Starting phenix.real_space_refine
on Wed Aug  5 05:37:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sj9_54941/08_2026/9sj9_54941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sj9_54941/08_2026/9sj9_54941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sj9_54941/08_2026/9sj9_54941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sj9_54941/08_2026/9sj9_54941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9sj9_54941/08_2026/9sj9_54941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sj9_54941/08_2026/9sj9_54941.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    5482      2.51       5
     N    1405      2.21       5
     O    1725      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8633
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4316
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 556, 4316
          Classifications: {'peptide': 556}
          Link IDs: {'PCIS': 4, 'PTRANS': 16, 'TRANS': 535}
    Chain: "B"
      Number of atoms: 4212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 4212
          Classifications: {'peptide': 546}
          Link IDs: {'PCIS': 6, 'PTRANS': 16, 'TRANS': 523}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'TCH': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 70
          Unusual residues: {'TCH': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.11, per 1000 atoms: 0.24
  Number of scatterers: 8633
  At special positions: 0
  Unit cell: (77.28, 93.24, 94.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O    1725      8.00
     N    1405      7.00
     C    5482      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: 0.70
  Conformation dependent library (CDL) restraints added in 423.5 milliseconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      26.5% alpha, 29.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 20
    Processing helix  chain 'A' and resid 42 through 49
      removed outlier: 3.735A  pdb=" N   ILE A  49 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 82
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 169 through 180
    Processing helix  chain 'A' and resid 185 through 189
      removed outlier: 3.521A  pdb=" N   ARG A 189 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 236
    Processing helix  chain 'A' and resid 256 through 266
      removed outlier: 4.616A  pdb=" N   ASN A 262 " --> pdb=" O   ASP A 259 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   ILE A 263 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 264 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 407
    Processing helix  chain 'A' and resid 423 through 427
    Processing helix  chain 'A' and resid 483 through 506
    Processing helix  chain 'A' and resid 508 through 513
    Processing helix  chain 'A' and resid 514 through 525
    Processing helix  chain 'A' and resid 545 through 557
    Processing helix  chain 'B' and resid 597 through 605
    Processing helix  chain 'B' and resid 606 through 609
      removed outlier: 5.739A  pdb=" N   GLN B 609 " --> pdb=" O   GLY B 606 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 606 through 609'
    Processing helix  chain 'B' and resid 629 through 636
    Processing helix  chain 'B' and resid 670 through 677
      removed outlier: 4.053A  pdb=" N   PHE B 674 " --> pdb=" O   GLY B 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 700 through 704
    Processing helix  chain 'B' and resid 736 through 746
    Processing helix  chain 'B' and resid 756 through 767
    Processing helix  chain 'B' and resid 798 through 816
    Processing helix  chain 'B' and resid 841 through 845
      removed outlier: 4.388A  pdb=" N   PHE B 844 " --> pdb=" O   LYS B 841 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 845 " --> pdb=" O   ALA B 842 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 841 through 845'
    Processing helix  chain 'B' and resid 982 through 986
    Processing helix  chain 'B' and resid 1062 through 1082
      removed outlier: 3.641A  pdb=" N   ALA B1066 " --> pdb=" O   GLY B1062 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1087 through 1091
    Processing helix  chain 'B' and resid 1092 through 1103
    Processing helix  chain 'B' and resid 1123 through 1132
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 206
      removed outlier: 9.696A  pdb=" N   ILE A 214 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   SER A  63 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67
    Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 148
      removed outlier: 5.163A  pdb=" N   VAL A 124 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   VAL A 199 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   TYR A 126 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   LYS A 201 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP A 128 " --> pdb=" O   LYS A 201 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU A 101 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   VAL A 103 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ILE A 104 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A 239 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   VAL A 272 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   ILE A 241 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   GLY A 274 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   LEU A 243 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 148
      removed outlier: 5.163A  pdb=" N   VAL A 124 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   VAL A 199 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   TYR A 126 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   LYS A 201 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP A 128 " --> pdb=" O   LYS A 201 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU A 101 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   VAL A 103 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ILE A 104 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A 239 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   VAL A 272 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   ILE A 241 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   GLY A 274 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   LEU A 243 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 462 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 288
    Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 325
      removed outlier: 6.162A  pdb=" N   LYS A 319 " --> pdb=" O   GLU A 390 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY A 381 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 611 through 615
      removed outlier: 6.081A  pdb=" N   PHE B 611 " --> pdb=" O   SER B 622 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   SER B 622 " --> pdb=" O   PHE B 611 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   LYS B 613 " --> pdb=" O   VAL B 620 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL B 620 " --> pdb=" O   LYS B 613 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG B 642 " --> pdb=" O   VAL B 593 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 796 through 797
      removed outlier: 4.164A  pdb=" N   TYR B 796 " --> pdb=" O   MET B 649 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 657
      removed outlier: 3.573A  pdb=" N   THR B1056 " --> pdb=" O   TYR B1052 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 732 through 735
      removed outlier: 4.824A  pdb=" N   ILE B 712 " --> pdb=" O   LEU B 784 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ILE B 786 " --> pdb=" O   ILE B 712 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TYR B 714 " --> pdb=" O   ILE B 786 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   LYS B 788 " --> pdb=" O   TYR B 714 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   TRP B 716 " --> pdb=" O   LYS B 788 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE B 689 " --> pdb=" O   ILE B 785 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   ILE B 787 " --> pdb=" O   ILE B 689 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE B 691 " --> pdb=" O   ILE B 787 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA B 692 " --> pdb=" O   ASN B 822 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   ILE B1011 " --> pdb=" O   LEU B 848 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE B 850 " --> pdb=" O   ILE B1011 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   ILE B1013 " --> pdb=" O   ILE B 850 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ALA B 852 " --> pdb=" O   ILE B1013 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   ALA B1015 " --> pdb=" O   ALA B 852 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 732 through 735
      removed outlier: 4.824A  pdb=" N   ILE B 712 " --> pdb=" O   LEU B 784 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ILE B 786 " --> pdb=" O   ILE B 712 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TYR B 714 " --> pdb=" O   ILE B 786 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   LYS B 788 " --> pdb=" O   TYR B 714 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   TRP B 716 " --> pdb=" O   LYS B 788 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE B 689 " --> pdb=" O   ILE B 785 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   ILE B 787 " --> pdb=" O   ILE B 689 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE B 691 " --> pdb=" O   ILE B 787 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA B 692 " --> pdb=" O   ASN B 822 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   ILE B1011 " --> pdb=" O   LEU B 848 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE B 850 " --> pdb=" O   ILE B1011 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   ILE B1013 " --> pdb=" O   ILE B 850 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ALA B 852 " --> pdb=" O   ILE B1013 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   ALA B1015 " --> pdb=" O   ALA B 852 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 863 through 867
      removed outlier: 3.568A  pdb=" N   GLN B 948 " --> pdb=" O   LEU B 894 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 899 through 905
      removed outlier: 6.309A  pdb=" N   LYS B 899 " --> pdb=" O   VAL B 969 " (cutoff:3.500A)

    366 hydrogen bonds defined for protein.
    954 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: 2.10

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2820
        1.34 -     1.46: 1596
        1.46 -     1.57: 4353
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 8805
  Sorted by residual:
  bond pdb=" O3S TCH A 601 "
       pdb=" S26 TCH A 601 "
    ideal  model  delta    sigma   weight residual
    1.475  1.548 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" O3S TCH B1202 "
       pdb=" S26 TCH B1202 "
    ideal  model  delta    sigma   weight residual
    1.475  1.540 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" O3S TCH B1201 "
       pdb=" S26 TCH B1201 "
    ideal  model  delta    sigma   weight residual
    1.475  1.534 -0.059 2.00e-02 2.50e+03 8.82e+00
  bond pdb=" O2S TCH B1201 "
       pdb=" S26 TCH B1201 "
    ideal  model  delta    sigma   weight residual
    1.476  1.430  0.046 2.00e-02 2.50e+03 5.37e+00
  bond pdb=" O1S TCH B1201 "
       pdb=" S26 TCH B1201 "
    ideal  model  delta    sigma   weight residual
    1.476  1.431  0.045 2.00e-02 2.50e+03 5.14e+00
  ... (remaining 8800 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 11581
        1.25 -     2.49: 330
        2.49 -     3.74: 75
        3.74 -     4.99: 16
        4.99 -     6.24: 9
  Bond angle restraints: 12011
  Sorted by residual:
  angle pdb=" CB  GLU B 840 "
        pdb=" CG  GLU B 840 "
        pdb=" CD  GLU B 840 "
      ideal   model   delta    sigma   weight residual
     112.60  117.95   -5.35 1.70e+00 3.46e-01 9.91e+00
  angle pdb=" CA  GLU B 840 "
        pdb=" CB  GLU B 840 "
        pdb=" CG  GLU B 840 "
      ideal   model   delta    sigma   weight residual
     114.10  120.34   -6.24 2.00e+00 2.50e-01 9.73e+00
  angle pdb=" N   ILE B1033 "
        pdb=" CA  ILE B1033 "
        pdb=" C   ILE B1033 "
      ideal   model   delta    sigma   weight residual
     112.98  109.13    3.85 1.25e+00 6.40e-01 9.48e+00
  angle pdb=" CA  GLU B 754 "
        pdb=" CB  GLU B 754 "
        pdb=" CG  GLU B 754 "
      ideal   model   delta    sigma   weight residual
     114.10  120.04   -5.94 2.00e+00 2.50e-01 8.83e+00
  angle pdb=" CB  GLU B 754 "
        pdb=" CG  GLU B 754 "
        pdb=" CD  GLU B 754 "
      ideal   model   delta    sigma   weight residual
     112.60  117.21   -4.61 1.70e+00 3.46e-01 7.35e+00
  ... (remaining 12006 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4734
       18.00 -    35.99: 474
       35.99 -    53.99: 121
       53.99 -    71.98: 29
       71.98 -    89.98: 19
  Dihedral angle restraints: 5377
    sinusoidal: 2211
      harmonic: 3166
  Sorted by residual:
  dihedral pdb=" CA  VAL A 252 "
           pdb=" C   VAL A 252 "
           pdb=" N   ALA A 253 "
           pdb=" CA  ALA A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.47  -16.53     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CB  GLU B 654 "
           pdb=" CG  GLU B 654 "
           pdb=" CD  GLU B 654 "
           pdb=" OE1 GLU B 654 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.98  -89.98     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CG  ARG A 386 "
           pdb=" CD  ARG A 386 "
           pdb=" NE  ARG A 386 "
           pdb=" CZ  ARG A 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.70   44.30     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 5374 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 769
       0.028 -    0.057: 359
       0.057 -    0.085: 139
       0.085 -    0.114: 104
       0.114 -    0.142: 25
  Chirality restraints: 1396
  Sorted by residual:
  chirality pdb=" CA  ILE A   8 "
            pdb=" N   ILE A   8 "
            pdb=" C   ILE A   8 "
            pdb=" CB  ILE A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  ILE B 785 "
            pdb=" N   ILE B 785 "
            pdb=" C   ILE B 785 "
            pdb=" CB  ILE B 785 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  ILE A 198 "
            pdb=" N   ILE A 198 "
            pdb=" C   ILE A 198 "
            pdb=" CB  ILE A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 1393 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 TCH A 601 "    0.030 2.00e-02 2.50e+03   1.21e-01 1.83e+02
        pdb=" C24 TCH A 601 "    0.033 2.00e-02 2.50e+03
        pdb=" C25 TCH A 601 "   -0.142 2.00e-02 2.50e+03
        pdb=" N24 TCH A 601 "    0.194 2.00e-02 2.50e+03
        pdb=" O24 TCH A 601 "   -0.115 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 TCH B1202 "   -0.093 2.00e-02 2.50e+03   1.03e-01 1.32e+02
        pdb=" C24 TCH B1202 "    0.035 2.00e-02 2.50e+03
        pdb=" C25 TCH B1202 "   -0.125 2.00e-02 2.50e+03
        pdb=" N24 TCH B1202 "    0.164 2.00e-02 2.50e+03
        pdb=" O24 TCH B1202 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C23 TCH B1201 "    0.021 2.00e-02 2.50e+03   2.26e-02 6.41e+00
        pdb=" C24 TCH B1201 "   -0.009 2.00e-02 2.50e+03
        pdb=" C25 TCH B1201 "    0.028 2.00e-02 2.50e+03
        pdb=" N24 TCH B1201 "   -0.035 2.00e-02 2.50e+03
        pdb=" O24 TCH B1201 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 4208
        2.97 -     3.45: 8461
        3.45 -     3.94: 15468
        3.94 -     4.42: 18067
        4.42 -     4.90: 29219
  Nonbonded interactions: 75423
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 754 "
            pdb=" OE1 GLU B 754 "
     model   vdw
     2.489 3.120
  nonbonded pdb=" N   GLU B 840 "
            pdb=" OE1 GLU B 840 "
     model   vdw
     2.503 3.120
  nonbonded pdb=" N   ASP A  93 "
            pdb=" OD1 ASP A  93 "
     model   vdw
     2.540 3.120
  nonbonded pdb=" N24 TCH B1201 "
            pdb=" O1S TCH B1201 "
     model   vdw
     2.545 3.120
  nonbonded pdb=" N24 TCH B1202 "
            pdb=" O1S TCH B1202 "
     model   vdw
     2.555 3.120
  ... (remaining 75418 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.700
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.320
  Find NCS groups from input model:        0.050
  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:7.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9293
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      :  0.004   0.073   8805  Z= 0.172
  Angle     :  0.559   6.237  12011  Z= 0.300
  Chirality :  0.045   0.142   1396
  Planarity :  0.006   0.121   1537
  Dihedral  : 16.448  89.976   3373
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 20.04 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.25), residues: 1098
  helix:  1.26 (0.35), residues: 230
  sheet:  0.40 (0.30), residues: 289
  loop : -0.31 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 610 
 TYR   0.010   0.001   TYR B 809 
 PHE   0.012   0.001   PHE A 359 
 TRP   0.008   0.001   TRP A 445 
 HIS   0.003   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.17 ( 8805)
  covalent geometry    : angle       0.55929 /  0.30 (12011)
  hydrogen bonds       : bond        0.13662 /  9.06 (  344)
  hydrogen bonds       : angle       6.55313 /  4.53 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8728 (tt0) cc_final: 0.8405 (tp40)
REVERT: A  342 TYR cc_start: 0.8915 (t80) cc_final: 0.8579 (t80)
REVERT: A  396 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8634 (mt-10)
  outliers start: 3
  outliers final: 4
  residues processed: 62
  average time/residue: 0.4931
  time to fit residues: 33.3358
Evaluate side-chains
  63 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain B residue  668 GLU
Chi-restraints excluded: chain B residue  677 ASN
Chi-restraints excluded: chain B residue  969 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.3031 r_free = 0.3031 target = 0.085356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.066668 restraints weight = 14228.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2685 rms_B_bonded: 2.14
r_work: 0.2560 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2431 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9294
moved from start:          0.0503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8805  Z= 0.130
  Angle     :  0.475   5.262  12011  Z= 0.253
  Chirality :  0.045   0.140   1396
  Planarity :  0.004   0.042   1537
  Dihedral  :  6.230  80.752   1440
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.95 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.25), residues: 1098
  helix:  1.72 (0.35), residues: 227
  sheet:  0.45 (0.30), residues: 283
  loop : -0.24 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 610 
 TYR   0.010   0.001   TYR B 809 
 PHE   0.011   0.001   PHE A 359 
 TRP   0.006   0.001   TRP A 445 
 HIS   0.003   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 8805)
  covalent geometry    : angle       0.47524 /  0.25 (12011)
  hydrogen bonds       : bond        0.03965 /  2.63 (  344)
  hydrogen bonds       : angle       5.51314 /  3.81 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8631 (tt0) cc_final: 0.8283 (tp40)
REVERT: A  342 TYR cc_start: 0.8995 (t80) cc_final: 0.8706 (t80)
REVERT: A  396 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8586 (mt-10)
REVERT: A  442 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8512 (t0)
  outliers start: 21
  outliers final: 9
  residues processed: 76
  average time/residue: 0.4910
  time to fit residues: 40.6555
Evaluate side-chains
  70 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  615 SER
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 91 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 37 optimal weight:    0.4980
   chunk 55 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    2.8986

-------------------------------------------------------------------------------
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 = 0.2994 r_free = 0.2994 target = 0.083335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.064666 restraints weight = 14314.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.2637 rms_B_bonded: 2.13
r_work: 0.2510 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2383 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9322
moved from start:          0.0812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   8805  Z= 0.202
  Angle     :  0.507   5.176  12011  Z= 0.270
  Chirality :  0.046   0.144   1396
  Planarity :  0.004   0.040   1537
  Dihedral  :  5.943  73.930   1433
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.16 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.25), residues: 1098
  helix:  1.70 (0.35), residues: 227
  sheet:  0.47 (0.30), residues: 280
  loop : -0.23 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 836 
 TYR   0.012   0.001   TYR B 938 
 PHE   0.014   0.001   PHE A 359 
 TRP   0.005   0.001   TRP A 445 
 HIS   0.003   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.20 ( 8805)
  covalent geometry    : angle       0.50747 /  0.27 (12011)
  hydrogen bonds       : bond        0.04345 /  2.89 (  344)
  hydrogen bonds       : angle       5.54191 /  3.84 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8643 (tt0) cc_final: 0.8303 (tp40)
REVERT: A  342 TYR cc_start: 0.9001 (t80) cc_final: 0.8734 (t80)
REVERT: A  396 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8591 (mt-10)
REVERT: A  442 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8578 (t0)
  outliers start: 23
  outliers final: 10
  residues processed: 80
  average time/residue: 0.5076
  time to fit residues: 44.0463
Evaluate side-chains
  73 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  668 GLU
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3013 r_free = 0.3013 target = 0.084399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.065774 restraints weight = 14432.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 2.14
r_work: 0.2539 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2412 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9307
moved from start:          0.0854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8805  Z= 0.147
  Angle     :  0.477   5.619  12011  Z= 0.254
  Chirality :  0.045   0.141   1396
  Planarity :  0.004   0.040   1537
  Dihedral  :  5.806  70.079   1433
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.59 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.25), residues: 1098
  helix:  1.81 (0.35), residues: 227
  sheet:  0.47 (0.30), residues: 271
  loop : -0.24 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 836 
 TYR   0.011   0.001   TYR A  85 
 PHE   0.012   0.001   PHE A 359 
 TRP   0.006   0.001   TRP A  54 
 HIS   0.002   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 8805)
  covalent geometry    : angle       0.47700 /  0.25 (12011)
  hydrogen bonds       : bond        0.03895 /  2.59 (  344)
  hydrogen bonds       : angle       5.33313 /  3.70 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8630 (tt0) cc_final: 0.8306 (tp40)
REVERT: A  342 TYR cc_start: 0.9001 (t80) cc_final: 0.8713 (t80)
REVERT: A  377 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8850 (m-30)
REVERT: A  396 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8608 (mt-10)
REVERT: A  442 ASP cc_start: 0.8882 (m-30) cc_final: 0.8609 (t0)
  outliers start: 23
  outliers final: 10
  residues processed: 78
  average time/residue: 0.4225
  time to fit residues: 36.4300
Evaluate side-chains
  70 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 45 optimal weight:   50.0000
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3013 r_free = 0.3013 target = 0.084313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.065612 restraints weight = 14318.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 2.13
r_work: 0.2541 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2413 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9307
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8805  Z= 0.147
  Angle     :  0.480   5.818  12011  Z= 0.253
  Chirality :  0.045   0.140   1396
  Planarity :  0.004   0.041   1537
  Dihedral  :  5.757  66.978   1433
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.63 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1098
  helix:  1.88 (0.35), residues: 227
  sheet:  0.49 (0.30), residues: 271
  loop : -0.24 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 836 
 TYR   0.013   0.001   TYR A  85 
 PHE   0.012   0.001   PHE A 359 
 TRP   0.005   0.001   TRP A  54 
 HIS   0.002   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 ( 8805)
  covalent geometry    : angle       0.48009 /  0.25 (12011)
  hydrogen bonds       : bond        0.03875 /  2.59 (  344)
  hydrogen bonds       : angle       5.30259 /  3.68 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8628 (tt0) cc_final: 0.8302 (tp40)
REVERT: A  342 TYR cc_start: 0.8998 (t80) cc_final: 0.8737 (t80)
REVERT: A  377 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8852 (m-30)
REVERT: A  396 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8605 (mt-10)
REVERT: A  442 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8633 (t0)
  outliers start: 27
  outliers final: 11
  residues processed: 81
  average time/residue: 0.4506
  time to fit residues: 39.9898
Evaluate side-chains
  71 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  668 GLU
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 77 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 95 optimal weight:    9.9990
   overall best weight:    3.7388

-------------------------------------------------------------------------------
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 = 0.2978 r_free = 0.2978 target = 0.082277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.063717 restraints weight = 14331.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.2622 rms_B_bonded: 2.08
r_work: 0.2497 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2370 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9327
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   8805  Z= 0.251
  Angle     :  0.533   6.260  12011  Z= 0.283
  Chirality :  0.047   0.143   1396
  Planarity :  0.004   0.040   1537
  Dihedral  :  6.023  66.753   1433
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.59 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.25), residues: 1098
  helix:  1.68 (0.34), residues: 227
  sheet:  0.56 (0.30), residues: 268
  loop : -0.29 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 836 
 TYR   0.015   0.002   TYR A  85 
 PHE   0.016   0.002   PHE A 359 
 TRP   0.005   0.001   TRP A  54 
 HIS   0.003   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00578 /  0.25 ( 8805)
  covalent geometry    : angle       0.53291 /  0.28 (12011)
  hydrogen bonds       : bond        0.04481 /  2.99 (  344)
  hydrogen bonds       : angle       5.49440 /  3.82 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8646 (tt0) cc_final: 0.8318 (tp40)
REVERT: A  342 TYR cc_start: 0.8991 (t80) cc_final: 0.8755 (t80)
REVERT: A  372 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8165 (tp30)
REVERT: A  396 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8626 (mt-10)
  outliers start: 24
  outliers final: 10
  residues processed: 75
  average time/residue: 0.4513
  time to fit residues: 37.2147
Evaluate side-chains
  69 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  668 GLU
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9980
   chunk 61 optimal weight:    8.9990
   chunk 78 optimal weight:    1.9990
   chunk 44 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3034 r_free = 0.3034 target = 0.085468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.067266 restraints weight = 14413.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 2.12
r_work: 0.2573 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2446 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9284
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8805  Z= 0.101
  Angle     :  0.458   5.999  12011  Z= 0.243
  Chirality :  0.044   0.139   1396
  Planarity :  0.003   0.041   1537
  Dihedral  :  5.645  61.954   1433
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.12 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1098
  helix:  2.01 (0.35), residues: 227
  sheet:  0.79 (0.31), residues: 263
  loop : -0.29 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 836 
 TYR   0.016   0.001   TYR A  85 
 PHE   0.009   0.001   PHE A 359 
 TRP   0.009   0.001   TRP A  54 
 HIS   0.002   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.10 ( 8805)
  covalent geometry    : angle       0.45753 /  0.24 (12011)
  hydrogen bonds       : bond        0.03450 /  2.30 (  344)
  hydrogen bonds       : angle       5.14237 /  3.58 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8628 (tt0) cc_final: 0.8300 (tp40)
REVERT: A  342 TYR cc_start: 0.9005 (t80) cc_final: 0.8736 (t80)
REVERT: A  377 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8809 (m-30)
REVERT: A  396 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8602 (mt-10)
REVERT: B  887 GLU cc_start: 0.8905 (tt0) cc_final: 0.8647 (mm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 76
  average time/residue: 0.4895
  time to fit residues: 40.6178
Evaluate side-chains
  70 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  668 GLU
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0020
   chunk 58 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   chunk 95 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 = 0.3060 r_free = 0.3060 target = 0.087128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.069020 restraints weight = 14230.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 2.12
r_work: 0.2608 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2481 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9265
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8805  Z= 0.092
  Angle     :  0.475  11.300  12011  Z= 0.248
  Chirality :  0.044   0.149   1396
  Planarity :  0.003   0.040   1537
  Dihedral  :  5.344  57.371   1433
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 18.55 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.25), residues: 1098
  helix:  2.13 (0.35), residues: 227
  sheet:  0.83 (0.31), residues: 270
  loop : -0.22 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 456 
 TYR   0.017   0.001   TYR A  85 
 PHE   0.009   0.001   PHE A 143 
 TRP   0.011   0.001   TRP A  54 
 HIS   0.002   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00199 /  0.09 ( 8805)
  covalent geometry    : angle       0.47550 /  0.25 (12011)
  hydrogen bonds       : bond        0.03225 /  2.15 (  344)
  hydrogen bonds       : angle       4.83739 /  3.38 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8627 (tt0) cc_final: 0.8273 (tp40)
REVERT: A  342 TYR cc_start: 0.8992 (t80) cc_final: 0.8711 (t80)
REVERT: A  377 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8785 (m-30)
REVERT: A  396 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8572 (mt-10)
REVERT: B  887 GLU cc_start: 0.8889 (tt0) cc_final: 0.8675 (mm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 85
  average time/residue: 0.4798
  time to fit residues: 44.4928
Evaluate side-chains
  75 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  668 GLU
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0970
   chunk 101 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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 = 0.3033 r_free = 0.3033 target = 0.085377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.066884 restraints weight = 14157.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.2691 rms_B_bonded: 2.12
r_work: 0.2566 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2439 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9292
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8805  Z= 0.132
  Angle     :  0.492   9.930  12011  Z= 0.260
  Chirality :  0.045   0.139   1396
  Planarity :  0.004   0.040   1537
  Dihedral  :  5.434  56.452   1433
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 19.19 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.25), residues: 1098
  helix:  2.13 (0.35), residues: 227
  sheet:  0.81 (0.31), residues: 268
  loop : -0.22 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1036 
 TYR   0.016   0.001   TYR A  85 
 PHE   0.010   0.001   PHE A 359 
 TRP   0.004   0.001   TRP A  54 
 HIS   0.002   0.001   HIS A 112 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 8805)
  covalent geometry    : angle       0.49214 /  0.26 (12011)
  hydrogen bonds       : bond        0.03617 /  2.41 (  344)
  hydrogen bonds       : angle       4.97796 /  3.47 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  301 GLN cc_start: 0.8645 (tt0) cc_final: 0.8324 (tp40)
REVERT: A  342 TYR cc_start: 0.9003 (t80) cc_final: 0.8725 (t80)
REVERT: A  377 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8888 (OUTLIER)
REVERT: A  396 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8578 (mt-10)
REVERT: B  887 GLU cc_start: 0.8928 (tt0) cc_final: 0.8679 (mm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 73
  average time/residue: 0.5014
  time to fit residues: 39.6564
Evaluate side-chains
  71 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 53 optimal weight:    0.1980
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 757 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.085811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.067408 restraints weight = 14180.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.2693 rms_B_bonded: 2.12
r_work: 0.2569 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2442 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9286
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8805  Z= 0.118
  Angle     :  0.486   9.924  12011  Z= 0.257
  Chirality :  0.045   0.174   1396
  Planarity :  0.004   0.040   1537
  Dihedral  :  5.391  54.915   1433
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.62 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.25), residues: 1098
  helix:  2.15 (0.35), residues: 227
  sheet:  0.81 (0.31), residues: 268
  loop : -0.23 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 836 
 TYR   0.017   0.001   TYR A  85 
 PHE   0.010   0.001   PHE A 143 
 TRP   0.006   0.001   TRP A  54 
 HIS   0.002   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 8805)
  covalent geometry    : angle       0.48588 /  0.26 (12011)
  hydrogen bonds       : bond        0.03495 /  2.34 (  344)
  hydrogen bonds       : angle       4.92940 /  3.44 (  954)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   26 MET cc_start: 0.9117 (mtt) cc_final: 0.7956 (mtt)
REVERT: A  301 GLN cc_start: 0.8624 (tt0) cc_final: 0.8271 (tp40)
REVERT: A  342 TYR cc_start: 0.9004 (t80) cc_final: 0.8692 (t80)
REVERT: A  377 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8840 (m-30)
REVERT: A  396 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8577 (mt-10)
REVERT: B  887 GLU cc_start: 0.8928 (tt0) cc_final: 0.8675 (mm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 71
  average time/residue: 0.3933
  time to fit residues: 30.2761
Evaluate side-chains
  70 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain B residue  719 THR
Chi-restraints excluded: chain B residue  720 LYS
Chi-restraints excluded: chain B residue  969 VAL
Chi-restraints excluded: chain B residue 1008 ASP
Chi-restraints excluded: chain B residue 1037 LEU
Chi-restraints excluded: chain B residue 1108 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.2993 r_free = 0.2993 target = 0.083100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.064960 restraints weight = 14333.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.2649 rms_B_bonded: 2.09
r_work: 0.2524 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2395 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9314
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8805  Z= 0.186
  Angle     :  0.534   9.759  12011  Z= 0.284
  Chirality :  0.046   0.174   1396
  Planarity :  0.004   0.039   1537
  Dihedral  :  5.661  55.593   1433
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.83 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.25), residues: 1098
  helix:  2.00 (0.35), residues: 227
  sheet:  0.68 (0.31), residues: 266
  loop : -0.29 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1036 
 TYR   0.019   0.001   TYR A  85 
 PHE   0.013   0.001   PHE A 359 
 TRP   0.005   0.001   TRP A  54 
 HIS   0.003   0.001   HIS B1069 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.19 ( 8805)
  covalent geometry    : angle       0.53426 /  0.28 (12011)
  hydrogen bonds       : bond        0.04057 /  2.74 (  344)
  hydrogen bonds       : angle       5.15066 /  3.60 (  954)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2351.21 seconds
wall clock time: 41 minutes 2.16 seconds (2462.16 seconds total)