Starting phenix.real_space_refine
on Mon Sep 23 22:33:44 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/09_2024/6hn4_0246.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/09_2024/6hn4_0246.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/09_2024/6hn4_0246.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/09_2024/6hn4_0246.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/09_2024/6hn4_0246.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/09_2024/6hn4_0246.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    3595      2.51       5
     N     981      2.21       5
     O    1078      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 5702
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1629
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 3989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3989
          Classifications: {'peptide': 498}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 466}
          Chain breaks: 4
    Chain: "F"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.11, per 1000 atoms: 0.72
  Number of scatterers: 5702
  At special positions: 0
  Unit cell: (100.88, 105.04, 102.96, 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      48     16.00
     O    1078      8.00
     N     981      7.00
     C    3595      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 647 " - pdb=" SG  CYS E 841 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 767 " - pdb=" SG  CYS E 776 " distance=2.05
    Simple disulfide: pdb=" SG  CYS F   8 " - pdb=" SG  CYS F  26 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 126 " - pdb=" SG  CYS F 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 159 " - pdb=" SG  CYS F 182 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 169 " - pdb=" SG  CYS F 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 192 " - pdb=" SG  CYS F 201 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 196 " - pdb=" SG  CYS F 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 208 " - pdb=" SG  CYS F 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 212 " - pdb=" SG  CYS F 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 228 " - pdb=" SG  CYS F 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 241 " - pdb=" SG  CYS F 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 259 " - pdb=" SG  CYS F 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 266 " - pdb=" SG  CYS F 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 288 " - pdb=" SG  CYS F 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 304 " - pdb=" SG  CYS F 308 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 647 " - pdb=" SG  CYS F 841 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 767 " - pdb=" SG  CYS F 776 " distance=2.05

  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
  Links applied
    NAG-ASN
      " NAG F1001 " - " ASN F  16 "
      " NAG F1002 " - " ASN F  25 "
      " NAG F1003 " - " ASN F 111 "
      " NAG F1004 " - " ASN F 606 "
      " NAG F1005 " - " ASN F 875 "
      " NAG F1006 " - " ASN F 215 "
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 671.2 milliseconds
  

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1326

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 16 sheets defined
      8.9% alpha, 37.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'E' and resid 638 through 644
      removed outlier: 4.029A  pdb=" N   LEU E 644 " --> pdb=" O   LEU E 641 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 844 through 851
    Processing helix  chain 'F' and resid 17 through 24
    Processing helix  chain 'F' and resid 42 through 48
      removed outlier: 3.801A  pdb=" N   PHE F  46 " --> pdb=" O   ARG F  42 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP F  48 " --> pdb=" O   GLU F  44 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 132 through 136
    Processing helix  chain 'F' and resid 255 through 266
      removed outlier: 3.507A  pdb=" N   CYS F 259 " --> pdb=" O   ASN F 255 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 638 through 644
      removed outlier: 4.039A  pdb=" N   LEU F 644 " --> pdb=" O   LEU F 641 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 844 through 851
    Processing sheet with id=AA1, first strand: chain 'E' and resid 599 through 604
      removed outlier: 6.521A  pdb=" N   LYS E 614 " --> pdb=" O   PRO E 601 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   SER E 603 " --> pdb=" O   ILE E 612 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ILE E 612 " --> pdb=" O   SER E 603 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 740 through 743
    Processing sheet with id=AA3, first strand: chain 'E' and resid 800 through 803
    Processing sheet with id=AA4, first strand: chain 'E' and resid 841 through 843
      removed outlier: 3.660A  pdb=" N   ALA E 869 " --> pdb=" O   GLY E 876 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 841 through 843
    Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 14
      removed outlier: 6.557A  pdb=" N   GLU F   6 " --> pdb=" O   VAL F  28 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLU F  30 " --> pdb=" O   GLU F   6 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   CYS F   8 " --> pdb=" O   GLU F  30 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   HIS F  32 " --> pdb=" O   CYS F   8 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   GLY F  10 " --> pdb=" O   HIS F  32 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   GLN F  34 " --> pdb=" O   GLY F  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ASP F  12 " --> pdb=" O   GLN F  34 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU F  36 " --> pdb=" O   ASP F  12 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ARG F  14 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET F  38 " --> pdb=" O   ARG F  14 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE F  82 " --> pdb=" O   ASN F 111 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 14
      removed outlier: 6.557A  pdb=" N   GLU F   6 " --> pdb=" O   VAL F  28 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLU F  30 " --> pdb=" O   GLU F   6 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   CYS F   8 " --> pdb=" O   GLU F  30 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   HIS F  32 " --> pdb=" O   CYS F   8 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   GLY F  10 " --> pdb=" O   HIS F  32 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   GLN F  34 " --> pdb=" O   GLY F  10 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ASP F  12 " --> pdb=" O   GLN F  34 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU F  36 " --> pdb=" O   ASP F  12 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ARG F  14 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET F  38 " --> pdb=" O   ARG F  14 " (cutoff:3.500A)
      removed outlier: 9.006A  pdb=" N   LEU F  62 " --> pdb=" O   GLY F  31 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU F  33 " --> pdb=" O   LEU F  62 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   PHE F  64 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE F  35 " --> pdb=" O   PHE F  64 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   VAL F  66 " --> pdb=" O   ILE F  35 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   LEU F  37 " --> pdb=" O   VAL F  66 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU F  61 " --> pdb=" O   VAL F  94 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   PHE F  96 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU F  63 " --> pdb=" O   PHE F  96 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   TYR F  91 " --> pdb=" O   SER F 116 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   ARG F 118 " --> pdb=" O   TYR F  91 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU F  93 " --> pdb=" O   ARG F 118 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   GLU F 120 " --> pdb=" O   LEU F  93 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ILE F  95 " --> pdb=" O   GLU F 120 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL F 117 " --> pdb=" O   HIS F 144 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   VAL F 146 " --> pdb=" O   VAL F 117 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE F 119 " --> pdb=" O   VAL F 146 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'F' and resid 171 through 173
    Processing sheet with id=AA9, first strand: chain 'F' and resid 231 through 233
    Processing sheet with id=AB1, first strand: chain 'F' and resid 252 through 254
      removed outlier: 6.728A  pdb=" N   HIS F 247 " --> pdb=" O   CYS F 284 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 292 through 295
      removed outlier: 3.516A  pdb=" N   LEU F 300 " --> pdb=" O   ASN F 295 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 599 through 604
      removed outlier: 6.540A  pdb=" N   LYS F 614 " --> pdb=" O   PRO F 601 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   SER F 603 " --> pdb=" O   ILE F 612 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE F 612 " --> pdb=" O   SER F 603 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 740 through 744
    Processing sheet with id=AB5, first strand: chain 'F' and resid 800 through 803
    Processing sheet with id=AB6, first strand: chain 'F' and resid 841 through 843
      removed outlier: 3.559A  pdb=" N   ALA F 869 " --> pdb=" O   GLY F 876 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 841 through 843

    167 hydrogen bonds defined for protein.
    387 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: 1.79

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1865
        1.35 -     1.48: 1492
        1.48 -     1.60: 2430
        1.60 -     1.73: 0
        1.73 -     1.86: 58
  Bond restraints: 5845
  Sorted by residual:
  bond pdb=" C   THR F 771 "
       pdb=" N   PRO F 772 "
    ideal  model  delta    sigma   weight residual
    1.334  1.427 -0.093 2.34e-02 1.83e+03 1.58e+01
  bond pdb=" CA  THR F 771 "
       pdb=" C   THR F 771 "
    ideal  model  delta    sigma   weight residual
    1.524  1.561 -0.037 1.26e-02 6.30e+03 8.83e+00
  bond pdb=" C1  NAG F1005 "
       pdb=" O5  NAG F1005 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.77e+00
  bond pdb=" C1  NAG F1004 "
       pdb=" O5  NAG F1004 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.57e+00
  bond pdb=" N   ASN F  90 "
       pdb=" CA  ASN F  90 "
    ideal  model  delta    sigma   weight residual
    1.460  1.498 -0.038 1.83e-02 2.99e+03 4.35e+00
  ... (remaining 5840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.00: 7817
        5.00 -     9.99: 110
        9.99 -    14.99: 6
       14.99 -    19.99: 0
       19.99 -    24.99: 2
  Bond angle restraints: 7935
  Sorted by residual:
  angle pdb=" C   LYS F 197 "
        pdb=" N   SER F 198 "
        pdb=" CA  SER F 198 "
      ideal   model   delta    sigma   weight residual
     122.06  109.66   12.40 1.86e+00 2.89e-01 4.45e+01
  angle pdb=" C   VAL F  99 "
        pdb=" N   HIS F 100 "
        pdb=" CA  HIS F 100 "
      ideal   model   delta    sigma   weight residual
     121.54  132.94  -11.40 1.91e+00 2.74e-01 3.56e+01
  angle pdb=" N   LYS F 197 "
        pdb=" CA  LYS F 197 "
        pdb=" C   LYS F 197 "
      ideal   model   delta    sigma   weight residual
     110.80  123.37  -12.57 2.13e+00 2.20e-01 3.48e+01
  angle pdb=" CA  GLU F 773 "
        pdb=" CB  GLU F 773 "
        pdb=" CG  GLU F 773 "
      ideal   model   delta    sigma   weight residual
     114.10  124.68  -10.58 2.00e+00 2.50e-01 2.80e+01
  angle pdb=" C   PRO E 816 "
        pdb=" N   LYS E 817 "
        pdb=" CA  LYS E 817 "
      ideal   model   delta    sigma   weight residual
     121.54  131.28   -9.74 1.91e+00 2.74e-01 2.60e+01
  ... (remaining 7930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 3405
       14.98 -    29.96: 183
       29.96 -    44.94: 41
       44.94 -    59.92: 7
       59.92 -    74.90: 3
  Dihedral angle restraints: 3639
    sinusoidal: 1591
      harmonic: 2048
  Sorted by residual:
  dihedral pdb=" CB  CYS E 647 "
           pdb=" SG  CYS E 647 "
           pdb=" SG  CYS E 841 "
           pdb=" CB  CYS E 841 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.92  -71.92     1      1.00e+01 1.00e-02 6.62e+01
  dihedral pdb=" C   THR F 771 "
           pdb=" N   THR F 771 "
           pdb=" CA  THR F 771 "
           pdb=" CB  THR F 771 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.47   13.47     0      2.50e+00 1.60e-01 2.90e+01
  dihedral pdb=" SG  CYS F 304 "
           pdb=" CB  CYS F 308 "
           pdb=" SG  CYS F 308 "
           pdb=" CA  CYS F 308 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    4.10   74.90     1      2.00e+01 2.50e-03 1.77e+01
  ... (remaining 3636 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 632
       0.075 -    0.149: 203
       0.149 -    0.224: 34
       0.224 -    0.299: 7
       0.299 -    0.373: 1
  Chirality restraints: 877
  Sorted by residual:
  chirality pdb=" CA  THR F 771 "
            pdb=" N   THR F 771 "
            pdb=" C   THR F 771 "
            pdb=" CB  THR F 771 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CB  VAL F 146 "
            pdb=" CA  VAL F 146 "
            pdb=" CG1 VAL F 146 "
            pdb=" CG2 VAL F 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  GLU F 773 "
            pdb=" N   GLU F 773 "
            pdb=" C   GLU F 773 "
            pdb=" CB  GLU F 773 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.99e+00
  ... (remaining 874 not shown)

  Planarity restraints: 1030
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU F 818 "   -0.016 2.00e-02 2.50e+03   3.13e-02 9.78e+00
        pdb=" CD  GLU F 818 "    0.054 2.00e-02 2.50e+03
        pdb=" OE1 GLU F 818 "   -0.020 2.00e-02 2.50e+03
        pdb=" OE2 GLU F 818 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 612 "   -0.015 2.00e-02 2.50e+03   3.11e-02 9.66e+00
        pdb=" C   ILE E 612 "    0.054 2.00e-02 2.50e+03
        pdb=" O   ILE E 612 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU E 613 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 612 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.33e+00
        pdb=" C   ILE F 612 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ILE F 612 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU F 613 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1027 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 327
        2.73 -     3.27: 5041
        3.27 -     3.81: 9021
        3.81 -     4.36: 10732
        4.36 -     4.90: 18402
  Nonbonded interactions: 43523
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 781 "
            pdb=" OH  TYR F  67 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OG  SER F 829 "
            pdb=" O   ARG F 866 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG  SER E 829 "
            pdb=" O   ARG E 866 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NE2 GLN F 610 "
            pdb=" OG  SER F 752 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   SER E 859 "
            pdb=" OH  TYR E 863 "
     model   vdw
     2.368 3.040
  ... (remaining 43518 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:             1.670
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.660
  Find NCS groups from input model:        0.060
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
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      :  0.007   0.093   5845  Z= 0.456
  Angle     :  1.497  24.985   7935  Z= 0.820
  Chirality :  0.075   0.373    877
  Planarity :  0.007   0.031   1024
  Dihedral  :  9.899  69.511   2259
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  1.75 %
    Allowed  :  6.87 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.30 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.30), residues: 684
  helix: -2.61 (0.76), residues: 28
  sheet: -1.98 (0.31), residues: 202
  loop : -1.09 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP F 878 
 HIS   0.021   0.002   HIS F  32 
 PHE   0.039   0.004   PHE F 231 
 TYR   0.021   0.004   TYR F  60 
 ARG   0.037   0.006   ARG F 866 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  600 ASP cc_start: 0.8950 (m-30) cc_final: 0.8727 (t0)
REVERT: E  740 PHE cc_start: 0.9044 (p90) cc_final: 0.8685 (p90)
REVERT: E  741 GLU cc_start: 0.8475 (tp30) cc_final: 0.7661 (tm-30)
REVERT: E  747 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8524 (mt-10)
REVERT: E  749 LEU cc_start: 0.8725 (tp) cc_final: 0.8498 (tp)
REVERT: E  800 THR cc_start: 0.9157 (m) cc_final: 0.8753 (p)
REVERT: E  802 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9055 (pt0)
REVERT: E  812 MET cc_start: 0.9457 (mtm) cc_final: 0.9029 (mpp)
REVERT: E  815 GLU cc_start: 0.9146 (pt0) cc_final: 0.8808 (tm-30)
REVERT: E  826 TYR cc_start: 0.8569 (m-80) cc_final: 0.8270 (m-80)
REVERT: E  885 TYR cc_start: 0.9234 (t80) cc_final: 0.8973 (t80)
REVERT: F   94 VAL cc_start: 0.8799 (t) cc_final: 0.8573 (t)
REVERT: F  125 LEU cc_start: 0.9035 (tp) cc_final: 0.8686 (tp)
REVERT: F  131 ILE cc_start: 0.8005 (mt) cc_final: 0.7755 (mt)
REVERT: F  249 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8403 (tp40)
REVERT: F  600 ASP cc_start: 0.8310 (m-30) cc_final: 0.7677 (t0)
REVERT: F  629 LEU cc_start: 0.8973 (tp) cc_final: 0.8474 (mt)
REVERT: F  757 PHE cc_start: 0.8658 (t80) cc_final: 0.8358 (t80)
REVERT: F  787 MET cc_start: 0.8877 (mtt) cc_final: 0.8146 (mtp)
REVERT: F  812 MET cc_start: 0.9095 (mtm) cc_final: 0.8653 (mpp)
REVERT: F  830 TYR cc_start: 0.8242 (p90) cc_final: 0.7950 (p90)
REVERT: F  870 THR cc_start: 0.9273 (m) cc_final: 0.9057 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2136
  time to fit residues: 45.7309
Evaluate side-chains
  96 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 52 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
E 610 GLN
** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 814 GLN
F  15 ASN
F 123 ASN
F 187 HIS
F 209 HIS
F 610 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5845  Z= 0.292
  Angle     :  0.776  13.641   7935  Z= 0.386
  Chirality :  0.048   0.245    877
  Planarity :  0.004   0.035   1024
  Dihedral  :  6.281  43.845    890
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.04 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.32), residues: 684
  helix: -0.53 (1.02), residues: 28
  sheet: -0.93 (0.34), residues: 188
  loop : -0.37 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 133 
 HIS   0.006   0.001   HIS F 264 
 PHE   0.012   0.002   PHE F  64 
 TYR   0.017   0.002   TYR E 628 
 ARG   0.007   0.001   ARG E 761 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  740 PHE cc_start: 0.8911 (p90) cc_final: 0.8654 (p90)
REVERT: E  812 MET cc_start: 0.9480 (mtm) cc_final: 0.9089 (mpp)
REVERT: E  826 TYR cc_start: 0.8862 (m-80) cc_final: 0.8358 (m-80)
REVERT: F   38 MET cc_start: 0.8839 (mtt) cc_final: 0.8213 (mmt)
REVERT: F  125 LEU cc_start: 0.8894 (tp) cc_final: 0.8577 (tp)
REVERT: F  246 TYR cc_start: 0.8708 (m-80) cc_final: 0.8474 (m-80)
REVERT: F  600 ASP cc_start: 0.8454 (m-30) cc_final: 0.8069 (t0)
REVERT: F  641 LEU cc_start: 0.9091 (mp) cc_final: 0.8705 (mt)
REVERT: F  757 PHE cc_start: 0.8776 (t80) cc_final: 0.8444 (t80)
REVERT: F  787 MET cc_start: 0.8778 (mtt) cc_final: 0.8061 (mtp)
REVERT: F  812 MET cc_start: 0.9011 (mtm) cc_final: 0.8611 (mpp)
REVERT: F  823 ILE cc_start: 0.7570 (mm) cc_final: 0.6842 (mm)
REVERT: F  830 TYR cc_start: 0.8861 (p90) cc_final: 0.8554 (p90)
REVERT: F  870 THR cc_start: 0.9275 (m) cc_final: 0.9017 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2256
  time to fit residues: 30.9307
Evaluate side-chains
  75 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 34 optimal weight:    0.1980
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 635 GLN
E 765 GLN
E 814 GLN
E 839 HIS
F 218 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5845  Z= 0.196
  Angle     :  0.669   9.495   7935  Z= 0.335
  Chirality :  0.046   0.157    877
  Planarity :  0.004   0.033   1024
  Dihedral  :  5.951  42.321    890
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.98 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.32), residues: 684
  helix:  0.53 (1.12), residues: 28
  sheet: -0.51 (0.35), residues: 190
  loop : -0.14 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 632 
 HIS   0.006   0.001   HIS F 264 
 PHE   0.023   0.001   PHE E 884 
 TYR   0.009   0.001   TYR F  60 
 ARG   0.009   0.001   ARG E 831 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  740 PHE cc_start: 0.8906 (p90) cc_final: 0.8601 (p90)
REVERT: E  800 THR cc_start: 0.8997 (p) cc_final: 0.8729 (p)
REVERT: E  826 TYR cc_start: 0.8800 (m-80) cc_final: 0.8462 (m-80)
REVERT: F   38 MET cc_start: 0.9010 (mtt) cc_final: 0.8177 (mmm)
REVERT: F  125 LEU cc_start: 0.8732 (tp) cc_final: 0.8457 (tp)
REVERT: F  600 ASP cc_start: 0.8568 (m-30) cc_final: 0.8100 (t0)
REVERT: F  637 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6063 (tm-30)
REVERT: F  638 ASP cc_start: 0.8892 (m-30) cc_final: 0.8610 (t70)
REVERT: F  787 MET cc_start: 0.8856 (mtt) cc_final: 0.8240 (mtp)
REVERT: F  812 MET cc_start: 0.8864 (mtm) cc_final: 0.8522 (mpp)
REVERT: F  827 GLU cc_start: 0.8496 (tp30) cc_final: 0.8214 (tp30)
REVERT: F  830 TYR cc_start: 0.8820 (p90) cc_final: 0.8558 (p90)
REVERT: F  870 THR cc_start: 0.9298 (m) cc_final: 0.9082 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1823
  time to fit residues: 23.3575
Evaluate side-chains
  72 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 635 GLN
E 814 GLN
F 218 GLN
F 610 GLN
F 814 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.5232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070   5845  Z= 0.478
  Angle     :  0.840   8.995   7935  Z= 0.425
  Chirality :  0.051   0.227    877
  Planarity :  0.005   0.047   1024
  Dihedral  :  6.226  44.543    890
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.82 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.32), residues: 684
  helix: -0.22 (0.89), residues: 34
  sheet: -0.48 (0.34), residues: 205
  loop : -0.26 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP F 133 
 HIS   0.011   0.002   HIS F 264 
 PHE   0.017   0.002   PHE F 231 
 TYR   0.018   0.002   TYR E 883 
 ARG   0.005   0.001   ARG E 738 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  817 LYS cc_start: 0.9127 (pttm) cc_final: 0.8668 (tppt)
REVERT: E  826 TYR cc_start: 0.8815 (m-80) cc_final: 0.8436 (m-80)
REVERT: F   38 MET cc_start: 0.8964 (mtt) cc_final: 0.8759 (mtt)
REVERT: F   98 MET cc_start: 0.8951 (mmp) cc_final: 0.8717 (mmt)
REVERT: F  600 ASP cc_start: 0.8823 (m-30) cc_final: 0.8290 (t0)
REVERT: F  638 ASP cc_start: 0.8877 (m-30) cc_final: 0.8397 (t70)
REVERT: F  787 MET cc_start: 0.8705 (mtt) cc_final: 0.8070 (mtp)
REVERT: F  870 THR cc_start: 0.9346 (m) cc_final: 0.9093 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1786
  time to fit residues: 19.7375
Evaluate side-chains
  52 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
E 610 GLN
E 814 GLN
F 218 GLN
F 769 GLN
F 814 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5845  Z= 0.191
  Angle     :  0.647   8.316   7935  Z= 0.329
  Chirality :  0.047   0.209    877
  Planarity :  0.004   0.030   1024
  Dihedral  :  5.597  42.421    890
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.25 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.32), residues: 684
  helix:  0.04 (0.84), residues: 40
  sheet: -0.15 (0.36), residues: 195
  loop : -0.23 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 813 
 HIS   0.012   0.001   HIS F 199 
 PHE   0.020   0.002   PHE E 884 
 TYR   0.013   0.001   TYR F 826 
 ARG   0.011   0.001   ARG E 851 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  812 MET cc_start: 0.9111 (mpp) cc_final: 0.8877 (mpp)
REVERT: E  817 LYS cc_start: 0.9120 (pttm) cc_final: 0.8775 (mmtt)
REVERT: F  600 ASP cc_start: 0.8843 (m-30) cc_final: 0.8340 (t0)
REVERT: F  638 ASP cc_start: 0.8868 (m-30) cc_final: 0.8394 (t70)
REVERT: F  827 GLU cc_start: 0.8354 (tp30) cc_final: 0.8104 (tp30)
REVERT: F  870 THR cc_start: 0.9250 (m) cc_final: 0.8967 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1847
  time to fit residues: 19.9175
Evaluate side-chains
  56 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
F 144 HIS
F 218 GLN
** F 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.6054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.079   5845  Z= 0.442
  Angle     :  0.786   9.240   7935  Z= 0.396
  Chirality :  0.050   0.214    877
  Planarity :  0.005   0.039   1024
  Dihedral  :  5.901  43.191    890
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.33), residues: 684
  helix:  0.87 (0.97), residues: 34
  sheet: -0.61 (0.35), residues: 206
  loop : -0.27 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP F 133 
 HIS   0.008   0.002   HIS F 199 
 PHE   0.017   0.002   PHE E 757 
 TYR   0.017   0.002   TYR E 883 
 ARG   0.006   0.001   ARG E 854 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  800 THR cc_start: 0.8726 (p) cc_final: 0.8450 (p)
REVERT: E  812 MET cc_start: 0.9134 (mpp) cc_final: 0.8736 (mpp)
REVERT: E  817 LYS cc_start: 0.9121 (pttm) cc_final: 0.8792 (mmtt)
REVERT: F   98 MET cc_start: 0.9038 (mmt) cc_final: 0.8718 (mmp)
REVERT: F  638 ASP cc_start: 0.8956 (m-30) cc_final: 0.8499 (t70)
REVERT: F  787 MET cc_start: 0.8676 (mtt) cc_final: 0.8022 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2094
  time to fit residues: 19.6262
Evaluate side-chains
  48 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0040
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
F 218 GLN
** F 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.5987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5845  Z= 0.189
  Angle     :  0.630   8.114   7935  Z= 0.322
  Chirality :  0.047   0.220    877
  Planarity :  0.004   0.028   1024
  Dihedral  :  5.326  38.094    890
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.33), residues: 684
  helix:  1.12 (0.98), residues: 34
  sheet: -0.31 (0.35), residues: 201
  loop : -0.14 (0.32), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 813 
 HIS   0.005   0.001   HIS F 199 
 PHE   0.011   0.001   PHE E 757 
 TYR   0.013   0.001   TYR F 826 
 ARG   0.013   0.000   ARG F  47 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
REVERT: E  800 THR cc_start: 0.8943 (p) cc_final: 0.8699 (p)
REVERT: E  812 MET cc_start: 0.9132 (mpp) cc_final: 0.8760 (mpp)
REVERT: E  826 TYR cc_start: 0.8446 (m-80) cc_final: 0.7807 (m-80)
REVERT: F  638 ASP cc_start: 0.8889 (m-30) cc_final: 0.8433 (t70)
REVERT: F  870 THR cc_start: 0.9227 (m) cc_final: 0.8947 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1722
  time to fit residues: 17.5940
Evaluate side-chains
  53 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 60 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
F 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.6171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5845  Z= 0.197
  Angle     :  0.623   8.023   7935  Z= 0.316
  Chirality :  0.046   0.220    877
  Planarity :  0.004   0.026   1024
  Dihedral  :  5.016  28.788    890
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.33), residues: 684
  helix:  0.12 (0.90), residues: 42
  sheet: -0.15 (0.36), residues: 201
  loop : -0.22 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 813 
 HIS   0.004   0.001   HIS F 199 
 PHE   0.012   0.001   PHE F  64 
 TYR   0.010   0.001   TYR F 830 
 ARG   0.007   0.000   ARG F 851 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  826 TYR cc_start: 0.8589 (m-80) cc_final: 0.8235 (m-80)
REVERT: E  845 LYS cc_start: 0.9446 (tmmt) cc_final: 0.9039 (mtpt)
REVERT: F  638 ASP cc_start: 0.9002 (m-30) cc_final: 0.8610 (t70)
REVERT: F  828 VAL cc_start: 0.9682 (t) cc_final: 0.9462 (t)
REVERT: F  870 THR cc_start: 0.9221 (m) cc_final: 0.8925 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1699
  time to fit residues: 17.3568
Evaluate side-chains
  55 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
F 123 ASN
F 218 GLN
F 814 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.6315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5845  Z= 0.189
  Angle     :  0.623   9.686   7935  Z= 0.314
  Chirality :  0.046   0.219    877
  Planarity :  0.004   0.028   1024
  Dihedral  :  4.902  23.724    890
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.16 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.33), residues: 684
  helix:  0.12 (0.89), residues: 42
  sheet: -0.01 (0.36), residues: 201
  loop : -0.23 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 813 
 HIS   0.004   0.001   HIS F 839 
 PHE   0.014   0.001   PHE E 757 
 TYR   0.010   0.001   TYR E 826 
 ARG   0.009   0.001   ARG F 851 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  826 TYR cc_start: 0.8561 (m-80) cc_final: 0.8189 (m-80)
REVERT: E  845 LYS cc_start: 0.9448 (tmmt) cc_final: 0.9028 (mtpt)
REVERT: F   98 MET cc_start: 0.8057 (mmt) cc_final: 0.7727 (mmt)
REVERT: F  638 ASP cc_start: 0.9107 (m-30) cc_final: 0.8516 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1842
  time to fit residues: 19.0025
Evaluate side-chains
  54 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 54 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
F 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.6404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5845  Z= 0.195
  Angle     :  0.619   9.565   7935  Z= 0.312
  Chirality :  0.046   0.220    877
  Planarity :  0.004   0.027   1024
  Dihedral  :  4.799  19.972    890
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.33), residues: 684
  helix: -0.05 (0.88), residues: 42
  sheet:  0.04 (0.36), residues: 201
  loop : -0.22 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 813 
 HIS   0.004   0.001   HIS F 839 
 PHE   0.016   0.001   PHE E 757 
 TYR   0.012   0.001   TYR F 826 
 ARG   0.008   0.000   ARG F 851 

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

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

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1368 Ramachandran restraints generated.
    684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  826 TYR cc_start: 0.8591 (m-80) cc_final: 0.8183 (m-80)
REVERT: E  845 LYS cc_start: 0.9465 (tmmt) cc_final: 0.9063 (mtpt)
REVERT: F   94 VAL cc_start: 0.8955 (t) cc_final: 0.8626 (p)
REVERT: F   98 MET cc_start: 0.8178 (mmt) cc_final: 0.7844 (mmt)
REVERT: F  638 ASP cc_start: 0.9100 (m-30) cc_final: 0.8534 (t70)
REVERT: F  781 TYR cc_start: 0.9187 (m-80) cc_final: 0.8618 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1868
  time to fit residues: 18.6216
Evaluate side-chains
  54 residues out of total 638 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
F 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.072291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.059613 restraints weight = 29176.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.061201 restraints weight = 18772.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.062359 restraints weight = 13622.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.6518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5845  Z= 0.227
  Angle     :  0.632   9.176   7935  Z= 0.320
  Chirality :  0.046   0.216    877
  Planarity :  0.004   0.027   1024
  Dihedral  :  4.958  31.987    890
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.33), residues: 684
  helix: -0.18 (0.87), residues: 42
  sheet:  0.05 (0.36), residues: 201
  loop : -0.29 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 813 
 HIS   0.004   0.001   HIS E 756 
 PHE   0.016   0.001   PHE E 757 
 TYR   0.014   0.001   TYR F 127 
 ARG   0.008   0.000   ARG F 851 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1513.13 seconds
wall clock time: 27 minutes 30.84 seconds (1650.84 seconds total)