Starting phenix.real_space_refine
on Thu Feb 13 15:30:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7un6_26614/02_2025/7un6_26614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7un6_26614/02_2025/7un6_26614.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7un6_26614/02_2025/7un6_26614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7un6_26614/02_2025/7un6_26614.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7un6_26614/02_2025/7un6_26614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7un6_26614/02_2025/7un6_26614.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=  -0.002 sd=   0.068
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      41      5.16       5
     C    5808      2.51       5
     N    1533      2.21       5
     O    1660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9042
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 648, 5186
          Classifications: {'peptide': 648}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 610}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 1965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1965
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 13, 'TRANS': 226}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1891
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 11, 'TRANS': 218}
          Chain breaks: 2
  Time building chain proxies: 5.90, per 1000 atoms: 0.65
  Number of scatterers: 9042
  At special positions: 0
  Unit cell: (90.75, 131.175, 135.3, 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      41     16.00
     O    1660      8.00
     N    1533      7.00
     C    5808      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: 2.31
  Conformation dependent library (CDL) restraints added in 972.2 milliseconds
  

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      31.8% alpha, 27.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 190 through 192
      No H-bonds generated for 'chain 'A' and resid 190 through 192'
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 4.091A  pdb=" N   SER A 275 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 334
      removed outlier: 4.179A  pdb=" N   GLY A 334 " --> pdb=" O   GLN A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 343
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 950 through 968
    Processing helix  chain 'A' and resid 1060 through 1071
    Processing helix  chain 'A' and resid 1083 through 1088
    Processing helix  chain 'A' and resid 1090 through 1118
      removed outlier: 3.535A  pdb=" N   ARG A1117 " --> pdb=" O   THR A1113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1146
      removed outlier: 3.751A  pdb=" N   ARG A1128 " --> pdb=" O   GLU A1124 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   THR A1133 " --> pdb=" O   GLN A1129 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   TRP A1136 " --> pdb=" O   SER A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1283
    Processing helix  chain 'B' and resid 74 through 122
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 169 through 178
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 189 through 194
    Processing helix  chain 'B' and resid 243 through 247
    Processing helix  chain 'B' and resid 296 through 301
    Processing helix  chain 'B' and resid 313 through 333
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.655A  pdb=" N   TYR B 341 " --> pdb=" O   ARG B 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 123
      Proline residue:  C 112  - end of helix
    Processing helix  chain 'C' and resid 169 through 177
    Processing helix  chain 'C' and resid 178 through 183
    Processing helix  chain 'C' and resid 189 through 194
    Processing helix  chain 'C' and resid 243 through 247
    Processing helix  chain 'C' and resid 296 through 302
    Processing helix  chain 'C' and resid 316 through 333
    Processing helix  chain 'C' and resid 337 through 343
    Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134
      removed outlier: 6.272A  pdb=" N   LEU A  65 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 188
      removed outlier: 6.668A  pdb=" N   ILE A 183 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU A 177 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   TYR A 185 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   VAL A 175 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP A 556 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   VAL A 169 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER A 554 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE A 171 " --> pdb=" O   MET A 552 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   MET A 552 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   CYS A 173 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   THR A 550 " --> pdb=" O   CYS A 173 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL A 175 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 548 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL A 546 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL A 557 " --> pdb=" O   CYS A 566 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   CYS A 566 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   TRP A 559 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL A 564 " --> pdb=" O   TRP A 559 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 356
      removed outlier: 6.662A  pdb=" N   VAL A 546 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 548 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL A 175 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   THR A 550 " --> pdb=" O   CYS A 173 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   CYS A 173 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   MET A 552 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE A 171 " --> pdb=" O   MET A 552 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER A 554 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   VAL A 169 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP A 556 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269
      removed outlier: 6.753A  pdb=" N   GLU A 297 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   LYS A 223 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ILE A 221 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   VAL A 301 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   GLN A 219 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 215 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280
      removed outlier: 5.963A  pdb=" N   TRP A 278 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   SER A 231 " --> pdb=" O   TRP A 278 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 215 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   GLN A 219 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   VAL A 301 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ILE A 221 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   LYS A 223 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   GLU A 297 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 291 through 306
    current: chain 'A' and resid 337 through 338
    Processing sheet with id=AA6, first strand: chain 'A' and resid 631 through 635
      removed outlier: 6.530A  pdb=" N   TRP A 621 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 631 through 635
      removed outlier: 6.530A  pdb=" N   TRP A 621 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   THR A 616 " --> pdb=" O   ASP A 611 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER A 609 " --> pdb=" O   MET A 618 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   LYS A 620 " --> pdb=" O   VAL A 607 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   VAL A 607 " --> pdb=" O   LYS A 620 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   PHE A 622 " --> pdb=" O   GLY A 605 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   GLY A 605 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   LEU A 624 " --> pdb=" O   VAL A 603 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   VAL A 603 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   VAL A 603 " --> pdb=" O   ASP A 592 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   ASP A 592 " --> pdb=" O   VAL A 603 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681
    Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 932
      removed outlier: 3.873A  pdb=" N   PHE A 978 " --> pdb=" O   LEU A 984 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   LEU A 984 " --> pdb=" O   PHE A 978 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   GLY A 991 " --> pdb=" O   GLY A1000 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   GLY A1000 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 196 through 203
      removed outlier: 4.035A  pdb=" N   LEU B 214 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LYS B 231 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ARG B 234 " --> pdb=" O   GLY B 254 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLY B 254 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   ARG B 236 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE B 252 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 278
    Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 203
    Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 235
      removed outlier: 5.790A  pdb=" N   ARG C 234 " --> pdb=" O   MET C 253 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 270 through 278

    353 hydrogen bonds defined for protein.
    990 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: 2.99

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2928
        1.34 -     1.46: 1983
        1.46 -     1.58: 4281
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 9253
  Sorted by residual:
  bond pdb=" C   PHE A 584 "
       pdb=" N   CYS A 585 "
    ideal  model  delta    sigma   weight residual
    1.329  1.248  0.081 1.86e-02 2.89e+03 1.87e+01
  bond pdb=" CG  LEU C  81 "
       pdb=" CD2 LEU C  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.30e+00
  bond pdb=" CB  VAL C 201 "
       pdb=" CG2 VAL C 201 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.99e-01
  bond pdb=" CB  GLU A1081 "
       pdb=" CG  GLU A1081 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.93e-01
  bond pdb=" CB  ILE B 192 "
       pdb=" CG1 ILE B 192 "
    ideal  model  delta    sigma   weight residual
    1.530  1.512  0.018 2.00e-02 2.50e+03 8.33e-01
  ... (remaining 9248 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 12111
        1.45 -     2.90: 316
        2.90 -     4.35: 74
        4.35 -     5.81: 5
        5.81 -     7.26: 4
  Bond angle restraints: 12510
  Sorted by residual:
  angle pdb=" N   GLU A 691 "
        pdb=" CA  GLU A 691 "
        pdb=" C   GLU A 691 "
      ideal   model   delta    sigma   weight residual
     111.07  115.58   -4.51 1.07e+00 8.73e-01 1.78e+01
  angle pdb=" CA  GLU A1081 "
        pdb=" CB  GLU A1081 "
        pdb=" CG  GLU A1081 "
      ideal   model   delta    sigma   weight residual
     114.10  121.36   -7.26 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" N   GLN B 111 "
        pdb=" CA  GLN B 111 "
        pdb=" C   GLN B 111 "
      ideal   model   delta    sigma   weight residual
     113.77  109.79    3.98 1.32e+00 5.74e-01 9.09e+00
  angle pdb=" N   VAL A 692 "
        pdb=" CA  VAL A 692 "
        pdb=" C   VAL A 692 "
      ideal   model   delta    sigma   weight residual
     107.75  111.45   -3.70 1.46e+00 4.69e-01 6.41e+00
  angle pdb=" C   ILE A 973 "
        pdb=" N   MET A 974 "
        pdb=" CA  MET A 974 "
      ideal   model   delta    sigma   weight residual
     121.80  117.67    4.13 1.71e+00 3.42e-01 5.82e+00
  ... (remaining 12505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 5060
       17.81 -    35.62: 413
       35.62 -    53.43: 61
       53.43 -    71.24: 17
       71.24 -    89.05: 14
  Dihedral angle restraints: 5565
    sinusoidal: 2315
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  GLU A 691 "
           pdb=" C   GLU A 691 "
           pdb=" N   VAL A 692 "
           pdb=" CA  VAL A 692 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.46  -27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ASN C 221 "
           pdb=" C   ASN C 221 "
           pdb=" N   GLU C 222 "
           pdb=" CA  GLU C 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.04   21.96     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  ILE A 973 "
           pdb=" C   ILE A 973 "
           pdb=" N   MET A 974 "
           pdb=" CA  MET A 974 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.11   21.89     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 5562 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 979
       0.039 -    0.078: 263
       0.078 -    0.117: 103
       0.117 -    0.156: 24
       0.156 -    0.195: 1
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CB  ILE B 192 "
            pdb=" CA  ILE B 192 "
            pdb=" CG1 ILE B 192 "
            pdb=" CG2 ILE B 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.20 2.00e-01 2.50e+01 9.54e-01
  chirality pdb=" CA  PHE C 216 "
            pdb=" N   PHE C 216 "
            pdb=" C   PHE C 216 "
            pdb=" CB  PHE C 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  ILE B 199 "
            pdb=" N   ILE B 199 "
            pdb=" C   ILE B 199 "
            pdb=" CB  ILE B 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 1367 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 154 "   -0.177 9.50e-02 1.11e+02   7.93e-02 4.03e+00
        pdb=" NE  ARG A 154 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 154 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 154 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 154 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 111 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO B 112 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 112 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 112 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 622 "    0.009 2.00e-02 2.50e+03   1.06e-02 1.97e+00
        pdb=" CG  PHE A 622 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 622 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 622 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 622 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 622 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 622 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 50
        2.48 -     3.09: 6799
        3.09 -     3.69: 13564
        3.69 -     4.30: 19819
        4.30 -     4.90: 32624
  Nonbonded interactions: 72856
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 233 "
            pdb=" OD1 ASP C 323 "
     model   vdw
     1.879 3.040
  nonbonded pdb=" OG  SER A 287 "
            pdb=" OD2 ASP C 248 "
     model   vdw
     1.955 3.040
  nonbonded pdb=" OH  TYR A 997 "
            pdb=" O   LEU A1029 "
     model   vdw
     1.985 3.040
  nonbonded pdb=" OH  TYR A  70 "
            pdb=" OE1 GLU A 129 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" OH  TYR B 233 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.126 3.040
  ... (remaining 72851 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 73 through 126 or resid 166 through 306 or resid 315 throu \ 
gh 349))
  selection = chain 'C'
}

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:             2.680
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     23.930
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5485
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   0.081   9253  Z= 0.243
  Angle     :  0.600   7.257  12510  Z= 0.331
  Chirality :  0.044   0.195   1370
  Planarity :  0.004   0.079   1608
  Dihedral  : 13.875  89.046   3455
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.25), residues: 1090
  helix:  0.66 (0.30), residues: 293
  sheet: -1.50 (0.32), residues: 218
  loop : -0.80 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 209 
 HIS   0.004   0.001   HIS A 577 
 PHE   0.024   0.002   PHE A 622 
 TYR   0.018   0.001   TYR A1034 
 ARG   0.007   0.000   ARG A 154 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.4564 (t80) cc_final: 0.3850 (p90)
REVERT: A  193 GLN cc_start: 0.6544 (mm110) cc_final: 0.6295 (mt0)
REVERT: A  206 TYR cc_start: 0.5558 (t80) cc_final: 0.5086 (t80)
REVERT: A  616 THR cc_start: 0.7799 (p) cc_final: 0.7590 (t)
REVERT: B   94 LYS cc_start: 0.6343 (mttp) cc_final: 0.5796 (mmtm)
REVERT: B  117 ARG cc_start: 0.6195 (ttp-170) cc_final: 0.3046 (tmm160)
REVERT: B  202 LYS cc_start: 0.6898 (mttm) cc_final: 0.6518 (mmmt)
REVERT: B  332 GLU cc_start: 0.5227 (pt0) cc_final: 0.5007 (pt0)
REVERT: B  337 ARG cc_start: 0.6925 (mtp180) cc_final: 0.6220 (mtt-85)
REVERT: C   76 ARG cc_start: 0.6178 (ttm170) cc_final: 0.5442 (tpt170)
REVERT: C  202 LYS cc_start: 0.6848 (mtpp) cc_final: 0.6250 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.2513
  time to fit residues: 62.6448
Evaluate side-chains
  116 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.0030
   chunk 84 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 44 optimal weight:   20.0000
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
A  75 HIS
A 346 GLN
A1018 HIS
A1101 ASN
A1129 GLN
B  85 GLN
B 226 ASN
C 100 HIS
C 221 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.280517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.231267 restraints weight = 8430.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4649 rms_B_bonded: 2.98
r_work: 0.4297 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9253  Z= 0.274
  Angle     :  0.683   8.158  12510  Z= 0.353
  Chirality :  0.047   0.181   1370
  Planarity :  0.005   0.069   1608
  Dihedral  :  5.238  27.565   1201
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  8.73 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.25), residues: 1090
  helix:  0.50 (0.29), residues: 300
  sheet: -1.37 (0.31), residues: 218
  loop : -0.52 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 171 
 HIS   0.006   0.001   HIS A 577 
 PHE   0.037   0.002   PHE C 212 
 TYR   0.016   0.002   TYR A1002 
 ARG   0.006   0.001   ARG C 117 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 LEU cc_start: 0.6859 (mt) cc_final: 0.6499 (mt)
REVERT: A  558 MET cc_start: 0.8132 (ttt) cc_final: 0.7882 (ttp)
REVERT: A  561 ASP cc_start: 0.7988 (p0) cc_final: 0.7742 (p0)
REVERT: B  231 LYS cc_start: 0.7623 (tttm) cc_final: 0.7208 (mtpp)
REVERT: B  337 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7568 (mtt-85)
REVERT: C   76 ARG cc_start: 0.6499 (ttm170) cc_final: 0.5646 (tpt170)
REVERT: C  170 PHE cc_start: 0.6413 (t80) cc_final: 0.6048 (t80)
REVERT: C  202 LYS cc_start: 0.6955 (mtpp) cc_final: 0.6612 (mmtt)
  outliers start: 19
  outliers final: 9
  residues processed: 134
  average time/residue: 0.1808
  time to fit residues: 35.7700
Evaluate side-chains
  113 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  226 ASN
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain C residue  216 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 102 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0470
   chunk 8 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0000
   chunk 63 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.3482

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

Flipped N/Q/H residues before XYZ refinement:
** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5052 r_free = 0.5052 target = 0.284567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.235094 restraints weight = 8547.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.4670 rms_B_bonded: 2.74
r_work: 0.4373 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9253  Z= 0.176
  Angle     :  0.579   7.811  12510  Z= 0.298
  Chirality :  0.044   0.173   1370
  Planarity :  0.004   0.059   1608
  Dihedral  :  4.904  25.201   1201
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.61 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.25), residues: 1090
  helix:  0.84 (0.30), residues: 294
  sheet: -1.13 (0.32), residues: 218
  loop : -0.25 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 171 
 HIS   0.006   0.001   HIS C 328 
 PHE   0.037   0.002   PHE C 212 
 TYR   0.016   0.002   TYR A 206 
 ARG   0.003   0.000   ARG C 117 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 LEU cc_start: 0.6799 (mt) cc_final: 0.6553 (mt)
REVERT: A  552 MET cc_start: 0.5304 (ptm) cc_final: 0.4082 (mmt)
REVERT: A  561 ASP cc_start: 0.7767 (p0) cc_final: 0.7482 (p0)
REVERT: B  117 ARG cc_start: 0.7052 (ttp-170) cc_final: 0.4408 (tmm160)
REVERT: B  226 ASN cc_start: 0.5155 (m-40) cc_final: 0.4416 (t0)
REVERT: B  231 LYS cc_start: 0.7488 (tttm) cc_final: 0.7048 (mtpp)
REVERT: B  337 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7455 (mtt-85)
REVERT: C   76 ARG cc_start: 0.6457 (ttm170) cc_final: 0.5560 (tpt170)
REVERT: C  170 PHE cc_start: 0.6465 (t80) cc_final: 0.6209 (t80)
REVERT: C  202 LYS cc_start: 0.6726 (mtpp) cc_final: 0.6376 (mmtt)
  outliers start: 13
  outliers final: 8
  residues processed: 125
  average time/residue: 0.1836
  time to fit residues: 33.6805
Evaluate side-chains
  119 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 101 optimal weight:    0.0000
   chunk 108 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:   40.0000
   chunk 59 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 162 GLN
B 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5031 r_free = 0.5031 target = 0.279625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.231399 restraints weight = 8574.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4660 rms_B_bonded: 3.31
r_work: 0.4253 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9253  Z= 0.216
  Angle     :  0.573   7.513  12510  Z= 0.295
  Chirality :  0.044   0.162   1370
  Planarity :  0.004   0.051   1608
  Dihedral  :  4.792  24.511   1201
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.80 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1090
  helix:  0.82 (0.30), residues: 295
  sheet: -1.05 (0.33), residues: 215
  loop : -0.15 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1136 
 HIS   0.009   0.001   HIS A  83 
 PHE   0.040   0.002   PHE C 212 
 TYR   0.011   0.002   TYR B 106 
 ARG   0.004   0.000   ARG B 117 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.6564 (t80) cc_final: 0.4191 (p90)
REVERT: A  552 MET cc_start: 0.5309 (ptm) cc_final: 0.4239 (mmt)
REVERT: A  561 ASP cc_start: 0.7831 (p0) cc_final: 0.7569 (p0)
REVERT: A  623 LYS cc_start: 0.8397 (ptpt) cc_final: 0.8006 (ptpp)
REVERT: B  226 ASN cc_start: 0.6054 (m110) cc_final: 0.5035 (t0)
REVERT: B  231 LYS cc_start: 0.7576 (tttm) cc_final: 0.7149 (mtpp)
REVERT: B  337 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7540 (mtt-85)
REVERT: C   76 ARG cc_start: 0.6609 (ttm170) cc_final: 0.5659 (tpt170)
REVERT: C  202 LYS cc_start: 0.6813 (mtpp) cc_final: 0.6456 (mmtt)
REVERT: C  233 TYR cc_start: 0.7437 (m-80) cc_final: 0.7150 (m-80)
REVERT: C  253 MET cc_start: 0.5834 (mmm) cc_final: 0.4668 (ptp)
  outliers start: 23
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1894
  time to fit residues: 36.1024
Evaluate side-chains
  120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 46 optimal weight:    0.0000
   chunk 95 optimal weight:    0.8980
   chunk 102 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   chunk 58 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5033 r_free = 0.5033 target = 0.280016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.230841 restraints weight = 8562.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.4647 rms_B_bonded: 3.28
r_work: 0.4262 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9253  Z= 0.197
  Angle     :  0.553   7.486  12510  Z= 0.284
  Chirality :  0.044   0.168   1370
  Planarity :  0.004   0.045   1608
  Dihedral  :  4.686  23.349   1201
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.79 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1090
  helix:  0.88 (0.30), residues: 295
  sheet: -0.90 (0.33), residues: 214
  loop : -0.09 (0.27), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 278 
 HIS   0.007   0.001   HIS C 328 
 PHE   0.037   0.002   PHE C 212 
 TYR   0.010   0.001   TYR C 223 
 ARG   0.004   0.000   ARG B 117 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.6470 (t80) cc_final: 0.4288 (p90)
REVERT: A  552 MET cc_start: 0.5274 (ptm) cc_final: 0.4259 (mmt)
REVERT: A  561 ASP cc_start: 0.7841 (p0) cc_final: 0.7593 (p0)
REVERT: A  623 LYS cc_start: 0.8338 (ptpt) cc_final: 0.7934 (ptpp)
REVERT: A  962 MET cc_start: 0.7576 (mtm) cc_final: 0.7196 (mmt)
REVERT: B  226 ASN cc_start: 0.6388 (m110) cc_final: 0.5170 (t0)
REVERT: B  231 LYS cc_start: 0.7565 (tttm) cc_final: 0.7093 (mtpp)
REVERT: C   76 ARG cc_start: 0.6618 (ttm170) cc_final: 0.5710 (tpt170)
REVERT: C  170 PHE cc_start: 0.6755 (t80) cc_final: 0.6524 (t80)
REVERT: C  202 LYS cc_start: 0.6848 (mtpp) cc_final: 0.6493 (mptt)
REVERT: C  233 TYR cc_start: 0.7403 (m-10) cc_final: 0.7088 (m-80)
REVERT: C  253 MET cc_start: 0.5904 (mmm) cc_final: 0.4776 (ptp)
  outliers start: 24
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1958
  time to fit residues: 35.9112
Evaluate side-chains
  124 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 81 optimal weight:   20.0000
   chunk 74 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 90 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 155 HIS
A 193 GLN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.276119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.224341 restraints weight = 8527.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.4590 rms_B_bonded: 3.43
r_work: 0.4200 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9253  Z= 0.277
  Angle     :  0.597   8.482  12510  Z= 0.307
  Chirality :  0.045   0.174   1370
  Planarity :  0.004   0.043   1608
  Dihedral  :  4.852  23.790   1201
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.29 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.26), residues: 1090
  helix:  0.75 (0.30), residues: 294
  sheet: -1.00 (0.33), residues: 214
  loop : -0.21 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 278 
 HIS   0.015   0.002   HIS A  83 
 PHE   0.049   0.002   PHE C 212 
 TYR   0.012   0.002   TYR B 106 
 ARG   0.004   0.000   ARG B 117 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.6507 (t80) cc_final: 0.4175 (p90)
REVERT: A  304 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5828 (pp)
REVERT: A  552 MET cc_start: 0.5326 (ptm) cc_final: 0.4236 (mmt)
REVERT: A  561 ASP cc_start: 0.7911 (p0) cc_final: 0.7657 (p0)
REVERT: A  623 LYS cc_start: 0.8355 (ptpt) cc_final: 0.7953 (ptpp)
REVERT: A  657 ASP cc_start: 0.6032 (OUTLIER) cc_final: 0.4751 (m-30)
REVERT: A  962 MET cc_start: 0.7571 (mtm) cc_final: 0.7112 (mmt)
REVERT: B  231 LYS cc_start: 0.7685 (tttm) cc_final: 0.7267 (mtpp)
REVERT: C   76 ARG cc_start: 0.6835 (ttm170) cc_final: 0.5919 (tpt170)
REVERT: C  202 LYS cc_start: 0.6835 (mtpp) cc_final: 0.6459 (mptt)
REVERT: C  224 PHE cc_start: 0.3734 (OUTLIER) cc_final: 0.2684 (p90)
REVERT: C  233 TYR cc_start: 0.7551 (m-10) cc_final: 0.7187 (m-80)
REVERT: C  253 MET cc_start: 0.6027 (mmm) cc_final: 0.4889 (ptp)
  outliers start: 31
  outliers final: 22
  residues processed: 139
  average time/residue: 0.1904
  time to fit residues: 38.4551
Evaluate side-chains
  135 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  155 HIS
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Chi-restraints excluded: chain C residue  224 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 71 optimal weight:    0.0570
   chunk 96 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 107 optimal weight:    1.9990
   overall best weight:    1.5704

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 193 GLN
C 122 ASN
C 221 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4984 r_free = 0.4984 target = 0.271864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.221895 restraints weight = 8698.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.4573 rms_B_bonded: 3.45
r_work: 0.4151 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   9253  Z= 0.373
  Angle     :  0.647   7.771  12510  Z= 0.336
  Chirality :  0.046   0.162   1370
  Planarity :  0.005   0.044   1608
  Dihedral  :  5.044  24.396   1201
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 14.19 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.26), residues: 1090
  helix:  0.61 (0.30), residues: 294
  sheet: -1.11 (0.34), residues: 216
  loop : -0.29 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 278 
 HIS   0.019   0.002   HIS A 155 
 PHE   0.053   0.003   PHE C 212 
 TYR   0.016   0.002   TYR B 106 
 ARG   0.016   0.001   ARG A 154 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.6542 (t80) cc_final: 0.4204 (p90)
REVERT: A  552 MET cc_start: 0.5375 (ptm) cc_final: 0.4301 (mmt)
REVERT: A  576 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7263 (t)
REVERT: A  623 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8007 (ptpp)
REVERT: A  657 ASP cc_start: 0.5983 (OUTLIER) cc_final: 0.4772 (m-30)
REVERT: A  962 MET cc_start: 0.7562 (mtm) cc_final: 0.7156 (mmt)
REVERT: B  179 ASP cc_start: 0.7602 (m-30) cc_final: 0.7306 (t0)
REVERT: B  231 LYS cc_start: 0.7819 (tttm) cc_final: 0.7404 (mtpp)
REVERT: B  305 GLU cc_start: 0.7402 (mp0) cc_final: 0.6814 (mp0)
REVERT: C   76 ARG cc_start: 0.6887 (ttm170) cc_final: 0.5942 (tpt170)
REVERT: C  183 ASP cc_start: 0.6393 (m-30) cc_final: 0.6170 (m-30)
REVERT: C  202 LYS cc_start: 0.6937 (mtpp) cc_final: 0.6480 (mmtt)
REVERT: C  224 PHE cc_start: 0.3799 (OUTLIER) cc_final: 0.3075 (p90)
REVERT: C  233 TYR cc_start: 0.7617 (m-10) cc_final: 0.7354 (m-80)
REVERT: C  253 MET cc_start: 0.6115 (mmm) cc_final: 0.4902 (ptp)
REVERT: C  330 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6995 (tt)
REVERT: C  345 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6440 (mt-10)
  outliers start: 39
  outliers final: 25
  residues processed: 145
  average time/residue: 0.1897
  time to fit residues: 40.1075
Evaluate side-chains
  136 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Chi-restraints excluded: chain C residue  221 ASN
Chi-restraints excluded: chain C residue  224 PHE
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 66 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 106 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 91 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 155 HIS
A 193 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5021 r_free = 0.5021 target = 0.277823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.227423 restraints weight = 8711.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.4608 rms_B_bonded: 3.51
r_work: 0.4233 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9253  Z= 0.194
  Angle     :  0.578   7.999  12510  Z= 0.297
  Chirality :  0.044   0.165   1370
  Planarity :  0.004   0.043   1608
  Dihedral  :  4.796  22.835   1201
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.38 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.26), residues: 1090
  helix:  0.78 (0.30), residues: 294
  sheet: -0.90 (0.35), residues: 205
  loop : -0.18 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 171 
 HIS   0.009   0.001   HIS C 328 
 PHE   0.045   0.002   PHE C 212 
 TYR   0.019   0.001   TYR C 223 
 ARG   0.006   0.000   ARG A 154 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 ILE cc_start: 0.7832 (tp) cc_final: 0.7523 (tp)
REVERT: A  185 TYR cc_start: 0.6382 (t80) cc_final: 0.4182 (p90)
REVERT: A  200 TYR cc_start: 0.7590 (m-80) cc_final: 0.7300 (m-80)
REVERT: A  552 MET cc_start: 0.5232 (ptm) cc_final: 0.4162 (mmt)
REVERT: A  623 LYS cc_start: 0.8357 (ptpt) cc_final: 0.7949 (ptpp)
REVERT: A  645 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6231 (tt)
REVERT: A  657 ASP cc_start: 0.5797 (OUTLIER) cc_final: 0.4484 (m-30)
REVERT: A  962 MET cc_start: 0.7489 (mtm) cc_final: 0.7069 (mmt)
REVERT: B  117 ARG cc_start: 0.7372 (ttp-170) cc_final: 0.5998 (tmm-80)
REVERT: B  179 ASP cc_start: 0.7436 (m-30) cc_final: 0.7139 (t0)
REVERT: B  231 LYS cc_start: 0.7435 (tttm) cc_final: 0.6923 (mtpp)
REVERT: C   76 ARG cc_start: 0.6780 (ttm170) cc_final: 0.5854 (tpt170)
REVERT: C   98 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7665 (mt-10)
REVERT: C  202 LYS cc_start: 0.6836 (mtpp) cc_final: 0.6391 (mmtt)
REVERT: C  224 PHE cc_start: 0.3751 (OUTLIER) cc_final: 0.2187 (p90)
REVERT: C  233 TYR cc_start: 0.7428 (m-10) cc_final: 0.7217 (m-80)
REVERT: C  253 MET cc_start: 0.5875 (mmm) cc_final: 0.4672 (ptp)
REVERT: C  330 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6795 (tt)
  outliers start: 32
  outliers final: 24
  residues processed: 141
  average time/residue: 0.2123
  time to fit residues: 42.8871
Evaluate side-chains
  140 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  155 HIS
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1111 SER
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Chi-restraints excluded: chain C residue  224 PHE
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 89 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 155 HIS
A 193 GLN
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 328 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.276723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.226481 restraints weight = 8682.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.4603 rms_B_bonded: 3.42
r_work: 0.4202 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9253  Z= 0.235
  Angle     :  0.588   8.190  12510  Z= 0.302
  Chirality :  0.044   0.158   1370
  Planarity :  0.004   0.050   1608
  Dihedral  :  4.813  23.351   1201
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 15.08 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.26), residues: 1090
  helix:  0.78 (0.30), residues: 294
  sheet: -0.94 (0.33), residues: 222
  loop : -0.20 (0.27), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 171 
 HIS   0.009   0.001   HIS A 155 
 PHE   0.041   0.002   PHE C 212 
 TYR   0.017   0.001   TYR C 223 
 ARG   0.008   0.000   ARG B  76 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 ILE cc_start: 0.7906 (tp) cc_final: 0.7588 (tp)
REVERT: A  185 TYR cc_start: 0.6333 (t80) cc_final: 0.4195 (p90)
REVERT: A  200 TYR cc_start: 0.7655 (m-80) cc_final: 0.7354 (m-80)
REVERT: A  552 MET cc_start: 0.5214 (ptm) cc_final: 0.4183 (mmt)
REVERT: A  623 LYS cc_start: 0.8338 (ptpt) cc_final: 0.7941 (ptpp)
REVERT: A  657 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.4601 (m-30)
REVERT: A  962 MET cc_start: 0.7531 (mtm) cc_final: 0.7085 (mmt)
REVERT: B  179 ASP cc_start: 0.7488 (m-30) cc_final: 0.7193 (t0)
REVERT: B  231 LYS cc_start: 0.7533 (tttm) cc_final: 0.7053 (mtpp)
REVERT: B  305 GLU cc_start: 0.7346 (mp0) cc_final: 0.6741 (mp0)
REVERT: C   76 ARG cc_start: 0.6837 (ttm170) cc_final: 0.5913 (tpt170)
REVERT: C  196 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5593 (tp)
REVERT: C  202 LYS cc_start: 0.6837 (mtpp) cc_final: 0.6421 (mmtt)
REVERT: C  224 PHE cc_start: 0.3648 (OUTLIER) cc_final: 0.2250 (p90)
REVERT: C  233 TYR cc_start: 0.7482 (m-10) cc_final: 0.7248 (m-80)
REVERT: C  253 MET cc_start: 0.5973 (mmm) cc_final: 0.4813 (ptp)
REVERT: C  330 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6850 (tt)
  outliers start: 33
  outliers final: 25
  residues processed: 136
  average time/residue: 0.1980
  time to fit residues: 39.3067
Evaluate side-chains
  136 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Chi-restraints excluded: chain C residue  224 PHE
Chi-restraints excluded: chain C residue  328 HIS
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0000
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 193 GLN
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 577 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 328 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5007 r_free = 0.5007 target = 0.275272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.226148 restraints weight = 8718.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.4601 rms_B_bonded: 3.45
r_work: 0.4209 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9253  Z= 0.254
  Angle     :  0.602   8.319  12510  Z= 0.310
  Chirality :  0.045   0.156   1370
  Planarity :  0.004   0.043   1608
  Dihedral  :  4.867  23.299   1201
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.48 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.26), residues: 1090
  helix:  0.74 (0.30), residues: 294
  sheet: -1.02 (0.33), residues: 224
  loop : -0.21 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 171 
 HIS   0.021   0.002   HIS C 328 
 PHE   0.049   0.002   PHE C 212 
 TYR   0.020   0.002   TYR B 223 
 ARG   0.007   0.000   ARG A 154 

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 ILE cc_start: 0.7868 (tp) cc_final: 0.7547 (tp)
REVERT: A  185 TYR cc_start: 0.6332 (t80) cc_final: 0.4248 (p90)
REVERT: A  200 TYR cc_start: 0.7649 (m-80) cc_final: 0.7333 (m-80)
REVERT: A  552 MET cc_start: 0.5221 (ptm) cc_final: 0.4187 (mmt)
REVERT: A  623 LYS cc_start: 0.8348 (ptpt) cc_final: 0.7947 (ptpp)
REVERT: A  657 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.4693 (m-30)
REVERT: A  962 MET cc_start: 0.7505 (mtm) cc_final: 0.7079 (mmt)
REVERT: B  179 ASP cc_start: 0.7505 (m-30) cc_final: 0.7225 (t0)
REVERT: B  231 LYS cc_start: 0.7568 (tttm) cc_final: 0.7086 (mtpp)
REVERT: B  305 GLU cc_start: 0.7372 (mp0) cc_final: 0.7021 (mp0)
REVERT: C   76 ARG cc_start: 0.6828 (ttm170) cc_final: 0.5929 (tpt170)
REVERT: C  196 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5677 (tp)
REVERT: C  202 LYS cc_start: 0.6811 (mtpp) cc_final: 0.6469 (mptt)
REVERT: C  224 PHE cc_start: 0.3608 (OUTLIER) cc_final: 0.2274 (p90)
REVERT: C  233 TYR cc_start: 0.7535 (m-10) cc_final: 0.7294 (m-80)
REVERT: C  253 MET cc_start: 0.5991 (mmm) cc_final: 0.4817 (ptp)
  outliers start: 29
  outliers final: 24
  residues processed: 127
  average time/residue: 0.1837
  time to fit residues: 34.3907
Evaluate side-chains
  133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  159 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  288 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  352 ARG
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 ASP
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1006 ILE
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  210 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  216 PHE
Chi-restraints excluded: chain C residue  224 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 104 optimal weight:   20.0000
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 74 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 193 GLN
A 344 HIS
A 577 HIS
C 217 HIS
C 328 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5011 r_free = 0.5011 target = 0.275912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.225392 restraints weight = 8658.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.4598 rms_B_bonded: 3.42
r_work: 0.4211 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9253  Z= 0.232
  Angle     :  0.587   8.116  12510  Z= 0.303
  Chirality :  0.044   0.156   1370
  Planarity :  0.004   0.042   1608
  Dihedral  :  4.813  22.613   1201
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.58 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.26), residues: 1090
  helix:  0.76 (0.30), residues: 294
  sheet: -0.84 (0.35), residues: 208
  loop : -0.22 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 694 
 HIS   0.012   0.001   HIS C 328 
 PHE   0.043   0.002   PHE C 212 
 TYR   0.021   0.001   TYR B 223 
 ARG   0.007   0.000   ARG A 154 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4646.69 seconds
wall clock time: 83 minutes 30.23 seconds (5010.23 seconds total)