Starting phenix.real_space_refine
on Fri Aug 22 20:58:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n2f_48837/08_2025/9n2f_48837.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n2f_48837/08_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_48837/08_2025/9n2f_48837.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n2f_48837/08_2025/9n2f_48837.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n2f_48837/08_2025/9n2f_48837.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n2f_48837/08_2025/9n2f_48837.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.90, per 1000 atoms: 0.25
  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: 0.63
  Conformation dependent library (CDL) restraints added in 398.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.20
  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: 1.42

  Time building geometry restraints manager: 0.86 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:             9.590
  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:          0.220
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.680
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.670
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.018   0.001   ARG A 225 
 TYR   0.024   0.001   TYR A 769 
 PHE   0.015   0.001   PHE A 894 
 TRP   0.002   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 

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

*********************** 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  : 0.352 
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: 0.1204
  time to fit residues: 32.4127
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  : 0.220 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 341 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.144373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.123595 restraints weight = 11870.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.127157 restraints weight = 5798.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.129344 restraints weight = 3502.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.130789 restraints weight = 2503.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.131557 restraints weight = 1998.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.0706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7775  Z= 0.172
  Angle     :  0.590   8.689  10494  Z= 0.317
  Chirality :  0.046   0.248   1099
  Planarity :  0.004   0.051   1360
  Dihedral  :  8.438  58.512   1139
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.21 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 32.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.29), residues: 943
  helix:  0.91 (0.31), residues: 280
  sheet:  0.44 (0.33), residues: 258
  loop : -1.83 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 544 
 TYR   0.015   0.001   TYR A 297 
 PHE   0.013   0.001   PHE A 552 
 TRP   0.007   0.001   TRP A 518 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7775)
  covalent geometry    : angle       0.59030 (10494)
  hydrogen bonds       : bond        0.04142 (  345)
  hydrogen bonds       : angle       4.80542 ( 1071)

*********************** 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
  223 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 185
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: F   87 TYR cc_start: 0.6335 (t80) cc_final: 0.6128 (t80)
REVERT: F  104 GLU cc_start: 0.8171 (tp30) cc_final: 0.7866 (tp30)
REVERT: F  108 LEU cc_start: 0.8168 (mm) cc_final: 0.7938 (mm)
REVERT: F  163 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7360 (ttpp)
REVERT: A  216 LYS cc_start: 0.6772 (mmtt) cc_final: 0.6152 (mmtt)
REVERT: A  243 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8192 (mtmm)
REVERT: A  260 TYR cc_start: 0.5299 (t80) cc_final: 0.3304 (t80)
REVERT: A  326 ASN cc_start: 0.8182 (t0) cc_final: 0.7589 (m110)
REVERT: A  428 GLU cc_start: 0.7093 (tp30) cc_final: 0.6759 (tp30)
REVERT: A  439 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7832 (p)
REVERT: A  459 TYR cc_start: 0.7484 (t80) cc_final: 0.7198 (t80)
REVERT: A  471 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.7617 (p)
REVERT: A  479 LYS cc_start: 0.7836 (mtpp) cc_final: 0.7636 (mtpp)
REVERT: A  499 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: A  525 VAL cc_start: 0.8186 (t) cc_final: 0.7840 (m)
REVERT: A  528 SER cc_start: 0.8153 (t) cc_final: 0.7504 (p)
REVERT: A  586 ASN cc_start: 0.7089 (m-40) cc_final: 0.6777 (m-40)
REVERT: A  613 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6975 (m-40)
REVERT: A  626 GLU cc_start: 0.6976 (tp30) cc_final: 0.6305 (tp30)
REVERT: A  627 PHE cc_start: 0.7012 (m-80) cc_final: 0.6266 (m-80)
REVERT: A  652 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7558 (mtpp)
REVERT: A  705 LYS cc_start: 0.7965 (tppp) cc_final: 0.7564 (ttpt)
REVERT: A  766 MET cc_start: 0.5753 (mmt) cc_final: 0.5485 (mmt)
REVERT: A  778 GLN cc_start: 0.7451 (tt0) cc_final: 0.6681 (tt0)
REVERT: A  780 ARG cc_start: 0.6108 (mtm-85) cc_final: 0.5688 (mtm-85)
REVERT: A  786 SER cc_start: 0.8387 (m) cc_final: 0.8137 (p)
REVERT: A  820 THR cc_start: 0.7337 (m) cc_final: 0.7121 (p)
REVERT: A  834 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6592 (mt-10)
REVERT: A  844 ASP cc_start: 0.6657 (p0) cc_final: 0.6246 (p0)
REVERT: A  852 ARG cc_start: 0.7454 (mtt90) cc_final: 0.6906 (mpp-170)
REVERT: A  862 MET cc_start: 0.7534 (mpp) cc_final: 0.7246 (mmp)
  outliers start: 38
  outliers final: 25
  residues processed: 209
  average time/residue: 0.1074
  time to fit residues: 28.0928
Evaluate side-chains
  209 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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  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 86 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0070
   chunk 66 optimal weight:    0.0770
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 809 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.123897 restraints weight = 11866.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.127449 restraints weight = 5774.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.129668 restraints weight = 3485.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.131072 restraints weight = 2471.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131717 restraints weight = 1984.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7775  Z= 0.160
  Angle     :  0.565   8.695  10494  Z= 0.304
  Chirality :  0.045   0.236   1099
  Planarity :  0.004   0.044   1360
  Dihedral  :  7.144  57.193   1096
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.10 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 30.90 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.29), residues: 943
  helix:  0.93 (0.32), residues: 286
  sheet:  0.39 (0.33), residues: 264
  loop : -1.73 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 225 
 TYR   0.012   0.001   TYR A 297 
 PHE   0.012   0.001   PHE F 107 
 TRP   0.005   0.001   TRP A 518 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7775)
  covalent geometry    : angle       0.56531 (10494)
  hydrogen bonds       : bond        0.03839 (  345)
  hydrogen bonds       : angle       4.59936 ( 1071)

*********************** 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
  231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: F  104 GLU cc_start: 0.8171 (tp30) cc_final: 0.7814 (tp30)
REVERT: F  108 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (mm)
REVERT: A  257 ARG cc_start: 0.7613 (ptm-80) cc_final: 0.7147 (mtp-110)
REVERT: A  260 TYR cc_start: 0.5231 (t80) cc_final: 0.3258 (t80)
REVERT: A  308 ILE cc_start: 0.7770 (mm) cc_final: 0.7320 (mt)
REVERT: A  326 ASN cc_start: 0.8197 (t0) cc_final: 0.7719 (m110)
REVERT: A  428 GLU cc_start: 0.7175 (tp30) cc_final: 0.6855 (tp30)
REVERT: A  439 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7816 (p)
REVERT: A  459 TYR cc_start: 0.7507 (t80) cc_final: 0.7215 (t80)
REVERT: A  471 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.7642 (p)
REVERT: A  479 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7660 (mtpp)
REVERT: A  493 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7500 (m-30)
REVERT: A  499 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8095 (tt)
REVERT: A  525 VAL cc_start: 0.8177 (t) cc_final: 0.7832 (m)
REVERT: A  528 SER cc_start: 0.8164 (t) cc_final: 0.7491 (p)
REVERT: A  586 ASN cc_start: 0.7072 (m-40) cc_final: 0.6762 (m-40)
REVERT: A  613 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6935 (m-40)
REVERT: A  626 GLU cc_start: 0.6999 (tp30) cc_final: 0.6309 (tp30)
REVERT: A  627 PHE cc_start: 0.7008 (m-80) cc_final: 0.6289 (m-80)
REVERT: A  652 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7515 (mtpp)
REVERT: A  705 LYS cc_start: 0.7956 (tppp) cc_final: 0.7558 (ttpt)
REVERT: A  766 MET cc_start: 0.5882 (mmt) cc_final: 0.5592 (mmt)
REVERT: A  780 ARG cc_start: 0.6110 (mtm-85) cc_final: 0.5635 (mtm-85)
REVERT: A  786 SER cc_start: 0.8410 (m) cc_final: 0.8130 (p)
REVERT: A  844 ASP cc_start: 0.6636 (p0) cc_final: 0.6226 (p0)
REVERT: A  852 ARG cc_start: 0.7426 (mtt90) cc_final: 0.7131 (mtm110)
REVERT: A  862 MET cc_start: 0.7515 (mpp) cc_final: 0.7228 (mmp)
  outliers start: 50
  outliers final: 28
  residues processed: 209
  average time/residue: 0.0989
  time to fit residues: 25.8542
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  : 0.176 
-------------------------------------------------------------------------------
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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 83 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.144240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.123176 restraints weight = 11770.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.126876 restraints weight = 5548.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.129104 restraints weight = 3291.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.130315 restraints weight = 2338.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131235 restraints weight = 1901.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7775  Z= 0.229
  Angle     :  0.603   8.773  10494  Z= 0.326
  Chirality :  0.047   0.267   1099
  Planarity :  0.004   0.041   1360
  Dihedral  :  7.173  58.338   1094
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.85 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 31.15 %
    Favored  : 63.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.29), residues: 943
  helix:  0.81 (0.31), residues: 286
  sheet:  0.34 (0.33), residues: 261
  loop : -1.73 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 225 
 TYR   0.016   0.002   TYR F 111 
 PHE   0.014   0.002   PHE A 741 
 TRP   0.009   0.001   TRP A 518 
 HIS   0.005   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 7775)
  covalent geometry    : angle       0.60288 (10494)
  hydrogen bonds       : bond        0.04227 (  345)
  hydrogen bonds       : angle       4.65861 ( 1071)

*********************** 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
  232 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 185
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: F  104 GLU cc_start: 0.8059 (tp30) cc_final: 0.7694 (tp30)
REVERT: F  108 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7997 (mm)
REVERT: A  215 MET cc_start: 0.6385 (ptp) cc_final: 0.6140 (ptp)
REVERT: A  257 ARG cc_start: 0.7482 (ptm-80) cc_final: 0.7232 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5418 (t80) cc_final: 0.3201 (t80)
REVERT: A  308 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7492 (mt)
REVERT: A  428 GLU cc_start: 0.7015 (tp30) cc_final: 0.6736 (tp30)
REVERT: A  459 TYR cc_start: 0.7483 (t80) cc_final: 0.7267 (t80)
REVERT: A  471 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7750 (p)
REVERT: A  493 ASP cc_start: 0.7784 (m-30) cc_final: 0.7582 (m-30)
REVERT: A  525 VAL cc_start: 0.8241 (t) cc_final: 0.7939 (m)
REVERT: A  528 SER cc_start: 0.8169 (t) cc_final: 0.7555 (p)
REVERT: A  586 ASN cc_start: 0.7015 (m-40) cc_final: 0.6797 (m-40)
REVERT: A  614 LYS cc_start: 0.7572 (mtpp) cc_final: 0.7348 (mtpp)
REVERT: A  626 GLU cc_start: 0.7086 (tp30) cc_final: 0.6377 (tp30)
REVERT: A  627 PHE cc_start: 0.6873 (m-80) cc_final: 0.6174 (m-80)
REVERT: A  652 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7561 (mtpp)
REVERT: A  705 LYS cc_start: 0.8009 (tppp) cc_final: 0.7719 (ttpt)
REVERT: A  725 TRP cc_start: 0.6191 (m-10) cc_final: 0.5977 (m-10)
REVERT: A  778 GLN cc_start: 0.7370 (tt0) cc_final: 0.6638 (tt0)
REVERT: A  780 ARG cc_start: 0.6082 (mtm-85) cc_final: 0.5779 (mtm-85)
REVERT: A  786 SER cc_start: 0.8373 (m) cc_final: 0.8097 (p)
REVERT: A  844 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6191 (p0)
REVERT: A  852 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7242 (mtm110)
REVERT: A  862 MET cc_start: 0.7374 (mpp) cc_final: 0.7144 (mmp)
  outliers start: 47
  outliers final: 32
  residues processed: 212
  average time/residue: 0.1065
  time to fit residues: 28.4666
Evaluate side-chains
  216 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 180
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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  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  308 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  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  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  822 LYS
Chi-restraints excluded: chain A residue  844 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 81 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0970
   chunk 72 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 15 optimal weight:    0.1980
   chunk 80 optimal weight:    0.2980
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.146133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.125637 restraints weight = 11782.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.129135 restraints weight = 5701.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.131313 restraints weight = 3436.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132412 restraints weight = 2447.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.133332 restraints weight = 2013.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.1365

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= 0.147
  Angle     :  0.569   9.125  10494  Z= 0.304
  Chirality :  0.045   0.256   1099
  Planarity :  0.004   0.039   1360
  Dihedral  :  6.968  57.639   1092
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.79 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 31.77 %
    Favored  : 62.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.29), residues: 943
  helix:  0.96 (0.32), residues: 286
  sheet:  0.61 (0.33), residues: 256
  loop : -1.68 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 225 
 TYR   0.011   0.001   TYR A 378 
 PHE   0.016   0.001   PHE A 741 
 TRP   0.005   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7775)
  covalent geometry    : angle       0.56924 (10494)
  hydrogen bonds       : bond        0.03595 (  345)
  hydrogen bonds       : angle       4.44420 ( 1071)

*********************** 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
  234 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 187
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 ARG cc_start: 0.7483 (ptm-80) cc_final: 0.6992 (mtp-110)
REVERT: A  260 TYR cc_start: 0.5358 (t80) cc_final: 0.3291 (t80)
REVERT: A  308 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7456 (mt)
REVERT: A  326 ASN cc_start: 0.8025 (t0) cc_final: 0.7801 (m-40)
REVERT: A  401 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7808 (mtpp)
REVERT: A  428 GLU cc_start: 0.6996 (tp30) cc_final: 0.6726 (tp30)
REVERT: A  459 TYR cc_start: 0.7489 (t80) cc_final: 0.7253 (t80)
REVERT: A  471 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7752 (p)
REVERT: A  493 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7517 (m-30)
REVERT: A  499 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8105 (tt)
REVERT: A  525 VAL cc_start: 0.8226 (t) cc_final: 0.7908 (m)
REVERT: A  528 SER cc_start: 0.8171 (t) cc_final: 0.7526 (p)
REVERT: A  586 ASN cc_start: 0.7011 (m-40) cc_final: 0.6793 (m-40)
REVERT: A  603 LEU cc_start: 0.8268 (tp) cc_final: 0.8052 (tt)
REVERT: A  626 GLU cc_start: 0.7131 (tp30) cc_final: 0.6421 (tp30)
REVERT: A  627 PHE cc_start: 0.6878 (m-80) cc_final: 0.6265 (m-80)
REVERT: A  652 LYS cc_start: 0.7885 (mtpp) cc_final: 0.7509 (mtpp)
REVERT: A  705 LYS cc_start: 0.7971 (tppp) cc_final: 0.7676 (ttpt)
REVERT: A  778 GLN cc_start: 0.7295 (tt0) cc_final: 0.6456 (tt0)
REVERT: A  780 ARG cc_start: 0.6075 (mtm-85) cc_final: 0.5755 (mtm-85)
REVERT: A  786 SER cc_start: 0.8354 (m) cc_final: 0.8084 (p)
REVERT: A  844 ASP cc_start: 0.6485 (p0) cc_final: 0.6145 (p0)
REVERT: A  852 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7198 (mtm110)
REVERT: A  862 MET cc_start: 0.7372 (mpp) cc_final: 0.7145 (mmp)
  outliers start: 47
  outliers final: 34
  residues processed: 211
  average time/residue: 0.1002
  time to fit residues: 26.5371
Evaluate side-chains
  216 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 178
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  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  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  553 ASN
Chi-restraints excluded: chain A residue  556 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  738 LEU
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  792 GLU
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 1 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 75 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0980
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   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 = 0.3832 r_free = 0.3832 target = 0.145843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.125373 restraints weight = 11744.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128832 restraints weight = 5695.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.130995 restraints weight = 3461.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.132144 restraints weight = 2471.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133147 restraints weight = 2024.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7775  Z= 0.157
  Angle     :  0.575   9.254  10494  Z= 0.306
  Chirality :  0.045   0.277   1099
  Planarity :  0.004   0.036   1360
  Dihedral  :  6.909  57.843   1092
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.21 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 32.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.29), residues: 943
  helix:  0.85 (0.32), residues: 292
  sheet:  0.60 (0.34), residues: 255
  loop : -1.55 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 225 
 TYR   0.012   0.001   TYR A 378 
 PHE   0.016   0.001   PHE A 741 
 TRP   0.006   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7775)
  covalent geometry    : angle       0.57549 (10494)
  hydrogen bonds       : bond        0.03604 (  345)
  hydrogen bonds       : angle       4.38534 ( 1071)

*********************** 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
  240 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 192
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 ILE cc_start: 0.6006 (pt) cc_final: 0.5709 (pt)
REVERT: A  257 ARG cc_start: 0.7488 (ptm-80) cc_final: 0.7001 (mtp-110)
REVERT: A  260 TYR cc_start: 0.5342 (t80) cc_final: 0.3271 (t80)
REVERT: A  308 ILE cc_start: 0.7858 (mm) cc_final: 0.7478 (mt)
REVERT: A  428 GLU cc_start: 0.6996 (tp30) cc_final: 0.6724 (tp30)
REVERT: A  471 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.7766 (p)
REVERT: A  499 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8107 (tt)
REVERT: A  525 VAL cc_start: 0.8226 (t) cc_final: 0.7918 (m)
REVERT: A  528 SER cc_start: 0.8166 (t) cc_final: 0.7533 (p)
REVERT: A  586 ASN cc_start: 0.7024 (m-40) cc_final: 0.6810 (m-40)
REVERT: A  603 LEU cc_start: 0.8267 (tp) cc_final: 0.8054 (tt)
REVERT: A  614 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7396 (mtpp)
REVERT: A  626 GLU cc_start: 0.7159 (tp30) cc_final: 0.6397 (tp30)
REVERT: A  627 PHE cc_start: 0.6865 (m-80) cc_final: 0.6146 (m-80)
REVERT: A  652 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7508 (mtpp)
REVERT: A  705 LYS cc_start: 0.7975 (tppp) cc_final: 0.7683 (ttpt)
REVERT: A  725 TRP cc_start: 0.6155 (OUTLIER) cc_final: 0.5915 (m-10)
REVERT: A  780 ARG cc_start: 0.6076 (mtm-85) cc_final: 0.5806 (mtm-85)
REVERT: A  786 SER cc_start: 0.8307 (m) cc_final: 0.8042 (p)
REVERT: A  844 ASP cc_start: 0.6456 (p0) cc_final: 0.6121 (p0)
REVERT: A  852 ARG cc_start: 0.7447 (mtt90) cc_final: 0.7201 (mtm110)
REVERT: A  862 MET cc_start: 0.7370 (mpp) cc_final: 0.7150 (mmp)
  outliers start: 48
  outliers final: 39
  residues processed: 220
  average time/residue: 0.1047
  time to fit residues: 29.1532
Evaluate side-chains
  225 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 183
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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  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 F residue  255 VAL
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  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  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  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  792 GLU
Chi-restraints excluded: chain A residue  822 LYS
Chi-restraints excluded: chain A residue  832 PHE
Chi-restraints excluded: chain A residue  870 ILE
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 73 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0270
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
** F  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3814 r_free = 0.3814 target = 0.144639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123820 restraints weight = 11680.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.127445 restraints weight = 5482.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.129727 restraints weight = 3259.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.130943 restraints weight = 2290.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.131955 restraints weight = 1858.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7775  Z= 0.236
  Angle     :  0.620   9.218  10494  Z= 0.333
  Chirality :  0.047   0.276   1099
  Planarity :  0.004   0.036   1360
  Dihedral  :  7.048  58.708   1090
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.42 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 31.77 %
    Favored  : 61.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.29), residues: 943
  helix:  0.62 (0.31), residues: 298
  sheet:  0.49 (0.33), residues: 256
  loop : -1.68 (0.34), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 859 
 TYR   0.018   0.002   TYR A 378 
 PHE   0.016   0.002   PHE A 741 
 TRP   0.009   0.001   TRP A 518 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 7775)
  covalent geometry    : angle       0.62023 (10494)
  hydrogen bonds       : bond        0.04157 (  345)
  hydrogen bonds       : angle       4.56805 ( 1071)

*********************** 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
  238 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 187
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   87 TYR cc_start: 0.6302 (t80) cc_final: 0.5962 (t80)
REVERT: F  104 GLU cc_start: 0.8118 (tp30) cc_final: 0.7868 (tp30)
REVERT: F  115 LYS cc_start: 0.8780 (mttp) cc_final: 0.8537 (mttp)
REVERT: F  133 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7971 (mttp)
REVERT: A  195 ILE cc_start: 0.6024 (pt) cc_final: 0.5523 (pt)
REVERT: A  231 LYS cc_start: 0.2557 (OUTLIER) cc_final: 0.0852 (mmmt)
REVERT: A  257 ARG cc_start: 0.7504 (ptm-80) cc_final: 0.7241 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5495 (t80) cc_final: 0.3175 (t80)
REVERT: A  308 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7632 (mt)
REVERT: A  428 GLU cc_start: 0.6966 (tp30) cc_final: 0.6682 (tp30)
REVERT: A  471 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.7749 (p)
REVERT: A  499 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8107 (tt)
REVERT: A  525 VAL cc_start: 0.8219 (t) cc_final: 0.7917 (m)
REVERT: A  528 SER cc_start: 0.8183 (t) cc_final: 0.7551 (p)
REVERT: A  586 ASN cc_start: 0.7019 (m-40) cc_final: 0.6805 (m-40)
REVERT: A  603 LEU cc_start: 0.8263 (tp) cc_final: 0.8058 (tt)
REVERT: A  614 LYS cc_start: 0.7670 (mtpp) cc_final: 0.7459 (mtpp)
REVERT: A  626 GLU cc_start: 0.7123 (tp30) cc_final: 0.6434 (tp30)
REVERT: A  627 PHE cc_start: 0.6854 (m-80) cc_final: 0.6139 (m-80)
REVERT: A  652 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7472 (mtpp)
REVERT: A  705 LYS cc_start: 0.7999 (tppp) cc_final: 0.7691 (ttpt)
REVERT: A  725 TRP cc_start: 0.6173 (OUTLIER) cc_final: 0.5904 (m-10)
REVERT: A  786 SER cc_start: 0.8390 (m) cc_final: 0.8094 (p)
REVERT: A  828 TYR cc_start: 0.7871 (p90) cc_final: 0.7506 (p90)
REVERT: A  844 ASP cc_start: 0.6528 (p0) cc_final: 0.6175 (p0)
REVERT: A  852 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7233 (mtm110)
REVERT: A  862 MET cc_start: 0.7433 (mpp) cc_final: 0.7196 (mmp)
  outliers start: 51
  outliers final: 40
  residues processed: 218
  average time/residue: 0.1018
  time to fit residues: 28.0798
Evaluate side-chains
  228 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 182
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
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  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  255 VAL
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  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  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  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  725 TRP
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  868 LEU
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 51 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 8 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.146184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.125329 restraints weight = 11773.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.129012 restraints weight = 5501.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.131274 restraints weight = 3250.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.132603 restraints weight = 2272.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.133576 restraints weight = 1820.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7775  Z= 0.171
  Angle     :  0.598   9.159  10494  Z= 0.318
  Chirality :  0.045   0.267   1099
  Planarity :  0.004   0.035   1360
  Dihedral  :  6.819  58.380   1088
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.42 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 32.39 %
    Favored  : 61.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.29), residues: 943
  helix:  0.90 (0.31), residues: 286
  sheet:  0.50 (0.33), residues: 255
  loop : -1.70 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 780 
 TYR   0.016   0.001   TYR F 141 
 PHE   0.035   0.001   PHE A 507 
 TRP   0.006   0.001   TRP A 518 
 HIS   0.003   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 7775)
  covalent geometry    : angle       0.59767 (10494)
  hydrogen bonds       : bond        0.03754 (  345)
  hydrogen bonds       : angle       4.42535 ( 1071)

*********************** 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
  231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   87 TYR cc_start: 0.6303 (t80) cc_final: 0.5956 (t80)
REVERT: F  133 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7992 (mttm)
REVERT: A  195 ILE cc_start: 0.5969 (pt) cc_final: 0.5499 (pt)
REVERT: A  231 LYS cc_start: 0.2490 (OUTLIER) cc_final: 0.0774 (mmmt)
REVERT: A  257 ARG cc_start: 0.7496 (ptm-80) cc_final: 0.7221 (ptm-80)
REVERT: A  260 TYR cc_start: 0.5371 (t80) cc_final: 0.3163 (t80)
REVERT: A  308 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7570 (mt)
REVERT: A  368 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5694 (mt-10)
REVERT: A  428 GLU cc_start: 0.6951 (tp30) cc_final: 0.6678 (tp30)
REVERT: A  471 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7737 (p)
REVERT: A  493 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7488 (m-30)
REVERT: A  499 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8103 (tt)
REVERT: A  525 VAL cc_start: 0.8222 (t) cc_final: 0.7916 (m)
REVERT: A  528 SER cc_start: 0.8186 (t) cc_final: 0.7545 (p)
REVERT: A  586 ASN cc_start: 0.7013 (m-40) cc_final: 0.6804 (m-40)
REVERT: A  603 LEU cc_start: 0.8261 (tp) cc_final: 0.8055 (tt)
REVERT: A  614 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7425 (mtpp)
REVERT: A  626 GLU cc_start: 0.7170 (tp30) cc_final: 0.6468 (tp30)
REVERT: A  627 PHE cc_start: 0.6865 (m-80) cc_final: 0.6289 (m-80)
REVERT: A  652 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7488 (mtpp)
REVERT: A  705 LYS cc_start: 0.7979 (tppp) cc_final: 0.7683 (ttpt)
REVERT: A  786 SER cc_start: 0.8318 (m) cc_final: 0.8012 (p)
REVERT: A  828 TYR cc_start: 0.7806 (p90) cc_final: 0.7475 (p90)
REVERT: A  844 ASP cc_start: 0.6482 (p0) cc_final: 0.6139 (p0)
REVERT: A  852 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7207 (mtm110)
REVERT: A  862 MET cc_start: 0.7419 (mpp) cc_final: 0.7184 (mmp)
  outliers start: 50
  outliers final: 40
  residues processed: 210
  average time/residue: 0.1086
  time to fit residues: 28.4272
Evaluate side-chains
  225 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 179
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
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  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  255 VAL
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  292 LEU
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  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  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  728 LYS
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  772 ASP
Chi-restraints excluded: chain A residue  792 GLU
Chi-restraints excluded: chain A residue  832 PHE
Chi-restraints excluded: chain A residue  886 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 65.5399 > 50:
  distance: 19 - 29:  23.631
  distance: 29 - 30:  28.476
  distance: 30 - 31:  13.670
  distance: 30 - 33:  19.986
  distance: 31 - 32:  22.428
  distance: 31 - 40:  19.570
  distance: 33 - 34:  17.464
  distance: 34 - 35:  11.463
  distance: 35 - 36:  43.470
  distance: 36 - 37:  65.540
  distance: 37 - 38:  58.620
  distance: 37 - 39:  53.116
  distance: 40 - 41:  15.002
  distance: 41 - 42:  28.059
  distance: 42 - 43:  22.583
  distance: 42 - 44:  26.478
  distance: 44 - 45:  29.380
  distance: 45 - 46:  50.750
  distance: 45 - 48:  25.320
  distance: 46 - 47:  36.089
  distance: 46 - 53:  59.356
  distance: 48 - 49:  10.402
  distance: 49 - 50:   7.228
  distance: 50 - 51:   8.257
  distance: 51 - 52:   4.481
  distance: 53 - 54:  52.268
  distance: 53 - 59:  31.253
  distance: 54 - 55:  39.171
  distance: 54 - 57:  28.507
  distance: 55 - 56:  15.145
  distance: 55 - 60:  25.054
  distance: 57 - 58:   9.396
  distance: 58 - 59:   9.487
  distance: 60 - 61:  12.815
  distance: 61 - 62:   6.311
  distance: 61 - 64:  14.636
  distance: 62 - 63:  22.309
  distance: 62 - 69:  24.281
  distance: 64 - 65:  13.484
  distance: 65 - 66:  20.401
  distance: 66 - 67:  17.985
  distance: 66 - 68:  26.984
  distance: 69 - 70:  57.869
  distance: 70 - 71:  57.675
  distance: 70 - 73:  26.393
  distance: 71 - 72:  40.015
  distance: 71 - 74:  59.898
  distance: 74 - 75:  43.312
  distance: 75 - 76:  52.336
  distance: 75 - 78:  35.432
  distance: 76 - 77:  13.065
  distance: 76 - 83:  27.253
  distance: 78 - 79:  10.255
  distance: 79 - 80:  17.089
  distance: 80 - 81:  14.365
  distance: 80 - 82:   8.752
  distance: 83 - 84:  23.298
  distance: 84 - 85:  37.142
  distance: 84 - 87:  32.038
  distance: 85 - 86:  23.668
  distance: 85 - 92:  36.374
  distance: 87 - 88:  15.703
  distance: 88 - 89:  22.096
  distance: 89 - 90:  15.970
  distance: 90 - 91:  28.507
  distance: 92 - 93:  47.899
  distance: 93 - 94:  38.882
  distance: 93 - 96:  50.030
  distance: 94 - 95:  18.242
  distance: 94 - 100:  30.739
  distance: 96 - 97:  17.907
  distance: 97 - 98:  17.973
  distance: 97 - 99:  19.168
  distance: 100 - 101:  52.817
  distance: 101 - 102:  42.938
  distance: 101 - 104:  45.999
  distance: 102 - 103:  54.459
  distance: 102 - 111:  25.550
  distance: 104 - 105:  63.141
  distance: 105 - 106:  51.940
  distance: 105 - 107:  46.671
  distance: 106 - 108:  30.641
  distance: 107 - 109:  22.396
  distance: 108 - 110:  33.668
  distance: 109 - 110:  48.145