6201 (m-30)
REVERT: A  583 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8245 (mp)
REVERT: B  596 LYS cc_start: 0.8811 (tptp) cc_final: 0.8556 (tptp)
REVERT: D  583 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8054 (mp)
REVERT: D  596 LYS cc_start: 0.8725 (tptp) cc_final: 0.8148 (tmtt)
REVERT: E  592 LEU cc_start: 0.8169 (pt) cc_final: 0.7719 (mt)
REVERT: F  575 ASP cc_start: 0.6656 (m-30) cc_final: 0.6105 (m-30)
REVERT: F  583 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8182 (mp)
REVERT: G  596 LYS cc_start: 0.8820 (tptp) cc_final: 0.8566 (tptp)
REVERT: I  596 LYS cc_start: 0.8751 (tptp) cc_final: 0.8175 (tmtt)
REVERT: J  592 LEU cc_start: 0.8164 (pt) cc_final: 0.7707 (mt)
  outliers start: 14
  outliers final: 7
  residues processed: 105
  average time/residue: 0.0934
  time to fit residues: 10.9626
Evaluate side-chains
  103 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [8, 7, 26, 24, 30, 1, 20, 5, 25, 37, 14]
   chunk 8 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 20 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    4.0788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 572 HIS
B 572 HIS
G 572 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.178470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.164333 restraints weight = 4131.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 3.21
r_work: 0.4312 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   3080  Z= 0.255
  Angle     :  0.749   5.891   4130  Z= 0.385
  Chirality :  0.048   0.129    520
  Planarity :  0.004   0.033    510
  Dihedral  :  7.709  29.766    440
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 26.00 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.35), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.004   ARG G 588 
 TYR   0.009   0.002   TYR A 571 
 HIS   0.001   0.001   HIS E 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00552 /  0.25 ( 3080)
  covalent geometry    : angle       0.74857 /  0.39 ( 4130)
  hydrogen bonds       : bond        0.05941 /  3.77 (   96)
  hydrogen bonds       : angle       7.69105 /  5.15 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7018 (m-30) cc_final: 0.6427 (m-30)
REVERT: A  583 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8230 (mp)
REVERT: F  575 ASP cc_start: 0.7059 (m-30) cc_final: 0.6493 (m-30)
REVERT: F  583 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8188 (mp)
  outliers start: 12
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0778
  time to fit residues: 7.3006
Evaluate side-chains
  87 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [26, 13, 32, 6, 39, 23, 21, 16, 14, 31, 37]
   chunk 26 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    3.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 593 GLN
H 593 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.179457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.165248 restraints weight = 4115.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.4442 rms_B_bonded: 3.35
r_work: 0.4340 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3080  Z= 0.228
  Angle     :  0.710   5.340   4130  Z= 0.367
  Chirality :  0.048   0.122    520
  Planarity :  0.004   0.028    510
  Dihedral  :  7.564  29.145    440
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 25.43 %
    Favored  : 69.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.35), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.003   ARG B 588 
 TYR   0.008   0.002   TYR F 571 
 HIS   0.002   0.001   HIS F 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.23 ( 3080)
  covalent geometry    : angle       0.70951 /  0.37 ( 4130)
  hydrogen bonds       : bond        0.05258 /  3.33 (   96)
  hydrogen bonds       : angle       7.36937 /  4.96 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7126 (m-30) cc_final: 0.6527 (m-30)
REVERT: A  583 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8276 (mp)
REVERT: E  583 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8163 (mp)
REVERT: F  575 ASP cc_start: 0.7152 (m-30) cc_final: 0.6555 (m-30)
REVERT: F  583 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8236 (mp)
REVERT: J  583 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (mp)
  outliers start: 17
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0886
  time to fit residues: 9.5018
Evaluate side-chains
  96 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain F residue  601 LEU
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  573 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [20, 30, 36, 18, 33, 4, 3, 11, 17, 15, 5]
   chunk 20 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 572 HIS
H 572 HIS
J 572 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.172648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.158351 restraints weight = 4203.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.4353 rms_B_bonded: 3.22
r_work: 0.4247 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.047   3080  Z= 0.409
  Angle     :  0.878   5.846   4130  Z= 0.460
  Chirality :  0.049   0.152    520
  Planarity :  0.004   0.024    510
  Dihedral  :  9.015  40.290    440
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 25.14 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.33), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.003   ARG A 588 
 TYR   0.013   0.003   TYR F 571 
 HIS   0.003   0.001   HIS G 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00898 /  0.41 ( 3080)
  covalent geometry    : angle       0.87813 /  0.46 ( 4130)
  hydrogen bonds       : bond        0.05957 /  3.77 (   96)
  hydrogen bonds       : angle       7.66550 /  5.17 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7278 (m-30) cc_final: 0.6654 (m-30)
REVERT: F  575 ASP cc_start: 0.7319 (m-30) cc_final: 0.6719 (m-30)
  outliers start: 23
  outliers final: 20
  residues processed: 84
  average time/residue: 0.0745
  time to fit residues: 7.3448
Evaluate side-chains
  90 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  573 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  573 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain G residue  573 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain G residue  608 VAL
Chi-restraints excluded: chain H residue  573 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  573 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  573 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [16, 6, 18, 10, 35, 8, 36, 29, 26, 24, 14]
   chunk 16 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 593 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.180064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.165601 restraints weight = 4110.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.4445 rms_B_bonded: 3.33
r_work: 0.4339 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3080  Z= 0.198
  Angle     :  0.708   5.341   4130  Z= 0.365
  Chirality :  0.049   0.115    520
  Planarity :  0.004   0.034    510
  Dihedral  :  7.570  29.397    440
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 29.14 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.07 (0.33), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.003   ARG A 588 
 TYR   0.006   0.001   TYR F 571 
 HIS   0.002   0.001   HIS H 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00431 /  0.20 ( 3080)
  covalent geometry    : angle       0.70798 /  0.37 ( 4130)
  hydrogen bonds       : bond        0.05259 /  3.29 (   96)
  hydrogen bonds       : angle       7.20296 /  4.89 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7100 (m-30) cc_final: 0.6478 (m-30)
REVERT: A  583 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8223 (mp)
REVERT: D  588 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7317 (mtt90)
REVERT: E  596 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8346 (tptt)
REVERT: F  575 ASP cc_start: 0.7137 (m-30) cc_final: 0.6523 (m-30)
REVERT: F  583 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8184 (mp)
REVERT: J  596 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8398 (tptt)
  outliers start: 20
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0792
  time to fit residues: 8.4213
Evaluate side-chains
  94 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  573 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain F residue  601 LEU
Chi-restraints excluded: chain G residue  573 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  573 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  573 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [38, 4, 20, 26, 8, 11, 10, 22, 27, 13, 6]
   chunk 38 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 593 GLN
F 593 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.174881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.160583 restraints weight = 4238.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.4387 rms_B_bonded: 3.30
r_work: 0.4282 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   3080  Z= 0.317
  Angle     :  0.803   5.665   4130  Z= 0.420
  Chirality :  0.049   0.138    520
  Planarity :  0.004   0.029    510
  Dihedral  :  8.497  36.116    440
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.08 %
    Favored  : 86.92 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 27.14 %
    Favored  : 66.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.32), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.003   ARG B 588 
 TYR   0.010   0.002   TYR F 571 
 HIS   0.002   0.001   HIS H 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00696 /  0.32 ( 3080)
  covalent geometry    : angle       0.80276 /  0.42 ( 4130)
  hydrogen bonds       : bond        0.05584 /  3.54 (   96)
  hydrogen bonds       : angle       7.42760 /  5.02 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7179 (m-30) cc_final: 0.6546 (m-30)
REVERT: A  583 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8216 (mp)
REVERT: D  588 ARG cc_start: 0.7593 (mtt90) cc_final: 0.7260 (mtt90)
REVERT: E  596 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8416 (tptt)
REVERT: F  575 ASP cc_start: 0.7340 (m-30) cc_final: 0.6726 (m-30)
REVERT: F  583 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: J  596 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8421 (tptt)
  outliers start: 24
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0634
  time to fit residues: 6.7298
Evaluate side-chains
  91 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  573 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain G residue  573 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain G residue  587 VAL
Chi-restraints excluded: chain H residue  573 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  573 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  573 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [35, 26, 21, 25, 12, 15, 16, 5, 17, 27, 10]
   chunk 35 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 15 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    2.0988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 593 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.185333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.170659 restraints weight = 4108.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4502 rms_B_bonded: 3.37
r_work: 0.4402 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3080  Z= 0.147
  Angle     :  0.674   5.191   4130  Z= 0.344
  Chirality :  0.048   0.113    520
  Planarity :  0.005   0.039    510
  Dihedral  :  7.043  27.259    440
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 30.29 %
    Favored  : 64.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.08 (0.33), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.004   ARG B 588 
 TYR   0.003   0.001   TYR F 571 
 HIS   0.001   0.001   HIS A 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 3080)
  covalent geometry    : angle       0.67437 /  0.34 ( 4130)
  hydrogen bonds       : bond        0.04924 /  3.08 (   96)
  hydrogen bonds       : angle       6.92005 /  4.70 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7041 (m-30) cc_final: 0.6432 (m-30)
REVERT: A  583 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8209 (mp)
REVERT: D  583 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7980 (mp)
REVERT: D  588 ARG cc_start: 0.7388 (mtt90) cc_final: 0.7103 (mtt90)
REVERT: D  591 SER cc_start: 0.8802 (m) cc_final: 0.8474 (p)
REVERT: F  575 ASP cc_start: 0.7101 (m-30) cc_final: 0.6494 (m-30)
REVERT: F  583 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: I  583 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7970 (mp)
REVERT: J  596 LYS cc_start: 0.8468 (tmtt) cc_final: 0.8204 (tptt)
  outliers start: 18
  outliers final: 11
  residues processed: 87
  average time/residue: 0.0507
  time to fit residues: 5.4169
Evaluate side-chains
  88 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  573 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  573 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain F residue  601 LEU
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  573 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [1, 27, 9, 11, 15, 25, 28, 37, 14, 8, 38]
   chunk 1 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 38 optimal weight:    0.0870
   overall best weight:    4.6166

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.177549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.162957 restraints weight = 4263.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4415 rms_B_bonded: 3.36
r_work: 0.4305 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3080  Z= 0.274
  Angle     :  0.768   5.389   4130  Z= 0.399
  Chirality :  0.049   0.132    520
  Planarity :  0.004   0.028    510
  Dihedral  :  8.059  34.402    440
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.79 %
    Favored  : 88.21 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 30.00 %
    Favored  : 64.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.22 (0.32), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.003   ARG B 588 
 TYR   0.008   0.002   TYR F 571 
 HIS   0.002   0.001   HIS G 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00606 /  0.27 ( 3080)
  covalent geometry    : angle       0.76843 /  0.40 ( 4130)
  hydrogen bonds       : bond        0.05401 /  3.40 (   96)
  hydrogen bonds       : angle       7.23704 /  4.88 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7148 (m-30) cc_final: 0.6516 (m-30)
REVERT: A  583 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8180 (mp)
REVERT: D  588 ARG cc_start: 0.7562 (mtt90) cc_final: 0.7298 (mtt90)
REVERT: D  592 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7743 (pt)
REVERT: E  596 LYS cc_start: 0.8676 (tmtt) cc_final: 0.8424 (tptt)
REVERT: F  575 ASP cc_start: 0.7223 (m-30) cc_final: 0.6595 (m-30)
REVERT: F  583 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8218 (mp)
  outliers start: 20
  outliers final: 16
  residues processed: 88
  average time/residue: 0.0625
  time to fit residues: 6.6376
Evaluate side-chains
  93 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  573 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain D residue  592 LEU
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  573 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain G residue  573 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  573 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  573 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [21, 31, 4, 0, 29, 5, 13, 36, 19, 15, 3]
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0670
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    2.8126

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.185384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.170971 restraints weight = 4069.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.4495 rms_B_bonded: 3.17
r_work: 0.4378 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3080  Z= 0.179
  Angle     :  0.707   5.207   4130  Z= 0.363
  Chirality :  0.049   0.118    520
  Planarity :  0.004   0.033    510
  Dihedral  :  7.372  28.986    440
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 31.43 %
    Favored  : 63.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.33), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.42 (0.25), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.003   ARG B 588 
 TYR   0.006   0.001   TYR B 571 
 HIS   0.001   0.001   HIS E 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.18 ( 3080)
  covalent geometry    : angle       0.70694 /  0.36 ( 4130)
  hydrogen bonds       : bond        0.04955 /  3.11 (   96)
  hydrogen bonds       : angle       7.00674 /  4.74 (  288)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  575 ASP cc_start: 0.7191 (m-30) cc_final: 0.6592 (m-30)
REVERT: A  583 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8189 (mp)
REVERT: D  583 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8047 (mp)
REVERT: D  588 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7212 (mtt90)
REVERT: D  592 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7489 (pt)
REVERT: E  596 LYS cc_start: 0.8493 (tmtt) cc_final: 0.8281 (tptt)
REVERT: F  575 ASP cc_start: 0.7161 (m-30) cc_final: 0.6542 (m-30)
REVERT: F  583 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8195 (mp)
REVERT: I  592 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7518 (pt)
  outliers start: 19
  outliers final: 14
  residues processed: 86
  average time/residue: 0.0618
  time to fit residues: 6.3272
Evaluate side-chains
  97 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  583 ILE
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  583 ILE
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  583 ILE
Chi-restraints excluded: chain D residue  573 ILE
Chi-restraints excluded: chain D residue  583 ILE
Chi-restraints excluded: chain D residue  592 LEU
Chi-restraints excluded: chain E residue  583 ILE
Chi-restraints excluded: chain F residue  573 ILE
Chi-restraints excluded: chain F residue  583 ILE
Chi-restraints excluded: chain G residue  573 ILE
Chi-restraints excluded: chain G residue  583 ILE
Chi-restraints excluded: chain H residue  583 ILE
Chi-restraints excluded: chain I residue  573 ILE
Chi-restraints excluded: chain I residue  583 ILE
Chi-restraints excluded: chain I residue  592 LEU
Chi-restraints excluded: chain J residue  583 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [39, 5, 4, 30, 23, 16, 25, 32, 11, 29, 8]
   chunk 39 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    6.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.172594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.158166 restraints weight = 4249.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.4347 rms_B_bonded: 3.27
r_work: 0.4242 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.058   3080  Z= 0.385
  Angle     :  0.895   5.924   4130  Z= 0.468
  Chirality :  0.050   0.141    520
  Planarity :  0.004   0.025    510
  Dihedral  :  9.154  42.771    440
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.85 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 31.14 %
    Favored  : 62.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.51 (0.31), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.003   ARG G 588 
 TYR   0.011   0.002   TYR E 571 
 HIS   0.004   0.002   HIS B 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00850 /  0.38 ( 3080)
  covalent geometry    : angle       0.89549 /  0.47 ( 4130)
  hydrogen bonds       : bond        0.05861 /  3.71 (   96)
  hydrogen bonds       : angle       7.50304 /  5.04 (  288)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 804.50 seconds
wall clock time: 14 minutes 27.73 seconds (867.73 seconds total)