Starting phenix.real_space_refine
on Tue Jul 29 20:30:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8thu_41272/07_2025/8thu_41272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8thu_41272/07_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_41272/07_2025/8thu_41272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8thu_41272/07_2025/8thu_41272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8thu_41272/07_2025/8thu_41272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8thu_41272/07_2025/8thu_41272.cif"
  }
  resolution = 3.1
  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=   0.004 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ARG:plan': 2, 'HIS:plan': 1}
          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: {'ARG:plan': 2, 'HIS:plan': 1}
          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: 7.40, per 1000 atoms: 0.62
  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: 2.93
  Conformation dependent library (CDL) restraints added in 961.5 milliseconds
  

  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: 5.87
  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: 4.18

  Time building geometry restraints manager: 3.26 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:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     32.540
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.050
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.810
-------------------------------------------------------------------------------
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 (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:  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
 HIS   0.004   0.001   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.029   0.002   TYR D  83 
 ARG   0.010   0.000   ARG D  79 

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

*********************** 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  : 0.868 
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: 0.3530
  time to fit residues: 60.5288
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  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   overall best weight:    1.7588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.052544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.038756 restraints weight = 50805.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 1.91
r_work: 0.2645 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.0815

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= 0.186
  Angle     :  0.559   5.205  18428  Z= 0.339
  Chirality :  0.033   0.129   2114
  Planarity :  0.004   0.042   1317
  Dihedral  : 30.928 173.146   4024
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.69 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.26 (0.31), residues: 744
  helix:  2.73 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.19 (0.36), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.020   0.001   TYR D  83 
 ARG   0.004   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05002 (  762)
  hydrogen bonds       : angle       2.76507 ( 1907)
  covalent geometry    : bond        0.00407 (12710)
  covalent geometry    : angle       0.55861 (18428)

*********************** 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
  139 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.797 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9626 (OUTLIER) cc_final: 0.9303 (mp)
REVERT: C   11 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: C   69 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8079 (tttm)
REVERT: C   83 ASP cc_start: 0.7820 (t0) cc_final: 0.7470 (t0)
REVERT: C   85 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8112 (mt-10)
REVERT: E  115 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8867 (mtmm)
REVERT: H   34 LYS cc_start: 0.8938 (mmpt) cc_final: 0.8639 (mmpt)
REVERT: H   71 GLU cc_start: 0.8880 (tp30) cc_final: 0.8660 (mm-30)
  outliers start: 14
  outliers final: 5
  residues processed: 133
  average time/residue: 0.3151
  time to fit residues: 55.2656
Evaluate side-chains
  127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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 E residue  115 LYS
Chi-restraints excluded: chain H residue  122 THR
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 4 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3207 r_free = 0.3207 target = 0.051125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.036860 restraints weight = 50155.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2722 rms_B_bonded: 1.90
r_work: 0.2580 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.1395

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= 0.290
  Angle     :  0.604   5.340  18428  Z= 0.365
  Chirality :  0.037   0.139   2114
  Planarity :  0.005   0.040   1317
  Dihedral  : 31.188 173.582   4024
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.86 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.28 (0.32), residues: 744
  helix:  2.79 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -2.37 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  49 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.035   0.002   TYR D  83 
 ARG   0.003   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06310 (  762)
  hydrogen bonds       : angle       3.05696 ( 1907)
  covalent geometry    : bond        0.00657 (12710)
  covalent geometry    : angle       0.60438 (18428)

*********************** 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
  135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.830 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9260 (mp)
REVERT: C   11 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8520 (tm-30)
REVERT: C   69 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8071 (tttt)
REVERT: E  115 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8945 (mtmm)
REVERT: H   34 LYS cc_start: 0.9015 (mmpt) cc_final: 0.8685 (mmpt)
REVERT: H   76 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8655 (mm-30)
  outliers start: 18
  outliers final: 10
  residues processed: 130
  average time/residue: 0.3221
  time to fit residues: 54.7651
Evaluate side-chains
  124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
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   37 LEU
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   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   66 ILE
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 65 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 52 optimal weight:    0.8980
   chunk 93 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3258 r_free = 0.3258 target = 0.053298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.039301 restraints weight = 50558.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 1.87
r_work: 0.2649 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.1248

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= 0.158
  Angle     :  0.537   6.662  18428  Z= 0.327
  Chirality :  0.032   0.132   2114
  Planarity :  0.004   0.040   1317
  Dihedral  : 30.705 174.453   4024
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.83 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.59 (0.32), residues: 744
  helix:  2.97 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.14 (0.37), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.023   0.001   TYR D  83 
 ARG   0.003   0.000   ARG C  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  762)
  hydrogen bonds       : angle       2.54797 ( 1907)
  covalent geometry    : bond        0.00337 (12710)
  covalent geometry    : angle       0.53692 (18428)

*********************** 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
  141 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.830 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9608 (OUTLIER) cc_final: 0.9303 (mp)
REVERT: C   11 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8520 (tm-30)
REVERT: C   33 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.8373 (m170)
REVERT: C   69 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8015 (tttm)
REVERT: C   83 ASP cc_start: 0.7910 (t0) cc_final: 0.7613 (t0)
REVERT: C   87 ASP cc_start: 0.8685 (t0) cc_final: 0.8361 (t0)
REVERT: C   91 LYS cc_start: 0.9372 (mmmt) cc_final: 0.9069 (mmtm)
REVERT: A   50 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8331 (mt-10)
REVERT: H   34 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8810 (mmtt)
  outliers start: 14
  outliers final: 5
  residues processed: 136
  average time/residue: 0.3062
  time to fit residues: 55.0258
Evaluate side-chains
  126 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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   49 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.3248 r_free = 0.3248 target = 0.052865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.038809 restraints weight = 50890.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 1.93
r_work: 0.2626 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.1323

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= 0.183
  Angle     :  0.548   8.566  18428  Z= 0.332
  Chirality :  0.033   0.130   2114
  Planarity :  0.004   0.038   1317
  Dihedral  : 30.775 174.264   4024
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.31 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.62 (0.32), residues: 744
  helix:  2.98 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -2.12 (0.37), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.011   0.001   TYR D  83 
 ARG   0.006   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  762)
  hydrogen bonds       : angle       2.61427 ( 1907)
  covalent geometry    : bond        0.00401 (12710)
  covalent geometry    : angle       0.54808 (18428)

*********************** 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
  135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.922 
Fit side-chains
REVERT: G   29 ARG cc_start: 0.8941 (tpp80) cc_final: 0.8660 (tpp80)
REVERT: G   47 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9311 (mp)
REVERT: C   11 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8373 (tm-30)
REVERT: C   33 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (m170)
REVERT: C   69 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8051 (tttm)
REVERT: C   83 ASP cc_start: 0.7937 (t0) cc_final: 0.7596 (t0)
REVERT: C   87 ASP cc_start: 0.8667 (t0) cc_final: 0.8359 (t0)
REVERT: C   91 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9099 (mmtm)
REVERT: D   79 ARG cc_start: 0.8898 (ttp-110) cc_final: 0.8690 (ttp80)
REVERT: D   86 ARG cc_start: 0.8762 (tpp80) cc_final: 0.8486 (tpp80)
REVERT: H   34 LYS cc_start: 0.9124 (mmpt) cc_final: 0.8894 (mmtt)
  outliers start: 12
  outliers final: 6
  residues processed: 131
  average time/residue: 0.3901
  time to fit residues: 67.7624
Evaluate side-chains
  127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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 H residue  123 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0000
   chunk 52 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0970
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.5382

-------------------------------------------------------------------------------
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**
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.054892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.041006 restraints weight = 51808.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 1.91
r_work: 0.2710 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.1653

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= 0.141
  Angle     :  0.521   6.318  18428  Z= 0.318
  Chirality :  0.032   0.130   2114
  Planarity :  0.004   0.037   1317
  Dihedral  : 30.514 175.240   4024
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.29 %
    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 (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:  2.78 (0.31), residues: 744
  helix:  3.05 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.91 (0.38), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS E 113 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.007   0.001   TYR H  40 
 ARG   0.005   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  762)
  hydrogen bonds       : angle       2.39594 ( 1907)
  covalent geometry    : bond        0.00295 (12710)
  covalent geometry    : angle       0.52112 (18428)

*********************** 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
  142 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.905 
Fit side-chains
REVERT: G   29 ARG cc_start: 0.8830 (tpp80) cc_final: 0.8608 (tpp80)
REVERT: G   47 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9280 (mp)
REVERT: C   11 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: C   33 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8279 (m170)
REVERT: C   69 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8037 (tttm)
REVERT: A   50 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8351 (mt-10)
  outliers start: 10
  outliers final: 6
  residues processed: 137
  average time/residue: 0.4729
  time to fit residues: 85.9259
Evaluate side-chains
  128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
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 B residue   43 VAL
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 40 optimal weight:    0.2980
   chunk 78 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    2.6588

-------------------------------------------------------------------------------
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 = 0.3244 r_free = 0.3244 target = 0.052377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.038312 restraints weight = 51177.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 1.92
r_work: 0.2620 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12710  Z= 0.235
  Angle     :  0.586   7.174  18428  Z= 0.351
  Chirality :  0.035   0.201   2114
  Planarity :  0.004   0.035   1317
  Dihedral  : 30.864 174.548   4024
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.48 %
    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 (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:  2.63 (0.32), residues: 744
  helix:  2.97 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -2.05 (0.37), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.016   0.002   TYR D 121 
 ARG   0.005   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05410 (  762)
  hydrogen bonds       : angle       2.81334 ( 1907)
  covalent geometry    : bond        0.00526 (12710)
  covalent geometry    : angle       0.58605 (18428)

*********************** 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
  133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.986 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9278 (mp)
REVERT: C   11 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: C   29 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7753 (mmm-85)
REVERT: C   33 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8454 (m170)
REVERT: C   69 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8031 (tttm)
REVERT: D   71 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8679 (mm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 129
  average time/residue: 0.3200
  time to fit residues: 55.4974
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  : 1.033 
-------------------------------------------------------------------------------
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 E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0570
   chunk 75 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    2.8106

-------------------------------------------------------------------------------
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 = 0.3234 r_free = 0.3234 target = 0.052047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.037990 restraints weight = 51215.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 1.92
r_work: 0.2608 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12710  Z= 0.241
  Angle     :  0.593   7.173  18428  Z= 0.355
  Chirality :  0.035   0.165   2114
  Planarity :  0.004   0.036   1317
  Dihedral  : 30.909 174.173   4024
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.77 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.52 (0.32), residues: 744
  helix:  2.90 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.06 (0.37), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  49 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.014   0.001   TYR D 121 
 ARG   0.005   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05408 (  762)
  hydrogen bonds       : angle       2.82634 ( 1907)
  covalent geometry    : bond        0.00540 (12710)
  covalent geometry    : angle       0.59309 (18428)

*********************** 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
  127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.982 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9626 (OUTLIER) cc_final: 0.9280 (mp)
REVERT: C   11 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8361 (tm-30)
REVERT: C   29 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7834 (mmm-85)
REVERT: C   33 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8463 (m170)
REVERT: C   69 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8096 (tttm)
REVERT: D   71 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8722 (mm-30)
REVERT: D  105 GLU cc_start: 0.8136 (pm20) cc_final: 0.7791 (pm20)
REVERT: H   71 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8726 (mm-30)
REVERT: H   76 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8742 (mm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 124
  average time/residue: 0.3162
  time to fit residues: 52.7399
Evaluate side-chains
  122 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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 E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3264 r_free = 0.3264 target = 0.053138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.039223 restraints weight = 50739.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 1.92
r_work: 0.2654 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.1550

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= 0.178
  Angle     :  0.562   6.636  18428  Z= 0.339
  Chirality :  0.033   0.159   2114
  Planarity :  0.004   0.036   1317
  Dihedral  : 30.725 174.300   4024
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 19.77 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.71 (0.32), residues: 744
  helix:  3.04 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.94 (0.38), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 109 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.013   0.001   TYR D 121 
 ARG   0.004   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04524 (  762)
  hydrogen bonds       : angle       2.61964 ( 1907)
  covalent geometry    : bond        0.00389 (12710)
  covalent geometry    : angle       0.56176 (18428)

*********************** 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
  126 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.840 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9299 (mp)
REVERT: C   11 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8362 (tm-30)
REVERT: C   29 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7747 (mmm-85)
REVERT: C   33 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.8462 (m170)
REVERT: C   69 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8021 (tttm)
REVERT: A   50 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: D   71 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8706 (mm-30)
REVERT: H   76 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8646 (mm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 123
  average time/residue: 0.2917
  time to fit residues: 48.3955
Evaluate side-chains
  124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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 E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 82 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0270
   chunk 54 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.9042

-------------------------------------------------------------------------------
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 = 0.3280 r_free = 0.3280 target = 0.054120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.040082 restraints weight = 50906.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 1.94
r_work: 0.2673 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12710  Z= 0.152
  Angle     :  0.556   8.204  18428  Z= 0.334
  Chirality :  0.032   0.147   2114
  Planarity :  0.004   0.036   1317
  Dihedral  : 30.588 174.824   4024
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.61 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.82 (0.32), residues: 744
  helix:  3.08 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.77 (0.39), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.006   0.001   PHE F  61 
 TYR   0.016   0.001   TYR D 121 
 ARG   0.004   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  762)
  hydrogen bonds       : angle       2.49029 ( 1907)
  covalent geometry    : bond        0.00325 (12710)
  covalent geometry    : angle       0.55650 (18428)

********************** 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
  132 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 1.859 
Fit side-chains
REVERT: G   47 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9307 (mp)
REVERT: C   11 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8378 (tm-30)
REVERT: C   33 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8346 (m170)
REVERT: C   69 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8025 (tttm)
REVERT: A   50 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8402 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 129
  average time/residue: 0.3835
  time to fit residues: 66.0733
Evaluate side-chains
  130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
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 E residue   76 GLN
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 95 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    8.9990
   chunk 82 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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 = 0.3202 r_free = 0.3202 target = 0.050900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.036681 restraints weight = 50751.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.2706 rms_B_bonded: 1.93
r_work: 0.2557 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8966
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.042  12710  Z= 0.367
  Angle     :  0.673   7.781  18428  Z= 0.397
  Chirality :  0.040   0.150   2114
  Planarity :  0.004   0.034   1317
  Dihedral  : 31.200 173.427   4024
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  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 (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:  2.29 (0.32), residues: 744
  helix:  2.73 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.14 (0.38), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  49 
 PHE   0.011   0.001   PHE D  65 
 TYR   0.019   0.002   TYR D 121 
 ARG   0.006   0.001   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06786 (  762)
  hydrogen bonds       : angle       3.19145 ( 1907)
  covalent geometry    : bond        0.00836 (12710)
  covalent geometry    : angle       0.67289 (18428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5166.94 seconds
wall clock time: 93 minutes 10.31 seconds (5590.31 seconds total)