Starting phenix.real_space_refine
on Fri Jul 25 17:35:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n2f_48837/07_2025/9n2f_48837.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n2f_48837/07_2025/9n2f_48837.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n2f_48837/07_2025/9n2f_48837.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n2f_48837/07_2025/9n2f_48837.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n2f_48837/07_2025/9n2f_48837.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n2f_48837/07_2025/9n2f_48837.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.013
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      12      5.16       5
     C    4874      2.51       5
     N    1251      2.21       5
     O    1463      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7600
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "F"
      Number of atoms: 1979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1979
          Classifications: {'peptide': 244}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 235}
    Chain: "A"
      Number of atoms: 5621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 704, 5621
          Classifications: {'peptide': 704}
          Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 677}
          Unresolved chain links: 1
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.04, per 1000 atoms: 0.93
  Number of scatterers: 7600
  At special positions: 0
  Unit cell: (128.832, 117.12, 109.8, 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      12     16.00
     O    1463      8.00
     N    1251      7.00
     C    4874      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: 1.68
  Conformation dependent library (CDL) restraints added in 998.2 milliseconds
  

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 7 sheets defined
      32.2% alpha, 28.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'F' and resid 21 through 26
      removed outlier: 3.856A  pdb=" N   LYS F  25 " --> pdb=" O   GLN F  21 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 28 through 43
    Processing helix  chain 'F' and resid 44 through 55
    Processing helix  chain 'F' and resid 70 through 80
      removed outlier: 3.676A  pdb=" N   TYR F  76 " --> pdb=" O   PHE F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 81 through 95
    Processing helix  chain 'F' and resid 101 through 115
    Processing helix  chain 'F' and resid 124 through 140
      removed outlier: 3.669A  pdb=" N   VAL F 128 " --> pdb=" O   GLN F 124 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS F 129 " --> pdb=" O   ALA F 125 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 146 through 175
      removed outlier: 4.268A  pdb=" N   TYR F 172 " --> pdb=" O   ASN F 168 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ASN F 173 " --> pdb=" O   ALA F 169 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE F 175 " --> pdb=" O   GLY F 171 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 186
      removed outlier: 3.831A  pdb=" N   ASP F 186 " --> pdb=" O   LEU F 182 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 197 through 215
      removed outlier: 3.642A  pdb=" N   SER F 208 " --> pdb=" O   TYR F 204 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASN F 215 " --> pdb=" O   GLN F 211 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 217 through 220
    Processing helix  chain 'F' and resid 221 through 239
    Processing helix  chain 'F' and resid 244 through 263
      removed outlier: 4.483A  pdb=" N   LYS F 261 " --> pdb=" O   THR F 257 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   PHE F 262 " --> pdb=" O   ASP F 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 215
      removed outlier: 4.059A  pdb=" N   MET A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 230
    Processing helix  chain 'A' and resid 233 through 252
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 315 through 324
    Processing helix  chain 'A' and resid 333 through 339
    Processing helix  chain 'A' and resid 386 through 392
      removed outlier: 3.867A  pdb=" N   ILE A 390 " --> pdb=" O   ASN A 386 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 392 " --> pdb=" O   HIS A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 418
      removed outlier: 4.341A  pdb=" N   GLY A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 641
      removed outlier: 4.022A  pdb=" N   PHE A 640 " --> pdb=" O   PRO A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 655
      removed outlier: 4.016A  pdb=" N   GLN A 651 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LYS A 652 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   GLU A 653 " --> pdb=" O   ASN A 650 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LYS A 655 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 711
    Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 201
      removed outlier: 4.035A  pdb=" N   TYR A 260 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   GLU A 279 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   ILE A 258 " --> pdb=" O   GLU A 279 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 292
      removed outlier: 7.086A  pdb=" N   LYS A 290 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ILE A 366 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LEU A 292 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   THR A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   THR A 355 " --> pdb=" O   THR A 359 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASP A 361 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 373 through 374
      removed outlier: 6.119A  pdb=" N   TYR A 373 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   ILE A 441 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374
      removed outlier: 6.119A  pdb=" N   TYR A 373 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   ILE A 441 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   THR A 438 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   VAL A 432 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN A 444 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 451 through 454
      removed outlier: 5.785A  pdb=" N   GLN A 495 " --> pdb=" O   ASN A 474 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   GLN A 550 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   SER A 812 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 810 " --> pdb=" O   GLU A 740 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR A 808 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 815 " --> pdb=" O   THR A 831 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ILE A 819 " --> pdb=" O   ILE A 827 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   ILE A 827 " --> pdb=" O   ILE A 819 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY A 855 " --> pdb=" O   PHE A 832 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 457 through 458
      removed outlier: 3.899A  pdb=" N   GLY A 855 " --> pdb=" O   PHE A 832 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   ILE A 827 " --> pdb=" O   ILE A 819 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ILE A 819 " --> pdb=" O   ILE A 827 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 815 " --> pdb=" O   THR A 831 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR A 808 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 810 " --> pdb=" O   GLU A 740 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   SER A 812 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 677 through 680
      removed outlier: 6.709A  pdb=" N   TYR A 677 " --> pdb=" O   VAL A 692 " (cutoff:3.500A)

    380 hydrogen bonds defined for protein.
    1071 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: 2.41

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2404
        1.34 -     1.46: 1488
        1.46 -     1.57: 3859
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 7775
  Sorted by residual:
  bond pdb=" C   LYS A 487 "
       pdb=" N   PRO A 488 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 2.34e-02 1.83e+03 3.22e+00
  bond pdb=" C   ALA F  56 "
       pdb=" N   PRO F  57 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 9.80e-03 1.04e+04 2.03e+00
  bond pdb=" CA  LYS A 487 "
       pdb=" C   LYS A 487 "
    ideal  model  delta    sigma   weight residual
    1.524  1.541 -0.017 1.26e-02 6.30e+03 1.78e+00
  bond pdb=" CB  ASN A 326 "
       pdb=" CG  ASN A 326 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.55e+00
  bond pdb=" N   THR A 776 "
       pdb=" CA  THR A 776 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.49e+00
  ... (remaining 7770 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 10224
        1.90 -     3.80: 228
        3.80 -     5.70: 30
        5.70 -     7.60: 8
        7.60 -     9.49: 4
  Bond angle restraints: 10494
  Sorted by residual:
  angle pdb=" N   VAL F 183 "
        pdb=" CA  VAL F 183 "
        pdb=" C   VAL F 183 "
      ideal   model   delta    sigma   weight residual
     113.43  108.72    4.71 1.09e+00 8.42e-01 1.87e+01
  angle pdb=" C   LYS A 487 "
        pdb=" CA  LYS A 487 "
        pdb=" CB  LYS A 487 "
      ideal   model   delta    sigma   weight residual
     110.17  117.73   -7.56 1.97e+00 2.58e-01 1.47e+01
  angle pdb=" CA  ARG A 225 "
        pdb=" CB  ARG A 225 "
        pdb=" CG  ARG A 225 "
      ideal   model   delta    sigma   weight residual
     114.10  121.76   -7.66 2.00e+00 2.50e-01 1.47e+01
  angle pdb=" CA  LYS A 487 "
        pdb=" C   LYS A 487 "
        pdb=" N   PRO A 488 "
      ideal   model   delta    sigma   weight residual
     118.44  124.28   -5.84 1.59e+00 3.96e-01 1.35e+01
  angle pdb=" CA  LYS A 487 "
        pdb=" CB  LYS A 487 "
        pdb=" CG  LYS A 487 "
      ideal   model   delta    sigma   weight residual
     114.10  121.41   -7.31 2.00e+00 2.50e-01 1.34e+01
  ... (remaining 10489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 3789
       17.03 -    34.06: 584
       34.06 -    51.09: 197
       51.09 -    68.12: 36
       68.12 -    85.15: 14
  Dihedral angle restraints: 4620
    sinusoidal: 1854
      harmonic: 2766
  Sorted by residual:
  dihedral pdb=" CA  VAL A 567 "
           pdb=" C   VAL A 567 "
           pdb=" N   PRO A 568 "
           pdb=" CA  PRO A 568 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.75   42.25     0      5.00e+00 4.00e-02 7.14e+01
  dihedral pdb=" CA  PHE A 832 "
           pdb=" C   PHE A 832 "
           pdb=" N   LEU A 833 "
           pdb=" CA  LEU A 833 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.87   24.13     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" C   LYS A 487 "
           pdb=" N   LYS A 487 "
           pdb=" CA  LYS A 487 "
           pdb=" CB  LYS A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.69   11.09     0      2.50e+00 1.60e-01 1.97e+01
  ... (remaining 4617 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 956
       0.068 -    0.135: 135
       0.135 -    0.203: 6
       0.203 -    0.270: 1
       0.270 -    0.338: 1
  Chirality restraints: 1099
  Sorted by residual:
  chirality pdb=" CA  LYS A 487 "
            pdb=" N   LYS A 487 "
            pdb=" C   LYS A 487 "
            pdb=" CB  LYS A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CB  VAL A 226 "
            pdb=" CA  VAL A 226 "
            pdb=" CG1 VAL A 226 "
            pdb=" CG2 VAL A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  ILE A 777 "
            pdb=" N   ILE A 777 "
            pdb=" C   ILE A 777 "
            pdb=" CB  ILE A 777 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.94e-01
  ... (remaining 1096 not shown)

  Planarity restraints: 1360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  56 "   -0.045 5.00e-02 4.00e+02   6.85e-02 7.52e+00
        pdb=" N   PRO F  57 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO F  57 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO F  57 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 225 "   -0.108 9.50e-02 1.11e+02   4.94e-02 2.49e+00
        pdb=" NE  ARG A 225 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 225 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 225 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 225 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 769 "    0.004 2.00e-02 2.50e+03   1.03e-02 2.14e+00
        pdb=" CG  TYR A 769 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 769 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 769 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 769 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 769 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 769 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 769 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1357 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 3192
        2.91 -     3.41: 7131
        3.41 -     3.91: 12246
        3.91 -     4.40: 13906
        4.40 -     4.90: 22995
  Nonbonded interactions: 59470
  Sorted by model distance:
  nonbonded pdb=" N   GLN F  21 "
            pdb=" NE2 GLN F  21 "
     model   vdw
     2.415 3.200
  nonbonded pdb=" O   PHE F 137 "
            pdb=" O   ASN F 140 "
     model   vdw
     2.558 3.040
  nonbonded pdb=" OE1 GLN A 205 "
            pdb=" OH  TYR A 253 "
     model   vdw
     2.588 3.040
  nonbonded pdb=" O   ASP A 208 "
            pdb=" OD1 ASP A 208 "
     model   vdw
     2.594 3.040
  nonbonded pdb=" N   SER A 504 "
            pdb=" O   SER A 504 "
     model   vdw
     2.607 2.496
  ... (remaining 59465 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.160
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
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   0.042   7775  Z= 0.172
  Angle     :  0.705   9.495  10494  Z= 0.408
  Chirality :  0.046   0.338   1099
  Planarity :  0.004   0.069   1360
  Dihedral  : 18.693  85.145   2876
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.26 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 33.00 %
    Favored  : 61.80 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.74 (0.29), residues: 943
  helix:  0.64 (0.32), residues: 274
  sheet:  0.36 (0.33), residues: 256
  loop : -1.87 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.015   0.001   PHE A 894 
 TYR   0.024   0.001   TYR A 769 
 ARG   0.018   0.001   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14582 (  345)
  hydrogen bonds       : angle       6.10222 ( 1071)
  covalent geometry    : bond        0.00354 ( 7775)
  covalent geometry    : angle       0.70522 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   21 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8584 (pm20)
REVERT: F  221 MET cc_start: 0.7671 (ttm) cc_final: 0.7232 (tpp)
REVERT: F  259 LEU cc_start: 0.7638 (tp) cc_final: 0.7383 (tt)
REVERT: A  216 LYS cc_start: 0.6737 (mmtt) cc_final: 0.6121 (mmtt)
REVERT: A  231 LYS cc_start: 0.1910 (OUTLIER) cc_final: 0.0361 (mmmt)
REVERT: A  243 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8177 (mtmm)
REVERT: A  250 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6811 (mp0)
REVERT: A  260 TYR cc_start: 0.5246 (t80) cc_final: 0.3277 (t80)
REVERT: A  454 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6538 (mm-30)
REVERT: A  459 TYR cc_start: 0.7451 (t80) cc_final: 0.7162 (t80)
REVERT: A  471 SER cc_start: 0.8357 (m) cc_final: 0.8001 (p)
REVERT: A  479 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7533 (mtpp)
REVERT: A  493 ASP cc_start: 0.7821 (m-30) cc_final: 0.7577 (m-30)
REVERT: A  525 VAL cc_start: 0.8167 (t) cc_final: 0.7818 (m)
REVERT: A  528 SER cc_start: 0.8166 (t) cc_final: 0.7490 (p)
REVERT: A  586 ASN cc_start: 0.7074 (m-40) cc_final: 0.6755 (m-40)
REVERT: A  613 ASN cc_start: 0.7292 (OUTLIER) cc_final: 0.6859 (m-40)
REVERT: A  626 GLU cc_start: 0.6928 (tp30) cc_final: 0.6272 (tp30)
REVERT: A  627 PHE cc_start: 0.7017 (m-80) cc_final: 0.6262 (m-80)
REVERT: A  652 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7482 (mtpp)
REVERT: A  705 LYS cc_start: 0.7944 (tppp) cc_final: 0.7542 (ttpt)
REVERT: A  769 TYR cc_start: 0.8073 (t80) cc_final: 0.7851 (t80)
REVERT: A  786 SER cc_start: 0.8333 (m) cc_final: 0.8128 (p)
REVERT: A  813 MET cc_start: 0.5996 (mpp) cc_final: 0.5723 (mpp)
REVERT: A  844 ASP cc_start: 0.6700 (p0) cc_final: 0.6292 (p0)
REVERT: A  852 ARG cc_start: 0.7420 (mtt90) cc_final: 0.6948 (mpp-170)
REVERT: A  862 MET cc_start: 0.7567 (mpp) cc_final: 0.7261 (mmp)
  outliers start: 42
  outliers final: 35
  residues processed: 214
  average time/residue: 0.2747
  time to fit residues: 73.4742
Evaluate side-chains
  221 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   21 GLN
Chi-restraints excluded: chain F residue   46 ASN
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue   67 LYS
Chi-restraints excluded: chain F residue   68 LEU
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  140 ASN
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  251 MET
Chi-restraints excluded: chain F residue  262 PHE
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  536 GLN
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  613 ASN
Chi-restraints excluded: chain A residue  672 ILE
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  784 ASN
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  809 ASN
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.4980
   chunk 71 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0470
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.3478

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

Flipped N/Q/H residues before XYZ refinement:
A 444 GLN
A 768 ASN
A 784 ASN
** A 802 GLN ** 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 = 0.3819 r_free = 0.3819 target = 0.145113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.124414 restraints weight = 11777.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.127959 restraints weight = 5761.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.130147 restraints weight = 3487.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.0676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7775  Z= 0.148
  Angle     :  0.579   8.688  10494  Z= 0.310
  Chirality :  0.045   0.250   1099
  Planarity :  0.004   0.051   1360
  Dihedral  :  8.403  58.187   1139
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.10 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 32.26 %
    Favored  : 62.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.48 (0.29), residues: 943
  helix:  0.96 (0.32), residues: 280
  sheet:  0.47 (0.33), residues: 258
  loop : -1.81 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 518 
 HIS   0.004   0.001   HIS A 388 
 PHE   0.012   0.001   PHE F 107 
 TYR   0.015   0.001   TYR A 297 
 ARG   0.003   0.000   ARG A 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04031 (  345)
  hydrogen bonds       : angle       4.76978 ( 1071)
  covalent geometry    : bond        0.00329 ( 7775)
  covalent geometry    : angle       0.57880 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 187
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: F   87 TYR cc_start: 0.6359 (t80) cc_final: 0.6134 (t80)
REVERT: F  104 GLU cc_start: 0.8181 (tp30) cc_final: 0.7856 (tp30)
REVERT: F  108 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7963 (mm)
REVERT: F  163 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7353 (ttpp)
REVERT: F  221 MET cc_start: 0.7605 (ttm) cc_final: 0.7150 (tpp)
REVERT: A  216 LYS cc_start: 0.6775 (mmtt) cc_final: 0.6146 (mmtt)
REVERT: A  243 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8189 (mtmm)
REVERT: A  260 TYR cc_start: 0.5224 (t80) cc_final: 0.3284 (t80)
REVERT: A  308 ILE cc_start: 0.7741 (mm) cc_final: 0.7277 (mt)
REVERT: A  326 ASN cc_start: 0.8193 (t0) cc_final: 0.7570 (m110)
REVERT: A  428 GLU cc_start: 0.7098 (tp30) cc_final: 0.6765 (tp30)
REVERT: A  439 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7870 (p)
REVERT: A  459 TYR cc_start: 0.7487 (t80) cc_final: 0.7196 (t80)
REVERT: A  471 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7556 (p)
REVERT: A  479 LYS cc_start: 0.7825 (mtpp) cc_final: 0.7620 (mtpp)
REVERT: A  499 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8084 (tt)
REVERT: A  525 VAL cc_start: 0.8189 (t) cc_final: 0.7850 (m)
REVERT: A  528 SER cc_start: 0.8156 (t) cc_final: 0.7509 (p)
REVERT: A  586 ASN cc_start: 0.7089 (m-40) cc_final: 0.6779 (m-40)
REVERT: A  613 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.6909 (m-40)
REVERT: A  626 GLU cc_start: 0.6945 (tp30) cc_final: 0.6262 (tp30)
REVERT: A  627 PHE cc_start: 0.7013 (m-80) cc_final: 0.6253 (m-80)
REVERT: A  652 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7543 (mtpp)
REVERT: A  705 LYS cc_start: 0.7974 (tppp) cc_final: 0.7568 (ttpt)
REVERT: A  766 MET cc_start: 0.5711 (mmt) cc_final: 0.5396 (mmt)
REVERT: A  778 GLN cc_start: 0.7444 (tt0) cc_final: 0.6730 (tt0)
REVERT: A  780 ARG cc_start: 0.6104 (mtm-85) cc_final: 0.5725 (mtm-85)
REVERT: A  786 SER cc_start: 0.8363 (m) cc_final: 0.8130 (p)
REVERT: A  834 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6565 (mt-10)
REVERT: A  844 ASP cc_start: 0.6694 (p0) cc_final: 0.6285 (p0)
REVERT: A  852 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7030 (mpp-170)
REVERT: A  862 MET cc_start: 0.7550 (mpp) cc_final: 0.7269 (mmp)
  outliers start: 39
  outliers final: 25
  residues processed: 211
  average time/residue: 0.2714
  time to fit residues: 71.7712
Evaluate side-chains
  212 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  163 LYS
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  338 TYR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  566 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  613 ASN
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0770
   chunk 57 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0970
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 444 GLN
A 768 ASN
** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 809 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.144730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.123878 restraints weight = 11936.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.127374 restraints weight = 5828.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.129729 restraints weight = 3520.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7775  Z= 0.161
  Angle     :  0.564   8.991  10494  Z= 0.303
  Chirality :  0.045   0.243   1099
  Planarity :  0.004   0.042   1360
  Dihedral  :  7.113  57.373   1096
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.21 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 31.40 %
    Favored  : 62.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.39 (0.29), residues: 943
  helix:  0.95 (0.32), residues: 286
  sheet:  0.53 (0.33), residues: 258
  loop : -1.74 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 518 
 HIS   0.004   0.001   HIS A 388 
 PHE   0.011   0.001   PHE F 107 
 TYR   0.020   0.001   TYR A 605 
 ARG   0.008   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03841 (  345)
  hydrogen bonds       : angle       4.58609 ( 1071)
  covalent geometry    : bond        0.00364 ( 7775)
  covalent geometry    : angle       0.56391 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 182
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: F  104 GLU cc_start: 0.8183 (tp30) cc_final: 0.7833 (tp30)
REVERT: F  108 LEU cc_start: 0.8197 (mm) cc_final: 0.7904 (mm)
REVERT: F  236 MET cc_start: 0.7343 (mmm) cc_final: 0.7102 (mmm)
REVERT: A  257 ARG cc_start: 0.7590 (ptm-80) cc_final: 0.7130 (mtp-110)
REVERT: A  260 TYR cc_start: 0.5272 (t80) cc_final: 0.3303 (t80)
REVERT: A  308 ILE cc_start: 0.7770 (mm) cc_final: 0.7316 (mt)
REVERT: A  326 ASN cc_start: 0.8194 (t0) cc_final: 0.7692 (m110)
REVERT: A  397 LYS cc_start: 0.8106 (mttm) cc_final: 0.7862 (mttm)
REVERT: A  428 GLU cc_start: 0.7175 (tp30) cc_final: 0.6853 (tp30)
REVERT: A  439 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7817 (p)
REVERT: A  459 TYR cc_start: 0.7514 (t80) cc_final: 0.7221 (t80)
REVERT: A  479 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7640 (mtpp)
REVERT: A  493 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7509 (m-30)
REVERT: A  499 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8073 (tt)
REVERT: A  525 VAL cc_start: 0.8201 (t) cc_final: 0.7845 (m)
REVERT: A  528 SER cc_start: 0.8171 (t) cc_final: 0.7510 (p)
REVERT: A  586 ASN cc_start: 0.7062 (m-40) cc_final: 0.6756 (m-40)
REVERT: A  613 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6902 (m-40)
REVERT: A  626 GLU cc_start: 0.6998 (tp30) cc_final: 0.6312 (tp30)
REVERT: A  627 PHE cc_start: 0.7006 (m-80) cc_final: 0.6269 (m-80)
REVERT: A  647 ASP cc_start: 0.7299 (p0) cc_final: 0.7079 (p0)
REVERT: A  652 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7513 (mtpp)
REVERT: A  705 LYS cc_start: 0.7974 (tppp) cc_final: 0.7569 (ttpt)
REVERT: A  766 MET cc_start: 0.5865 (mmt) cc_final: 0.5517 (mmt)
REVERT: A  778 GLN cc_start: 0.7440 (tt0) cc_final: 0.6258 (tt0)
REVERT: A  780 ARG cc_start: 0.6093 (mtm-85) cc_final: 0.5611 (mtm-85)
REVERT: A  786 SER cc_start: 0.8410 (m) cc_final: 0.8135 (p)
REVERT: A  844 ASP cc_start: 0.6679 (p0) cc_final: 0.6269 (p0)
REVERT: A  852 ARG cc_start: 0.7437 (mtt90) cc_final: 0.7007 (mpp-170)
REVERT: A  862 MET cc_start: 0.7565 (mpp) cc_final: 0.7278 (mmp)
  outliers start: 47
  outliers final: 27
  residues processed: 208
  average time/residue: 0.2787
  time to fit residues: 72.2632
Evaluate side-chains
  212 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  338 TYR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  613 ASN
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  822 LYS
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 15 optimal weight:    0.1980
   chunk 47 optimal weight:    0.0570
   chunk 62 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 68 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 444 GLN
A 768 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.147544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.126953 restraints weight = 11690.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.130478 restraints weight = 5670.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.132426 restraints weight = 3421.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7775  Z= 0.149
  Angle     :  0.560   8.770  10494  Z= 0.299
  Chirality :  0.045   0.256   1099
  Planarity :  0.004   0.037   1360
  Dihedral  :  6.924  57.391   1094
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.53 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 32.51 %
    Favored  : 62.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.35 (0.29), residues: 943
  helix:  1.00 (0.32), residues: 286
  sheet:  0.46 (0.33), residues: 264
  loop : -1.69 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 518 
 HIS   0.002   0.001   HIS A 388 
 PHE   0.013   0.001   PHE A 741 
 TYR   0.015   0.001   TYR A 605 
 ARG   0.008   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03599 (  345)
  hydrogen bonds       : angle       4.43171 ( 1071)
  covalent geometry    : bond        0.00336 ( 7775)
  covalent geometry    : angle       0.55969 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 188
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: F  104 GLU cc_start: 0.8062 (tp30) cc_final: 0.7702 (tp30)
REVERT: F  108 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: A  257 ARG cc_start: 0.7483 (ptm-80) cc_final: 0.7180 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5353 (t80) cc_final: 0.3348 (t80)
REVERT: A  308 ILE cc_start: 0.7806 (mm) cc_final: 0.7375 (mt)
REVERT: A  326 ASN cc_start: 0.8102 (t0) cc_final: 0.7812 (m110)
REVERT: A  428 GLU cc_start: 0.7001 (tp30) cc_final: 0.6730 (tp30)
REVERT: A  439 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7927 (p)
REVERT: A  459 TYR cc_start: 0.7503 (t80) cc_final: 0.7263 (t80)
REVERT: A  471 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7688 (p)
REVERT: A  499 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8099 (tt)
REVERT: A  525 VAL cc_start: 0.8261 (t) cc_final: 0.7952 (m)
REVERT: A  528 SER cc_start: 0.8169 (t) cc_final: 0.7527 (p)
REVERT: A  586 ASN cc_start: 0.7012 (m-40) cc_final: 0.6795 (m-40)
REVERT: A  613 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6894 (m-40)
REVERT: A  626 GLU cc_start: 0.7083 (tp30) cc_final: 0.6360 (tp30)
REVERT: A  627 PHE cc_start: 0.6900 (m-80) cc_final: 0.6266 (m-80)
REVERT: A  647 ASP cc_start: 0.7280 (p0) cc_final: 0.7013 (p0)
REVERT: A  652 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7508 (mtpp)
REVERT: A  705 LYS cc_start: 0.7991 (tppp) cc_final: 0.7698 (ttpt)
REVERT: A  780 ARG cc_start: 0.6032 (mtm-85) cc_final: 0.5827 (mtm-85)
REVERT: A  786 SER cc_start: 0.8355 (m) cc_final: 0.8089 (p)
REVERT: A  834 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6457 (mt-10)
REVERT: A  844 ASP cc_start: 0.6490 (p0) cc_final: 0.6159 (p0)
REVERT: A  852 ARG cc_start: 0.7457 (mtt90) cc_final: 0.7066 (mpp-170)
REVERT: A  862 MET cc_start: 0.7409 (mpp) cc_final: 0.7174 (mmp)
  outliers start: 43
  outliers final: 29
  residues processed: 212
  average time/residue: 0.2656
  time to fit residues: 70.7542
Evaluate side-chains
  212 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 178
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  338 TYR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  404 LYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  613 ASN
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0570
   chunk 43 optimal weight:    0.0970
   overall best weight:    0.2994

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 444 GLN
A 768 ASN
A 785 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.148066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.127647 restraints weight = 11621.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.131065 restraints weight = 5614.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.133223 restraints weight = 3410.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7775  Z= 0.131
  Angle     :  0.556   8.977  10494  Z= 0.295
  Chirality :  0.044   0.251   1099
  Planarity :  0.004   0.035   1360
  Dihedral  :  6.823  56.965   1094
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.89 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 32.39 %
    Favored  : 62.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.24 (0.29), residues: 943
  helix:  0.96 (0.32), residues: 292
  sheet:  0.54 (0.33), residues: 261
  loop : -1.54 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.014   0.001   PHE A 741 
 TYR   0.017   0.001   TYR A 769 
 ARG   0.010   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03384 (  345)
  hydrogen bonds       : angle       4.31723 ( 1071)
  covalent geometry    : bond        0.00296 ( 7775)
  covalent geometry    : angle       0.55585 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 187
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: F  104 GLU cc_start: 0.8050 (tp30) cc_final: 0.7671 (tp30)
REVERT: F  108 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7879 (mm)
REVERT: A  215 MET cc_start: 0.6308 (ptp) cc_final: 0.5998 (ptp)
REVERT: A  250 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7160 (mm-30)
REVERT: A  257 ARG cc_start: 0.7457 (ptm-80) cc_final: 0.7168 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5374 (t80) cc_final: 0.3422 (t80)
REVERT: A  308 ILE cc_start: 0.7807 (mm) cc_final: 0.7377 (mt)
REVERT: A  326 ASN cc_start: 0.8116 (t0) cc_final: 0.7827 (m-40)
REVERT: A  328 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7930 (ptmt)
REVERT: A  368 GLU cc_start: 0.6034 (mt-10) cc_final: 0.5596 (mt-10)
REVERT: A  397 LYS cc_start: 0.8132 (mttm) cc_final: 0.7915 (mttm)
REVERT: A  428 GLU cc_start: 0.6989 (tp30) cc_final: 0.6723 (tp30)
REVERT: A  439 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7916 (p)
REVERT: A  459 TYR cc_start: 0.7451 (t80) cc_final: 0.7217 (t80)
REVERT: A  471 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7710 (p)
REVERT: A  499 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8098 (tt)
REVERT: A  525 VAL cc_start: 0.8258 (t) cc_final: 0.7946 (m)
REVERT: A  528 SER cc_start: 0.8169 (t) cc_final: 0.7530 (p)
REVERT: A  586 ASN cc_start: 0.7008 (m-40) cc_final: 0.6799 (m-40)
REVERT: A  602 ASN cc_start: 0.8091 (t0) cc_final: 0.7829 (t0)
REVERT: A  613 ASN cc_start: 0.7127 (OUTLIER) cc_final: 0.6877 (m-40)
REVERT: A  626 GLU cc_start: 0.7132 (tp30) cc_final: 0.6398 (tp30)
REVERT: A  627 PHE cc_start: 0.6884 (m-80) cc_final: 0.6266 (m-80)
REVERT: A  652 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7478 (mtpp)
REVERT: A  705 LYS cc_start: 0.7986 (tppp) cc_final: 0.7697 (ttpt)
REVERT: A  769 TYR cc_start: 0.8140 (t80) cc_final: 0.7899 (t80)
REVERT: A  778 GLN cc_start: 0.7306 (tt0) cc_final: 0.6501 (tt0)
REVERT: A  780 ARG cc_start: 0.6024 (mtm-85) cc_final: 0.5806 (mtm-85)
REVERT: A  834 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6450 (mt-10)
REVERT: A  844 ASP cc_start: 0.6475 (p0) cc_final: 0.6165 (p0)
REVERT: A  852 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7032 (mpp-170)
REVERT: A  862 MET cc_start: 0.7390 (mpp) cc_final: 0.6978 (mmp)
  outliers start: 44
  outliers final: 30
  residues processed: 210
  average time/residue: 0.2622
  time to fit residues: 69.1692
Evaluate side-chains
  218 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 183
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  108 LEU
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  338 TYR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  613 ASN
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  822 LYS
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0770
   chunk 91 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 444 GLN
A 768 ASN
A 785 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.146495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.125880 restraints weight = 11661.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.129334 restraints weight = 5663.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131546 restraints weight = 3443.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7775  Z= 0.179
  Angle     :  0.583   9.133  10494  Z= 0.311
  Chirality :  0.046   0.279   1099
  Planarity :  0.004   0.034   1360
  Dihedral  :  6.829  57.716   1092
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.53 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 31.15 %
    Favored  : 62.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.24 (0.29), residues: 943
  helix:  0.92 (0.32), residues: 292
  sheet:  0.66 (0.33), residues: 255
  loop : -1.56 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 518 
 HIS   0.004   0.001   HIS A 388 
 PHE   0.015   0.001   PHE A 741 
 TYR   0.014   0.001   TYR A 378 
 ARG   0.010   0.000   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  345)
  hydrogen bonds       : angle       4.38939 ( 1071)
  covalent geometry    : bond        0.00409 ( 7775)
  covalent geometry    : angle       0.58319 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 190
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: F  115 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8486 (mttp)
REVERT: A  228 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5903 (mttp)
REVERT: A  257 ARG cc_start: 0.7458 (ptm-80) cc_final: 0.6971 (mtp-110)
REVERT: A  260 TYR cc_start: 0.5372 (t80) cc_final: 0.3295 (t80)
REVERT: A  308 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7470 (mt)
REVERT: A  368 GLU cc_start: 0.6151 (mt-10) cc_final: 0.5746 (mt-10)
REVERT: A  401 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7819 (mtpp)
REVERT: A  428 GLU cc_start: 0.6992 (tp30) cc_final: 0.6729 (tp30)
REVERT: A  471 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7695 (p)
REVERT: A  499 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8090 (tt)
REVERT: A  525 VAL cc_start: 0.8252 (t) cc_final: 0.7943 (m)
REVERT: A  528 SER cc_start: 0.8170 (t) cc_final: 0.7535 (p)
REVERT: A  586 ASN cc_start: 0.7013 (m-40) cc_final: 0.6808 (m-40)
REVERT: A  603 LEU cc_start: 0.8261 (tp) cc_final: 0.8046 (tt)
REVERT: A  613 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6895 (m-40)
REVERT: A  614 LYS cc_start: 0.7567 (mtpp) cc_final: 0.7324 (mtpp)
REVERT: A  626 GLU cc_start: 0.7104 (tp30) cc_final: 0.6377 (tp30)
REVERT: A  627 PHE cc_start: 0.6885 (m-80) cc_final: 0.6267 (m-80)
REVERT: A  652 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7506 (mtpp)
REVERT: A  705 LYS cc_start: 0.7998 (tppp) cc_final: 0.7701 (ttpt)
REVERT: A  769 TYR cc_start: 0.8201 (t80) cc_final: 0.7792 (t80)
REVERT: A  844 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6174 (p0)
REVERT: A  852 ARG cc_start: 0.7460 (mtt90) cc_final: 0.7196 (mtm110)
REVERT: A  862 MET cc_start: 0.7424 (mpp) cc_final: 0.7183 (mmp)
  outliers start: 51
  outliers final: 37
  residues processed: 216
  average time/residue: 0.2560
  time to fit residues: 69.5083
Evaluate side-chains
  228 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 184
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  115 LYS
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  338 TYR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  404 LYS
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  613 ASN
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  844 ASP
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0470
   chunk 47 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0870
   chunk 29 optimal weight:    0.5980
   chunk 92 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.2656

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 444 GLN
A 613 ASN
A 768 ASN
A 785 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.148169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.127674 restraints weight = 11576.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.131128 restraints weight = 5624.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.133265 restraints weight = 3414.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7775  Z= 0.126
  Angle     :  0.563   8.993  10494  Z= 0.298
  Chirality :  0.044   0.252   1099
  Planarity :  0.003   0.033   1360
  Dihedral  :  6.731  56.943   1092
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.00 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 31.77 %
    Favored  : 62.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.14 (0.29), residues: 943
  helix:  1.01 (0.32), residues: 292
  sheet:  0.71 (0.34), residues: 255
  loop : -1.52 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 518 
 HIS   0.002   0.001   HIS A 388 
 PHE   0.012   0.001   PHE A 741 
 TYR   0.011   0.001   TYR A 605 
 ARG   0.004   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03314 (  345)
  hydrogen bonds       : angle       4.22604 ( 1071)
  covalent geometry    : bond        0.00285 ( 7775)
  covalent geometry    : angle       0.56278 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 186
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
REVERT: F  115 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8420 (mttp)
REVERT: A  250 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7162 (mm-30)
REVERT: A  257 ARG cc_start: 0.7432 (ptm-80) cc_final: 0.7159 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5377 (t80) cc_final: 0.3384 (t80)
REVERT: A  308 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7403 (mt)
REVERT: A  428 GLU cc_start: 0.6911 (tp30) cc_final: 0.6650 (tp30)
REVERT: A  471 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7717 (p)
REVERT: A  499 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8089 (tt)
REVERT: A  525 VAL cc_start: 0.8249 (t) cc_final: 0.7941 (m)
REVERT: A  528 SER cc_start: 0.8167 (t) cc_final: 0.7540 (p)
REVERT: A  559 VAL cc_start: 0.8299 (t) cc_final: 0.8072 (p)
REVERT: A  586 ASN cc_start: 0.7003 (m-40) cc_final: 0.6801 (m-40)
REVERT: A  602 ASN cc_start: 0.8090 (t0) cc_final: 0.7807 (t0)
REVERT: A  603 LEU cc_start: 0.8260 (tp) cc_final: 0.7936 (tt)
REVERT: A  626 GLU cc_start: 0.7158 (tp30) cc_final: 0.6400 (tp30)
REVERT: A  627 PHE cc_start: 0.6897 (m-80) cc_final: 0.6271 (m-80)
REVERT: A  652 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7459 (mtpp)
REVERT: A  705 LYS cc_start: 0.7992 (tppp) cc_final: 0.7698 (ttpt)
REVERT: A  769 TYR cc_start: 0.8173 (t80) cc_final: 0.7749 (t80)
REVERT: A  828 TYR cc_start: 0.7824 (p90) cc_final: 0.7473 (p90)
REVERT: A  852 ARG cc_start: 0.7437 (mtt90) cc_final: 0.7032 (mpp-170)
REVERT: A  862 MET cc_start: 0.7420 (mpp) cc_final: 0.7027 (mmp)
  outliers start: 49
  outliers final: 37
  residues processed: 209
  average time/residue: 0.2680
  time to fit residues: 70.1645
Evaluate side-chains
  223 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 182
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  115 LYS
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  338 TYR
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  404 LYS
Chi-restraints excluded: chain A residue  416 GLN
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  822 LYS
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 47 optimal weight:    0.3980
   chunk 82 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 2 optimal weight:    2.9990
   chunk 44 optimal weight:    0.1980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 444 GLN
A 768 ASN
A 785 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.146736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126153 restraints weight = 11793.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.129654 restraints weight = 5710.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131587 restraints weight = 3459.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7775  Z= 0.158
  Angle     :  0.589   9.261  10494  Z= 0.312
  Chirality :  0.045   0.273   1099
  Planarity :  0.004   0.032   1360
  Dihedral  :  6.668  57.516   1090
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.53 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 32.14 %
    Favored  : 62.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.17 (0.29), residues: 943
  helix:  1.00 (0.31), residues: 292
  sheet:  0.67 (0.34), residues: 255
  loop : -1.53 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.013   0.001   PHE A 741 
 TYR   0.014   0.001   TYR F 111 
 ARG   0.019   0.001   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  345)
  hydrogen bonds       : angle       4.26567 ( 1071)
  covalent geometry    : bond        0.00362 ( 7775)
  covalent geometry    : angle       0.58904 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 186
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: F  115 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8458 (mttp)
REVERT: A  250 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7171 (mm-30)
REVERT: A  257 ARG cc_start: 0.7451 (ptm-80) cc_final: 0.7159 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5384 (t80) cc_final: 0.3337 (t80)
REVERT: A  308 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7457 (mt)
REVERT: A  428 GLU cc_start: 0.6926 (tp30) cc_final: 0.6656 (tp30)
REVERT: A  471 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7720 (p)
REVERT: A  499 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8090 (tt)
REVERT: A  525 VAL cc_start: 0.8249 (t) cc_final: 0.7940 (m)
REVERT: A  528 SER cc_start: 0.8164 (t) cc_final: 0.7553 (p)
REVERT: A  559 VAL cc_start: 0.8306 (t) cc_final: 0.8071 (p)
REVERT: A  603 LEU cc_start: 0.8265 (tp) cc_final: 0.8058 (tt)
REVERT: A  626 GLU cc_start: 0.7121 (tp30) cc_final: 0.6393 (tp30)
REVERT: A  627 PHE cc_start: 0.6890 (m-80) cc_final: 0.6264 (m-80)
REVERT: A  652 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7455 (mtpp)
REVERT: A  705 LYS cc_start: 0.8004 (tppp) cc_final: 0.7710 (ttpt)
REVERT: A  769 TYR cc_start: 0.8213 (t80) cc_final: 0.7794 (t80)
REVERT: A  828 TYR cc_start: 0.7820 (p90) cc_final: 0.7382 (p90)
REVERT: A  844 ASP cc_start: 0.6458 (p0) cc_final: 0.6145 (p0)
REVERT: A  852 ARG cc_start: 0.7454 (mtt90) cc_final: 0.7070 (mpp-170)
REVERT: A  862 MET cc_start: 0.7444 (mpp) cc_final: 0.7196 (mmp)
  outliers start: 47
  outliers final: 37
  residues processed: 209
  average time/residue: 0.2734
  time to fit residues: 71.8654
Evaluate side-chains
  225 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 184
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  115 LYS
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  140 ASN
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  536 GLN
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  822 LYS
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0970
   chunk 17 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0770
   chunk 40 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 444 GLN
A 768 ASN
A 785 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.147477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.127122 restraints weight = 11811.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130610 restraints weight = 5689.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.132759 restraints weight = 3432.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7775  Z= 0.137
  Angle     :  0.584   9.160  10494  Z= 0.309
  Chirality :  0.044   0.268   1099
  Planarity :  0.003   0.034   1360
  Dihedral  :  6.611  56.988   1090
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.21 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 32.01 %
    Favored  : 61.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.11 (0.29), residues: 943
  helix:  1.08 (0.31), residues: 292
  sheet:  0.71 (0.34), residues: 255
  loop : -1.51 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.011   0.001   PHE A 741 
 TYR   0.011   0.001   TYR A 605 
 ARG   0.005   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  345)
  hydrogen bonds       : angle       4.20091 ( 1071)
  covalent geometry    : bond        0.00315 ( 7775)
  covalent geometry    : angle       0.58432 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: F  115 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8426 (mttp)
REVERT: F  133 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (mttm)
REVERT: A  231 LYS cc_start: 0.2467 (OUTLIER) cc_final: 0.1038 (mmmt)
REVERT: A  250 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7155 (mm-30)
REVERT: A  257 ARG cc_start: 0.7429 (ptm-80) cc_final: 0.7149 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5407 (t80) cc_final: 0.3399 (t80)
REVERT: A  308 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7446 (mt)
REVERT: A  428 GLU cc_start: 0.6910 (tp30) cc_final: 0.6643 (tp30)
REVERT: A  471 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7719 (p)
REVERT: A  499 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8092 (tt)
REVERT: A  525 VAL cc_start: 0.8243 (t) cc_final: 0.7935 (m)
REVERT: A  528 SER cc_start: 0.8157 (t) cc_final: 0.7547 (p)
REVERT: A  559 VAL cc_start: 0.8303 (t) cc_final: 0.8077 (p)
REVERT: A  602 ASN cc_start: 0.8104 (t0) cc_final: 0.7823 (t0)
REVERT: A  603 LEU cc_start: 0.8261 (tp) cc_final: 0.7950 (tt)
REVERT: A  614 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7459 (mtpp)
REVERT: A  626 GLU cc_start: 0.7149 (tp30) cc_final: 0.6379 (tp30)
REVERT: A  627 PHE cc_start: 0.6889 (m-80) cc_final: 0.6160 (m-80)
REVERT: A  652 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7503 (mtpp)
REVERT: A  705 LYS cc_start: 0.7999 (tppp) cc_final: 0.7693 (ttpt)
REVERT: A  725 TRP cc_start: 0.6157 (OUTLIER) cc_final: 0.5925 (m-10)
REVERT: A  769 TYR cc_start: 0.8197 (t80) cc_final: 0.7765 (t80)
REVERT: A  828 TYR cc_start: 0.7768 (p90) cc_final: 0.7356 (p90)
REVERT: A  852 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7049 (mpp-170)
REVERT: A  862 MET cc_start: 0.7434 (mpp) cc_final: 0.7183 (mmp)
  outliers start: 50
  outliers final: 39
  residues processed: 207
  average time/residue: 0.2661
  time to fit residues: 68.8366
Evaluate side-chains
  224 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 178
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  115 LYS
Chi-restraints excluded: chain F residue  133 LYS
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  140 ASN
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  456 GLN
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  536 GLN
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  822 LYS
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 42 optimal weight:    0.2980
   chunk 55 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 11 optimal weight:    0.2980
   chunk 40 optimal weight:    0.4980
   chunk 78 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
F  21 GLN
A 326 ASN
A 444 GLN
A 768 ASN
A 785 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.147124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.126728 restraints weight = 11818.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.130202 restraints weight = 5710.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.132269 restraints weight = 3449.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7775  Z= 0.159
  Angle     :  0.603   9.215  10494  Z= 0.319
  Chirality :  0.045   0.274   1099
  Planarity :  0.003   0.031   1360
  Dihedral  :  6.651  57.592   1090
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.74 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 32.39 %
    Favored  : 61.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.13 (0.29), residues: 943
  helix:  1.07 (0.31), residues: 292
  sheet:  0.69 (0.34), residues: 255
  loop : -1.53 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 518 
 HIS   0.004   0.001   HIS A 388 
 PHE   0.012   0.001   PHE A 741 
 TYR   0.020   0.001   TYR A 696 
 ARG   0.005   0.000   ARG A 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  345)
  hydrogen bonds       : angle       4.24966 ( 1071)
  covalent geometry    : bond        0.00367 ( 7775)
  covalent geometry    : angle       0.60320 (10494)

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 182
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: F  115 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8459 (mttp)
REVERT: F  133 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8018 (mttm)
REVERT: A  231 LYS cc_start: 0.2518 (OUTLIER) cc_final: 0.0862 (mmmt)
REVERT: A  250 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7143 (mm-30)
REVERT: A  257 ARG cc_start: 0.7442 (ptm-80) cc_final: 0.7153 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5417 (t80) cc_final: 0.3362 (t80)
REVERT: A  308 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7468 (mt)
REVERT: A  428 GLU cc_start: 0.6925 (tp30) cc_final: 0.6655 (tp30)
REVERT: A  471 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7747 (p)
REVERT: A  499 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8088 (tt)
REVERT: A  525 VAL cc_start: 0.8241 (t) cc_final: 0.7934 (m)
REVERT: A  528 SER cc_start: 0.8164 (t) cc_final: 0.7555 (p)
REVERT: A  559 VAL cc_start: 0.8301 (t) cc_final: 0.8066 (p)
REVERT: A  603 LEU cc_start: 0.8266 (tp) cc_final: 0.8064 (tt)
REVERT: A  614 LYS cc_start: 0.7682 (mtpp) cc_final: 0.7454 (mtpp)
REVERT: A  626 GLU cc_start: 0.7139 (tp30) cc_final: 0.6403 (tp30)
REVERT: A  627 PHE cc_start: 0.6893 (m-80) cc_final: 0.6265 (m-80)
REVERT: A  705 LYS cc_start: 0.8010 (tppp) cc_final: 0.7709 (ttpt)
REVERT: A  828 TYR cc_start: 0.7722 (p90) cc_final: 0.7350 (p90)
REVERT: A  844 ASP cc_start: 0.6461 (p0) cc_final: 0.6133 (p0)
REVERT: A  852 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7052 (mpp-170)
REVERT: A  862 MET cc_start: 0.7461 (mpp) cc_final: 0.7208 (mmp)
  outliers start: 47
  outliers final: 38
  residues processed: 205
  average time/residue: 0.2575
  time to fit residues: 66.1385
Evaluate side-chains
  229 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 185
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   58 THR
Chi-restraints excluded: chain F residue   60 ARG
Chi-restraints excluded: chain F residue  113 TYR
Chi-restraints excluded: chain F residue  115 LYS
Chi-restraints excluded: chain F residue  133 LYS
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  140 ASN
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  242 THR
Chi-restraints excluded: chain F residue  247 LYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  248 TYR
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  456 GLN
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  470 LEU
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 PHE
Chi-restraints excluded: chain A residue  483 LYS
Chi-restraints excluded: chain A residue  493 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  508 GLN
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  536 GLN
Chi-restraints excluded: chain A residue  553 ASN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  606 THR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 50 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0470
   chunk 19 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 4 optimal weight:    0.1980
   overall best weight:    0.3278

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

Flipped N/Q/H residues before XYZ refinement:
A 444 GLN
A 768 ASN
A 785 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.147563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.126922 restraints weight = 11614.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130512 restraints weight = 5508.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132742 restraints weight = 3292.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7775  Z= 0.142
  Angle     :  0.603   9.175  10494  Z= 0.317
  Chirality :  0.045   0.270   1099
  Planarity :  0.003   0.031   1360
  Dihedral  :  6.463  56.946   1088
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.89 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 33.00 %
    Favored  : 61.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    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: -0.10 (0.29), residues: 943
  helix:  1.11 (0.31), residues: 292
  sheet:  0.72 (0.34), residues: 255
  loop : -1.53 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 
 PHE   0.011   0.001   PHE A 741 
 TYR   0.012   0.001   TYR A 696 
 ARG   0.004   0.000   ARG A 780 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (  345)
  hydrogen bonds       : angle       4.20870 ( 1071)
  covalent geometry    : bond        0.00328 ( 7775)
  covalent geometry    : angle       0.60314 (10494)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3593.24 seconds
wall clock time: 62 minutes 51.21 seconds (3771.21 seconds total)