Starting phenix.real_space_refine
on Sat Aug 23 11:10:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8thu_41272/08_2025/8thu_41272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8thu_41272/08_2025/8thu_41272.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2025/8thu_41272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2025/8thu_41272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2025/8thu_41272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8thu_41272/08_2025/8thu_41272.cif"
  }
  resolution = 3.1
  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=   0.004 sd=   0.029
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: 5
    Type Number    sf(0)   Gaussians
     P     291      5.49       5
     S      12      5.16       5
     C    6569      2.51       5
     N    2223      2.21       5
     O    2807      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 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: 11902
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "G"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 803
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 773
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 657
          Classifications: {'peptide': 84}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 718
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 657
          Classifications: {'peptide': 84}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
  Time building chain proxies: 2.43, per 1000 atoms: 0.20
  Number of scatterers: 11902
  At special positions: 0
  Unit cell: (123.54, 124.392, 78.384, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     291     15.00
     O    2807      8.00
     N    2223      7.00
     C    6569      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: 0.71
  Conformation dependent library (CDL) restraints added in 297.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 7 sheets defined
      71.2% alpha, 1.8% beta
      144 base pairs and 254 stacking pairs defined.
    Time for finding SS restraints: 1.63
  Creating SS restraints...
    Processing helix  chain 'G' and resid 8 through 13
      removed outlier: 3.838A  pdb=" N   ALA G  13 " --> pdb=" O   ARG G   9 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 28
    Processing helix  chain 'G' and resid 37 through 65
      removed outlier: 3.799A  pdb=" N   ALA G  41 " --> pdb=" O   GLY G  37 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL G  42 " --> pdb=" O   ALA G  38 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU G  58 " --> pdb=" O   GLU G  54 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 72 through 83
    Processing helix  chain 'G' and resid 84 through 90
    Processing helix  chain 'C' and resid 8 through 13
      removed outlier: 3.581A  pdb=" N   ALA C  13 " --> pdb=" O   ARG C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 28
    Processing helix  chain 'C' and resid 37 through 66
      removed outlier: 3.819A  pdb=" N   ALA C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL C  42 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU C  58 " --> pdb=" O   GLU C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 83
      removed outlier: 3.513A  pdb=" N   LEU C  76 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 90
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.771A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.727A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 4.062A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.619A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.559A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
    Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 36
      removed outlier: 7.232A  pdb=" N   ARG G  35 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'G' and resid 93 through 94
      removed outlier: 6.243A  pdb=" N   THR G  93 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 35 through 36
      removed outlier: 7.002A  pdb=" N   ARG C  35 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 94
      removed outlier: 6.444A  pdb=" N   THR C  93 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.755A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119

    395 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      367 hydrogen bonds
      734 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      254 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2785
        1.34 -     1.46: 4202
        1.46 -     1.58: 5121
        1.58 -     1.70: 580
        1.70 -     1.82: 22
  Bond restraints: 12710
  Sorted by residual:
  bond pdb=" N   VAL D  69 "
       pdb=" CA  VAL D  69 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.51e+00
  bond pdb=" N   VAL H  69 "
       pdb=" CA  VAL H  69 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.40e+00
  bond pdb=" N   ASP C  83 "
       pdb=" CA  ASP C  83 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.27e-02 6.20e+03 6.32e+00
  bond pdb=" N   GLU C  84 "
       pdb=" CA  GLU C  84 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.28e-02 6.10e+03 5.57e+00
  bond pdb=" N   ASN D  67 "
       pdb=" CA  ASN D  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.56e+00
  ... (remaining 12705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 18330
        2.93 -     5.87: 82
        5.87 -     8.80: 11
        8.80 -    11.73: 4
       11.73 -    14.66: 1
  Bond angle restraints: 18428
  Sorted by residual:
  angle pdb=" CB  MET A  90 "
        pdb=" CG  MET A  90 "
        pdb=" SD  MET A  90 "
      ideal   model   delta    sigma   weight residual
     112.70  127.36  -14.66 3.00e+00 1.11e-01 2.39e+01
  angle pdb=" N   GLY C  34 "
        pdb=" CA  GLY C  34 "
        pdb=" C   GLY C  34 "
      ideal   model   delta    sigma   weight residual
     111.36  116.78   -5.42 1.17e+00 7.31e-01 2.14e+01
  angle pdb=" CA  LYS H  34 "
        pdb=" CB  LYS H  34 "
        pdb=" CG  LYS H  34 "
      ideal   model   delta    sigma   weight residual
     114.10  123.27   -9.17 2.00e+00 2.50e-01 2.10e+01
  angle pdb=" CA  GLN C  11 "
        pdb=" CB  GLN C  11 "
        pdb=" CG  GLN C  11 "
      ideal   model   delta    sigma   weight residual
     114.10  122.42   -8.32 2.00e+00 2.50e-01 1.73e+01
  angle pdb=" CB  LYS C  91 "
        pdb=" CG  LYS C  91 "
        pdb=" CD  LYS C  91 "
      ideal   model   delta    sigma   weight residual
     111.30  120.23   -8.93 2.30e+00 1.89e-01 1.51e+01
  ... (remaining 18423 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.71: 5372
       34.71 -    69.43: 1478
       69.43 -   104.14: 17
      104.14 -   138.86: 1
      138.86 -   173.57: 2
  Dihedral angle restraints: 6870
    sinusoidal: 4666
      harmonic: 2204
  Sorted by residual:
  dihedral pdb=" CA  THR C  31 "
           pdb=" C   THR C  31 "
           pdb=" N   SER C  32 "
           pdb=" CA  SER C  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" C4'  DC J   3 "
           pdb=" C3'  DC J   3 "
           pdb=" O3'  DC J   3 "
           pdb=" P    DG J   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.57 -173.57     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT I 134 "
           pdb=" C3'  DT I 134 "
           pdb=" O3'  DT I 134 "
           pdb=" P    DA I 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.93  168.07     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 6867 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1535
       0.034 -    0.069: 440
       0.069 -    0.103: 108
       0.103 -    0.137: 27
       0.137 -    0.171: 4
  Chirality restraints: 2114
  Sorted by residual:
  chirality pdb=" CA  VAL H  69 "
            pdb=" N   VAL H  69 "
            pdb=" C   VAL H  69 "
            pdb=" CB  VAL H  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" CA  VAL D  69 "
            pdb=" N   VAL D  69 "
            pdb=" C   VAL D  69 "
            pdb=" CB  VAL D  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.22e-01
  chirality pdb=" P    DA I 135 "
            pdb=" OP1  DA I 135 "
            pdb=" OP2  DA I 135 "
            pdb=" O5'  DA I 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.50   -0.15 2.00e-01 2.50e+01 5.76e-01
  ... (remaining 2111 not shown)

  Planarity restraints: 1317
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  81 "    0.263 9.50e-02 1.11e+02   1.18e-01 8.56e+00
        pdb=" NE  ARG C  81 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  81 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  81 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  81 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP G  87 "   -0.010 2.00e-02 2.50e+03   2.09e-02 4.36e+00
        pdb=" CG  ASP G  87 "    0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASP G  87 "   -0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP G  87 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 121 "   -0.028 2.00e-02 2.50e+03   1.16e-02 4.03e+00
        pdb=" N9   DG I 121 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DG I 121 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I 121 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I 121 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I 121 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I 121 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I 121 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I 121 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I 121 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I 121 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I 121 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1314 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.20: 4
        2.20 -     2.88: 3707
        2.88 -     3.55: 16699
        3.55 -     4.23: 31285
        4.23 -     4.90: 47126
  Nonbonded interactions: 98821
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG G  29 "
            pdb=" OE1 GLU H  71 "
     model   vdw
     1.528 3.120
  nonbonded pdb=" NH2 ARG B  92 "
            pdb=" CD2 LEU D 101 "
     model   vdw
     1.954 3.540
  nonbonded pdb=" CZ  ARG G  29 "
            pdb=" OE1 GLU H  71 "
     model   vdw
     1.976 3.270
  nonbonded pdb=" NH2 ARG G  29 "
            pdb=" OE1 GLU H  71 "
     model   vdw
     2.055 3.120
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.208 3.040
  ... (remaining 98816 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and (resid 6 through 66 or (resid 67 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 68 through 108))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 59 through 124))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.760
  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:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.930
  Find NCS groups from input model:        0.090
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
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   0.052  12710  Z= 0.191
  Angle     :  0.681  14.663  18428  Z= 0.401
  Chirality :  0.036   0.171   2114
  Planarity :  0.006   0.118   1317
  Dihedral  : 28.562 173.573   5446
  Min Nonbonded Distance : 1.528

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.48 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.30), residues: 744
  helix:  2.07 (0.22), residues: 529
  sheet:  None (None), residues: 0
  loop : -2.14 (0.34), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  79 
 TYR   0.029   0.002   TYR D  83 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12710)
  covalent geometry    : angle       0.68128 (18428)
  hydrogen bonds       : bond        0.10874 (  762)
  hydrogen bonds       : angle       3.34017 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C   69 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7608 (tttt)
REVERT: D   68 ASP cc_start: 0.9168 (t0) cc_final: 0.8951 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1389
  time to fit residues: 23.7420
Evaluate side-chains
  115 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.053958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.039887 restraints weight = 50826.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.03
r_work: 0.2679 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.0956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12710  Z= 0.155
  Angle     :  0.542   4.749  18428  Z= 0.330
  Chirality :  0.032   0.131   2114
  Planarity :  0.004   0.043   1317
  Dihedral  : 30.763 173.724   4024
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.21 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.31), residues: 744
  helix:  2.75 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -2.06 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.017   0.001   TYR D  83 
 PHE   0.007   0.001   PHE H  70 
 HIS   0.002   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12710)
  covalent geometry    : angle       0.54164 (18428)
  hydrogen bonds       : bond        0.04277 (  762)
  hydrogen bonds       : angle       2.64169 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.337 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9579 (OUTLIER) cc_final: 0.9256 (mp)
REVERT: C   11 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8556 (tm-30)
REVERT: C   69 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8084 (tttm)
REVERT: C   85 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8132 (mt-10)
  outliers start: 12
  outliers final: 4
  residues processed: 136
  average time/residue: 0.1311
  time to fit residues: 23.4905
Evaluate side-chains
  130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue   85 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.051911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.037607 restraints weight = 50894.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 1.97
r_work: 0.2598 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  12710  Z= 0.248
  Angle     :  0.575   5.040  18428  Z= 0.349
  Chirality :  0.036   0.168   2114
  Planarity :  0.004   0.040   1317
  Dihedral  : 30.993 174.372   4024
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.18 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.32), residues: 744
  helix:  2.88 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -2.18 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  35 
 TYR   0.033   0.002   TYR D  83 
 PHE   0.009   0.001   PHE B  61 
 HIS   0.003   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 (12710)
  covalent geometry    : angle       0.57494 (18428)
  hydrogen bonds       : bond        0.05663 (  762)
  hydrogen bonds       : angle       2.89307 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.338 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9601 (OUTLIER) cc_final: 0.9259 (mp)
REVERT: C   11 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8561 (tm-30)
REVERT: C   69 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8031 (tttm)
REVERT: E  115 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8931 (mtmm)
REVERT: F   79 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8772 (tppt)
  outliers start: 15
  outliers final: 7
  residues processed: 127
  average time/residue: 0.1399
  time to fit residues: 23.2284
Evaluate side-chains
  123 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0980
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.052574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.038542 restraints weight = 51410.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 1.93
r_work: 0.2622 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12710  Z= 0.185
  Angle     :  0.546   6.449  18428  Z= 0.332
  Chirality :  0.033   0.132   2114
  Planarity :  0.004   0.039   1317
  Dihedral  : 30.809 174.420   4024
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.21 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.32), residues: 744
  helix:  2.94 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.11 (0.37), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  29 
 TYR   0.034   0.001   TYR D  83 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (12710)
  covalent geometry    : angle       0.54647 (18428)
  hydrogen bonds       : bond        0.04738 (  762)
  hydrogen bonds       : angle       2.67208 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.305 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9622 (OUTLIER) cc_final: 0.9297 (mp)
REVERT: C   11 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8555 (tm-30)
REVERT: C   33 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8354 (m170)
REVERT: C   69 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8085 (tttm)
REVERT: C   83 ASP cc_start: 0.8036 (t0) cc_final: 0.7703 (t0)
REVERT: D   79 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8684 (ttp80)
REVERT: F   79 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8855 (tppt)
REVERT: H   76 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8653 (mm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 133
  average time/residue: 0.1416
  time to fit residues: 24.9277
Evaluate side-chains
  129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue   33 HIS
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.052667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.038534 restraints weight = 51059.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 1.93
r_work: 0.2622 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12710  Z= 0.184
  Angle     :  0.544   5.685  18428  Z= 0.332
  Chirality :  0.033   0.129   2114
  Planarity :  0.004   0.037   1317
  Dihedral  : 30.806 174.468   4024
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.50 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.32), residues: 744
  helix:  2.95 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -2.08 (0.37), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  35 
 TYR   0.030   0.001   TYR D  83 
 PHE   0.007   0.001   PHE B  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (12710)
  covalent geometry    : angle       0.54420 (18428)
  hydrogen bonds       : bond        0.04751 (  762)
  hydrogen bonds       : angle       2.66205 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: G   47 ILE cc_start: 0.9624 (OUTLIER) cc_final: 0.9300 (mp)
REVERT: C   11 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: C   33 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8403 (m170)
REVERT: C   69 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8079 (tttm)
REVERT: C   83 ASP cc_start: 0.8009 (t0) cc_final: 0.7654 (t0)
REVERT: C   87 ASP cc_start: 0.8674 (t0) cc_final: 0.8363 (t0)
REVERT: C   91 LYS cc_start: 0.9388 (mmmt) cc_final: 0.9100 (mmtm)
REVERT: A   50 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8398 (mt-10)
REVERT: E  115 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8744 (mtmm)
REVERT: F   79 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8848 (tppt)
  outliers start: 15
  outliers final: 8
  residues processed: 132
  average time/residue: 0.1419
  time to fit residues: 24.9809
Evaluate side-chains
  129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue   33 HIS
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.0170
   chunk 17 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.054343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.040450 restraints weight = 51094.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 1.93
r_work: 0.2690 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12710  Z= 0.147
  Angle     :  0.531   8.129  18428  Z= 0.322
  Chirality :  0.032   0.151   2114
  Planarity :  0.004   0.037   1317
  Dihedral  : 30.558 175.118   4024
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 18.96 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.79 (0.32), residues: 744
  helix:  3.07 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.91 (0.38), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.017   0.001   TYR D  83 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (12710)
  covalent geometry    : angle       0.53053 (18428)
  hydrogen bonds       : bond        0.03837 (  762)
  hydrogen bonds       : angle       2.44995 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.249 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9284 (mp)
REVERT: C   11 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: C   33 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8318 (m170)
REVERT: C   69 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7979 (tttm)
REVERT: A   50 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8353 (mt-10)
REVERT: D   86 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8341 (tpp80)
REVERT: F   79 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8818 (tppt)
REVERT: H   76 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8656 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 136
  average time/residue: 0.1387
  time to fit residues: 25.0052
Evaluate side-chains
  131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue   33 HIS
Chi-restraints excluded: chain C residue   84 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   79 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0980
   chunk 42 optimal weight:    0.0770
   chunk 10 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.2142

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.054066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.039994 restraints weight = 51003.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 1.93
r_work: 0.2670 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12710  Z= 0.161
  Angle     :  0.543   6.795  18428  Z= 0.328
  Chirality :  0.032   0.172   2114
  Planarity :  0.004   0.035   1317
  Dihedral  : 30.607 175.082   4024
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.12 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.31), residues: 744
  helix:  3.08 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.90 (0.38), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.019   0.001   TYR D  83 
 PHE   0.006   0.001   PHE F  61 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12710)
  covalent geometry    : angle       0.54260 (18428)
  hydrogen bonds       : bond        0.04157 (  762)
  hydrogen bonds       : angle       2.50339 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: G   47 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9300 (mp)
REVERT: C   11 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: C   33 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8338 (m170)
REVERT: C   69 LYS cc_start: 0.8349 (ttmm) cc_final: 0.7982 (tttm)
REVERT: A   50 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8380 (mt-10)
REVERT: A   59 GLU cc_start: 0.7637 (pm20) cc_final: 0.7433 (pm20)
REVERT: D   86 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8324 (tpp80)
REVERT: F   79 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8868 (tppt)
  outliers start: 10
  outliers final: 6
  residues processed: 133
  average time/residue: 0.1424
  time to fit residues: 24.9825
Evaluate side-chains
  132 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue   33 HIS
Chi-restraints excluded: chain C residue   84 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   79 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 42 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0980
   chunk 58 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.053704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.039668 restraints weight = 50450.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 1.90
r_work: 0.2656 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8847
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12710  Z= 0.168
  Angle     :  0.548   7.201  18428  Z= 0.331
  Chirality :  0.033   0.160   2114
  Planarity :  0.004   0.035   1317
  Dihedral  : 30.627 175.227   4024
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.12 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.84 (0.31), residues: 744
  helix:  3.10 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.90 (0.38), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.035   0.002   TYR D  83 
 PHE   0.007   0.001   PHE B  61 
 HIS   0.002   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12710)
  covalent geometry    : angle       0.54836 (18428)
  hydrogen bonds       : bond        0.04385 (  762)
  hydrogen bonds       : angle       2.54669 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.410 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9614 (OUTLIER) cc_final: 0.9308 (mp)
REVERT: C   11 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: C   33 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8311 (m170)
REVERT: C   69 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8003 (tttm)
REVERT: C   83 ASP cc_start: 0.8034 (t0) cc_final: 0.7630 (t0)
REVERT: A   50 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8338 (mt-10)
REVERT: F   79 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8864 (tppt)
  outliers start: 11
  outliers final: 7
  residues processed: 133
  average time/residue: 0.1410
  time to fit residues: 24.7881
Evaluate side-chains
  131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue   33 HIS
Chi-restraints excluded: chain C residue   84 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   79 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.053126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.039126 restraints weight = 50664.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 1.92
r_work: 0.2650 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12710  Z= 0.192
  Angle     :  0.564   7.658  18428  Z= 0.339
  Chirality :  0.033   0.154   2114
  Planarity :  0.004   0.035   1317
  Dihedral  : 30.725 174.941   4024
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.80 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.32), residues: 744
  helix:  3.06 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.98 (0.37), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  92 
 TYR   0.044   0.002   TYR D  83 
 PHE   0.008   0.001   PHE B  61 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (12710)
  covalent geometry    : angle       0.56435 (18428)
  hydrogen bonds       : bond        0.04835 (  762)
  hydrogen bonds       : angle       2.64840 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: G   47 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9274 (mp)
REVERT: C   11 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: C   33 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8409 (m170)
REVERT: C   69 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8051 (tttm)
REVERT: A   50 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8368 (mt-10)
REVERT: F   79 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8903 (tppt)
REVERT: H   76 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8689 (mm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 131
  average time/residue: 0.1427
  time to fit residues: 24.9280
Evaluate side-chains
  130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain C residue   33 HIS
Chi-restraints excluded: chain C residue   84 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.054156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.040000 restraints weight = 50511.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 1.92
r_work: 0.2673 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12710  Z= 0.163
  Angle     :  0.553   8.246  18428  Z= 0.332
  Chirality :  0.032   0.145   2114
  Planarity :  0.004   0.035   1317
  Dihedral  : 30.589 175.175   4024
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.12 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.88 (0.32), residues: 744
  helix:  3.12 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.84 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  92 
 TYR   0.030   0.001   TYR D  83 
 PHE   0.006   0.001   PHE B  61 
 HIS   0.002   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12710)
  covalent geometry    : angle       0.55313 (18428)
  hydrogen bonds       : bond        0.04238 (  762)
  hydrogen bonds       : angle       2.50483 ( 1907)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: G   47 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9298 (mp)
REVERT: G   57 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8779 (tt0)
REVERT: C   11 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: C   33 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8401 (m170)
REVERT: C   69 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8000 (tttm)
REVERT: A   50 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8350 (mt-10)
REVERT: F   79 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8788 (tppt)
REVERT: H   76 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8675 (mm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 130
  average time/residue: 0.1357
  time to fit residues: 23.4082
Evaluate side-chains
  133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain C residue   33 HIS
Chi-restraints excluded: chain C residue   84 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   79 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 71 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.051202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.037058 restraints weight = 50956.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 1.91
r_work: 0.2570 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8955
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  12710  Z= 0.328
  Angle     :  0.654   7.831  18428  Z= 0.387
  Chirality :  0.039   0.148   2114
  Planarity :  0.004   0.034   1317
  Dihedral  : 31.141 173.806   4024
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.29 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.32), residues: 744
  helix:  2.77 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -2.21 (0.38), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  79 
 TYR   0.053   0.002   TYR D  83 
 PHE   0.009   0.001   PHE B  61 
 HIS   0.005   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00745 (12710)
  covalent geometry    : angle       0.65389 (18428)
  hydrogen bonds       : bond        0.06493 (  762)
  hydrogen bonds       : angle       3.09667 ( 1907)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2318.06 seconds
wall clock time: 40 minutes 31.41 seconds (2431.41 seconds total)