Starting phenix.real_space_refine
on Sat Nov 16 12:09:48 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua7_42053/11_2024/8ua7_42053.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua7_42053/11_2024/8ua7_42053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua7_42053/11_2024/8ua7_42053.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua7_42053/11_2024/8ua7_42053.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua7_42053/11_2024/8ua7_42053.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ua7_42053/11_2024/8ua7_42053.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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     259      5.49       5
     S      22      5.16       5
     C    6251      2.51       5
     N    2081      2.21       5
     O    2650      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 11263
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 826
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 1, 'TRANS': 107}
    Chain: "B"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 633
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 2, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 754
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "D"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 755
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 3, 'TRANS': 97}
    Chain: "E"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 826
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 1, 'TRANS': 107}
    Chain: "F"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 633
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 2, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 754
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "H"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 755
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 3, 'TRANS': 97}
    Chain: "I"
      Number of atoms: 2676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 2676
          Classifications: {'DNA': 130}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 129}
    Chain: "J"
      Number of atoms: 2651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 2651
          Classifications: {'DNA': 130}
          Link IDs: {'rna3p': 129}
  Time building chain proxies: 7.14, per 1000 atoms: 0.63
  Number of scatterers: 11263
  At special positions: 0
  Unit cell: (88.27, 117.37, 129.01, 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      22     16.00
     P     259     15.00
     O    2650      8.00
     N    2081      7.00
     C    6251      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: 3.04
  Conformation dependent library (CDL) restraints added in 824.6 milliseconds
  

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      66.2% alpha, 0.0% beta
      89 base pairs and 214 stacking pairs defined.
    Time for finding SS restraints: 4.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 59
      removed outlier: 3.522A  pdb=" N   LYS A  53 " --> pdb=" O   ARG A  49 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLN A  55 " --> pdb=" O   SER A  51 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   LYS A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 78
      removed outlier: 4.551A  pdb=" N   ILE A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   THR A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 3.552A  pdb=" N   GLN A  97 " --> pdb=" O   ASP A  93 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY A  98 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LEU A 101 " --> pdb=" O   GLN A  97 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A 117 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 134
      removed outlier: 4.009A  pdb=" N   ILE A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU A 129 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
      removed outlier: 3.562A  pdb=" N   ALA A 143 " --> pdb=" O   ASP A 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 33
      removed outlier: 3.516A  pdb=" N   VAL B  26 " --> pdb=" O   GLY B  22 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   THR B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 69
      removed outlier: 3.735A  pdb=" N   LYS B  46 " --> pdb=" O   THR B  42 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS B  48 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   LYS B  49 " --> pdb=" O   PRO B  45 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   SER B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ILE B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ALA B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER B  69 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 86
    Processing helix  chain 'C' and resid 62 through 67
    Processing helix  chain 'C' and resid 72 through 81
      removed outlier: 3.608A  pdb=" N   ILE C  76 " --> pdb=" O   PRO C  72 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE C  79 " --> pdb=" O   ARG C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 119
      removed outlier: 4.233A  pdb=" N   VAL C  97 " --> pdb=" O   PRO C  93 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   PHE C  98 " --> pdb=" O   THR C  94 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU C  99 " --> pdb=" O   ALA C  95 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU C 119 " --> pdb=" O   ASP C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 133
      removed outlier: 3.637A  pdb=" N   LYS C 133 " --> pdb=" O   GLN C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 145
      removed outlier: 4.129A  pdb=" N   ILE C 145 " --> pdb=" O   ALA C 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 77
    Processing helix  chain 'D' and resid 92 through 122
      removed outlier: 3.932A  pdb=" N   MET D  96 " --> pdb=" O   SER D  92 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLU D  97 " --> pdb=" O   ALA D  93 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL D  98 " --> pdb=" O   LYS D  94 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   VAL D 103 " --> pdb=" O   LEU D  99 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   THR D 111 " --> pdb=" O   ALA D 107 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU D 117 " --> pdb=" O   VAL D 113 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA D 118 " --> pdb=" O   ALA D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 141
      removed outlier: 4.146A  pdb=" N   THR D 133 " --> pdb=" O   GLY D 129 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ALA D 134 " --> pdb=" O   ASP D 130 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL D 137 " --> pdb=" O   THR D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 166
      removed outlier: 4.143A  pdb=" N   ALA D 151 " --> pdb=" O   ALA D 147 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   LEU D 152 " --> pdb=" O   THR D 148 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER D 166 " --> pdb=" O   LYS D 162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 57
      removed outlier: 3.616A  pdb=" N   LYS E  56 " --> pdb=" O   LYS E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 78
      removed outlier: 3.529A  pdb=" N   SER E  78 " --> pdb=" O   ARG E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 117
      removed outlier: 3.551A  pdb=" N   LEU E  94 " --> pdb=" O   ASN E  90 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU E 101 " --> pdb=" O   GLN E  97 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASP E 105 " --> pdb=" O   LEU E 101 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU E 106 " --> pdb=" O   TYR E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 134
      removed outlier: 4.150A  pdb=" N   ILE E 127 " --> pdb=" O   MET E 123 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP E 128 " --> pdb=" O   GLY E 124 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU E 129 " --> pdb=" O   LYS E 125 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE E 130 " --> pdb=" O   ASP E 126 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 148
      removed outlier: 3.538A  pdb=" N   ALA E 143 " --> pdb=" O   ASP E 139 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 22 through 32
      removed outlier: 3.837A  pdb=" N   VAL F  26 " --> pdb=" O   GLY F  22 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ARG F  27 " --> pdb=" O   ASN F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 42 through 69
      removed outlier: 3.984A  pdb=" N   LYS F  46 " --> pdb=" O   THR F  42 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU F  57 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA F  62 " --> pdb=" O   ALA F  58 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER F  69 " --> pdb=" O   ALA F  65 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 86
    Processing helix  chain 'G' and resid 62 through 67
      removed outlier: 3.983A  pdb=" N   ALA G  67 " --> pdb=" O   ALA G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 72 through 83
      removed outlier: 3.907A  pdb=" N   ILE G  76 " --> pdb=" O   PRO G  72 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE G  79 " --> pdb=" O   ARG G  75 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASN G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 121
      removed outlier: 4.204A  pdb=" N   VAL G  97 " --> pdb=" O   PRO G  93 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE G  98 " --> pdb=" O   THR G  94 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS G 116 " --> pdb=" O   LYS G 112 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LYS G 117 " --> pdb=" O   GLY G 113 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU G 119 " --> pdb=" O   ASP G 115 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU G 120 " --> pdb=" O   LYS G 116 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG G 121 " --> pdb=" O   LYS G 117 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 127 through 133
    Processing helix  chain 'G' and resid 140 through 145
      removed outlier: 4.245A  pdb=" N   ILE G 145 " --> pdb=" O   ALA G 141 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 72 through 78
      removed outlier: 3.677A  pdb=" N   ALA H  77 " --> pdb=" O   ALA H  73 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 95 through 121
      removed outlier: 4.012A  pdb=" N   VAL H 103 " --> pdb=" O   LEU H  99 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LYS H 104 " --> pdb=" O   GLU H 100 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL H 113 " --> pdb=" O   GLU H 109 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   HIS H 120 " --> pdb=" O   GLU H 116 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   GLN H 121 " --> pdb=" O   LEU H 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 129 through 141
    Processing helix  chain 'H' and resid 145 through 166
      removed outlier: 3.908A  pdb=" N   VAL H 149 " --> pdb=" O   GLU H 145 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU H 152 " --> pdb=" O   THR H 148 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   SER H 166 " --> pdb=" O   LYS H 162 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      235 hydrogen bonds
      462 hydrogen bond angles
      0 basepair planarities
      89 basepair parallelities
      214 stacking parallelities
  Total time for adding SS restraints: 3.86

  Time building geometry restraints manager: 3.48 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1902
        1.33 -     1.45: 4030
        1.45 -     1.57: 5478
        1.57 -     1.70: 517
        1.70 -     1.82: 44
  Bond restraints: 11971
  Sorted by residual:
  bond pdb=" C   LYS E 145 "
       pdb=" O   LYS E 145 "
    ideal  model  delta    sigma   weight residual
    1.236  1.312 -0.075 1.24e-02 6.50e+03 3.70e+01
  bond pdb=" N   LYS E 145 "
       pdb=" CA  LYS E 145 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.040 1.27e-02 6.20e+03 9.92e+00
  bond pdb=" N   LEU D 117 "
       pdb=" CA  LEU D 117 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.28e-02 6.10e+03 8.99e+00
  bond pdb=" N   ILE B  14 "
       pdb=" CA  ILE B  14 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.80e+00
  bond pdb=" N   THR C 136 "
       pdb=" CA  THR C 136 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.21e-02 6.83e+03 8.16e+00
  ... (remaining 11966 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 17055
        2.47 -     4.94: 176
        4.94 -     7.41: 16
        7.41 -     9.87: 2
        9.87 -    12.34: 1
  Bond angle restraints: 17250
  Sorted by residual:
  angle pdb=" N   ASN B  16 "
        pdb=" CA  ASN B  16 "
        pdb=" C   ASN B  16 "
      ideal   model   delta    sigma   weight residual
     110.35   98.01   12.34 1.36e+00 5.41e-01 8.24e+01
  angle pdb=" N   ASP A 126 "
        pdb=" CA  ASP A 126 "
        pdb=" C   ASP A 126 "
      ideal   model   delta    sigma   weight residual
     112.90  107.33    5.57 1.31e+00 5.83e-01 1.81e+01
  angle pdb=" N   SER C 152 "
        pdb=" CA  SER C 152 "
        pdb=" C   SER C 152 "
      ideal   model   delta    sigma   weight residual
     107.73  112.51   -4.78 1.34e+00 5.57e-01 1.27e+01
  angle pdb=" C   ALA E 144 "
        pdb=" N   LYS E 145 "
        pdb=" CA  LYS E 145 "
      ideal   model   delta    sigma   weight residual
     120.38  115.37    5.01 1.46e+00 4.69e-01 1.18e+01
  angle pdb=" CA  GLY C 154 "
        pdb=" C   GLY C 154 "
        pdb=" O   GLY C 154 "
      ideal   model   delta    sigma   weight residual
     121.63  117.97    3.66 1.07e+00 8.73e-01 1.17e+01
  ... (remaining 17245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.21: 5225
       34.21 -    68.43: 1299
       68.43 -   102.64: 31
      102.64 -   136.85: 1
      136.85 -   171.06: 5
  Dihedral angle restraints: 6561
    sinusoidal: 4335
      harmonic: 2226
  Sorted by residual:
  dihedral pdb=" CD  ARG G  75 "
           pdb=" NE  ARG G  75 "
           pdb=" CZ  ARG G  75 "
           pdb=" NH1 ARG G  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   63.64  -63.64     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CA  GLY A  70 "
           pdb=" C   GLY A  70 "
           pdb=" N   ARG A  71 "
           pdb=" CA  ARG A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.69   23.31     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  ARG A  71 "
           pdb=" C   ARG A  71 "
           pdb=" N   ILE A  72 "
           pdb=" CA  ILE A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.52  -22.48     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 6558 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1734
       0.052 -    0.105: 220
       0.105 -    0.157: 30
       0.157 -    0.209: 6
       0.209 -    0.262: 1
  Chirality restraints: 1991
  Sorted by residual:
  chirality pdb=" CA  ASN B  16 "
            pdb=" N   ASN B  16 "
            pdb=" C   ASN B  16 "
            pdb=" CB  ASN B  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  ILE D 142 "
            pdb=" CA  ILE D 142 "
            pdb=" CG1 ILE D 142 "
            pdb=" CG2 ILE D 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.54e-01
  chirality pdb=" CA  ILE E 138 "
            pdb=" N   ILE E 138 "
            pdb=" C   ILE E 138 "
            pdb=" CB  ILE E 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.40e-01
  ... (remaining 1988 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  75 "   -0.982 9.50e-02 1.11e+02   4.40e-01 1.17e+02
        pdb=" NE  ARG G  75 "    0.059 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  75 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  75 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  75 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  14 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.22e+00
        pdb=" C   ILE B  14 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ILE B  14 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LYS B  15 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 143 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.22e+00
        pdb=" C   ALA D 143 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ALA D 143 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ARG D 144 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 325
        2.66 -     3.22: 9772
        3.22 -     3.78: 19471
        3.78 -     4.34: 25040
        4.34 -     4.90: 36539
  Nonbonded interactions: 91147
  Sorted by model distance:
  nonbonded pdb=" N2   DG I  29 "
            pdb=" O2   DC J -29 "
     model   vdw
     2.099 2.496
  nonbonded pdb=" NH1 ARG A 119 "
            pdb=" OD2 ASP A 126 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" NE2 HIS B  68 "
            pdb=" OD1 ASP D 130 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   TYR G 134 "
            pdb=" N   ASN G 138 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   SER F  69 "
            pdb=" OG  SER F  69 "
     model   vdw
     2.218 3.040
  ... (remaining 91142 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'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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:             1.970
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     30.950
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.060
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
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   0.075  11971  Z= 0.245
  Angle     :  0.674  12.344  17250  Z= 0.413
  Chirality :  0.037   0.262   1991
  Planarity :  0.013   0.440   1272
  Dihedral  : 28.716 171.063   5117
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.63 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 33.07 %
    Favored  : 61.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.00 (0.32), residues: 762
  helix:  0.56 (0.25), residues: 485
  sheet:  None (None), residues: 0
  loop : -2.98 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  68 
 PHE   0.012   0.001   PHE C  98 
 TYR   0.009   0.001   TYR B  56 
 ARG   0.003   0.000   ARG H  87 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 0.679 
Fit side-chains
REVERT: C   66 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7020 (mpt180)
REVERT: C   81 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8328 (tppt)
REVERT: C  109 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7547 (tm-30)
REVERT: D  104 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6809 (mptt)
REVERT: E   52 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8145 (mmmt)
REVERT: E   66 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6884 (mpt180)
REVERT: E  123 MET cc_start: 0.7594 (mtp) cc_final: 0.7373 (mtp)
REVERT: H   97 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7282 (tp30)
  outliers start: 35
  outliers final: 26
  residues processed: 166
  average time/residue: 0.3306
  time to fit residues: 70.9747
Evaluate side-chains
  161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain C residue   66 ARG
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain E residue   52 LYS
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue  105 ASP
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue  110 ILE
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain H residue   70 ASP
Chi-restraints excluded: chain H residue   97 GLU
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  142 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
C  77 GLN
G  83 ASN
H 115 ASN
** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11971  Z= 0.315
  Angle     :  0.652   6.325  17250  Z= 0.374
  Chirality :  0.038   0.182   1991
  Planarity :  0.005   0.050   1272
  Dihedral  : 30.845 154.484   3703
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 10.50 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  9.97 %
    Allowed  : 31.65 %
    Favored  : 58.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.31), residues: 762
  helix:  0.70 (0.25), residues: 486
  sheet:  None (None), residues: 0
  loop : -3.16 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 120 
 PHE   0.021   0.003   PHE B  47 
 TYR   0.012   0.002   TYR G 134 
 ARG   0.004   0.001   ARG B  71 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 132
  time to evaluate  : 0.809 
Fit side-chains
REVERT: B   60 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7862 (m-40)
REVERT: C   81 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8443 (tppt)
REVERT: C  109 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: D  104 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6866 (mptt)
REVERT: D  124 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6666 (mt0)
REVERT: E   52 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8193 (mmmt)
REVERT: E  123 MET cc_start: 0.7779 (mtp) cc_final: 0.7474 (mtp)
REVERT: G  140 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7759 (mt-10)
REVERT: G  153 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.6049 (p-80)
REVERT: H  132 ARG cc_start: 0.8087 (tmm-80) cc_final: 0.7696 (ttm170)
  outliers start: 63
  outliers final: 46
  residues processed: 180
  average time/residue: 0.3028
  time to fit residues: 71.9508
Evaluate side-chains
  176 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 126
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain G residue   78 LYS
Chi-restraints excluded: chain G residue  110 ILE
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  142 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
G  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11971  Z= 0.272
  Angle     :  0.630   8.771  17250  Z= 0.362
  Chirality :  0.036   0.209   1991
  Planarity :  0.004   0.052   1272
  Dihedral  : 30.858 154.426   3677
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  9.97 %
    Favored  : 89.50 %
  Rotamer:
    Outliers : 10.60 %
    Allowed  : 30.70 %
    Favored  : 58.70 %
  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: -0.75 (0.32), residues: 762
  helix:  0.87 (0.25), residues: 483
  sheet:  None (None), residues: 0
  loop : -3.09 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 120 
 PHE   0.018   0.002   PHE H  91 
 TYR   0.010   0.001   TYR B  56 
 ARG   0.003   0.000   ARG D 132 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 129
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8323 (mtmm)
REVERT: C   81 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8339 (tppt)
REVERT: C  109 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7587 (tm-30)
REVERT: D  104 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6852 (mptt)
REVERT: D  124 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6676 (mt0)
REVERT: E   52 LYS cc_start: 0.8617 (mmtp) cc_final: 0.8196 (mmmt)
REVERT: G  140 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7735 (mt-10)
REVERT: G  153 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.6065 (p-80)
REVERT: H  132 ARG cc_start: 0.8066 (tmm-80) cc_final: 0.7675 (ttm170)
  outliers start: 67
  outliers final: 56
  residues processed: 176
  average time/residue: 0.2972
  time to fit residues: 69.4259
Evaluate side-chains
  187 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 127
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  105 ASP
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain G residue  110 ILE
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  142 ILE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  164 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0870
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0040
   chunk 80 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    1.4176

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

Flipped N/Q/H residues before XYZ refinement:
G  83 ASN
** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11971  Z= 0.240
  Angle     :  0.613   8.772  17250  Z= 0.353
  Chirality :  0.035   0.199   1991
  Planarity :  0.004   0.053   1272
  Dihedral  : 30.798 153.851   3674
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.10 %
    Favored  : 89.50 %
  Rotamer:
    Outliers : 11.55 %
    Allowed  : 30.06 %
    Favored  : 58.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.32), residues: 762
  helix:  1.04 (0.25), residues: 484
  sheet:  None (None), residues: 0
  loop : -2.99 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 120 
 PHE   0.016   0.002   PHE B  47 
 TYR   0.010   0.001   TYR F  56 
 ARG   0.003   0.000   ARG D 132 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 127
  time to evaluate  : 0.922 
Fit side-chains
REVERT: B   49 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8417 (mtmm)
REVERT: B   60 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7794 (m-40)
REVERT: C   81 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8328 (tppt)
REVERT: C   90 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7351 (mmm160)
REVERT: C  109 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7592 (tm-30)
REVERT: D  104 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6832 (mptt)
REVERT: D  124 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6620 (mt0)
REVERT: E   52 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8191 (mmmt)
REVERT: F   71 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6946 (mtm-85)
REVERT: G  140 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7651 (mt-10)
REVERT: G  153 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5968 (p-80)
REVERT: H   96 MET cc_start: 0.8427 (mmm) cc_final: 0.8200 (tpp)
REVERT: H  124 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6308 (pm20)
REVERT: H  132 ARG cc_start: 0.8035 (tmm-80) cc_final: 0.7667 (ttm170)
  outliers start: 73
  outliers final: 52
  residues processed: 178
  average time/residue: 0.3008
  time to fit residues: 70.6216
Evaluate side-chains
  184 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 124
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   90 ARG
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue  105 ASP
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   30 VAL
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   71 ARG
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain G residue  110 ILE
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   91 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain H residue  142 ILE
Chi-restraints excluded: chain H residue  160 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0970
   chunk 87 optimal weight:    6.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
G  83 ASN
** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11971  Z= 0.234
  Angle     :  0.612   7.376  17250  Z= 0.351
  Chirality :  0.035   0.139   1991
  Planarity :  0.004   0.054   1272
  Dihedral  : 30.787 153.178   3669
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.97 %
    Favored  : 89.63 %
  Rotamer:
    Outliers : 11.87 %
    Allowed  : 29.75 %
    Favored  : 58.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.32), residues: 762
  helix:  1.06 (0.25), residues: 486
  sheet:  None (None), residues: 0
  loop : -2.96 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 120 
 PHE   0.016   0.002   PHE B  47 
 TYR   0.010   0.001   TYR F  56 
 ARG   0.004   0.000   ARG D 144 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 129
  time to evaluate  : 0.933 
Fit side-chains
REVERT: B   49 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8379 (mtmm)
REVERT: B   60 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7763 (m-40)
REVERT: C   81 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8314 (tppt)
REVERT: C  109 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7671 (tm-30)
REVERT: D  104 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6807 (mptt)
REVERT: D  124 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6723 (mt0)
REVERT: D  158 LYS cc_start: 0.8217 (tppt) cc_final: 0.7987 (tptt)
REVERT: E   52 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8165 (mmmt)
REVERT: G  140 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7651 (mt-10)
REVERT: G  153 HIS cc_start: 0.6153 (OUTLIER) cc_final: 0.5892 (p-80)
REVERT: H  124 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6318 (pm20)
REVERT: H  132 ARG cc_start: 0.8019 (tmm-80) cc_final: 0.7662 (ttm170)
  outliers start: 75
  outliers final: 58
  residues processed: 183
  average time/residue: 0.2848
  time to fit residues: 70.1684
Evaluate side-chains
  191 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 127
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  105 ASP
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain G residue  110 ILE
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   91 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain H residue  130 ASP
Chi-restraints excluded: chain H residue  160 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
G  83 ASN
** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11971  Z= 0.241
  Angle     :  0.623   7.349  17250  Z= 0.356
  Chirality :  0.035   0.140   1991
  Planarity :  0.004   0.054   1272
  Dihedral  : 30.802 152.240   3665
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.10 %
    Favored  : 89.50 %
  Rotamer:
    Outliers : 11.87 %
    Allowed  : 29.91 %
    Favored  : 58.23 %
  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: -0.50 (0.32), residues: 762
  helix:  1.04 (0.25), residues: 486
  sheet:  None (None), residues: 0
  loop : -2.97 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 120 
 PHE   0.015   0.002   PHE B  47 
 TYR   0.010   0.001   TYR F  56 
 ARG   0.004   0.000   ARG D 144 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 130
  time to evaluate  : 0.839 
Fit side-chains
REVERT: B   60 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7758 (m-40)
REVERT: B   80 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7130 (ttp-170)
REVERT: C   81 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8316 (tppt)
REVERT: C  109 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7681 (tm-30)
REVERT: D  104 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6806 (mptt)
REVERT: D  124 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6736 (mt0)
REVERT: D  158 LYS cc_start: 0.8234 (tppt) cc_final: 0.8023 (tptt)
REVERT: E   52 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8164 (mmmt)
REVERT: G  133 LYS cc_start: 0.8143 (tppt) cc_final: 0.7934 (tppt)
REVERT: G  140 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7663 (mt-10)
REVERT: G  153 HIS cc_start: 0.6171 (OUTLIER) cc_final: 0.5909 (p-80)
REVERT: H  124 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6295 (pm20)
REVERT: H  132 ARG cc_start: 0.8014 (tmm-80) cc_final: 0.7655 (ttm170)
  outliers start: 75
  outliers final: 57
  residues processed: 187
  average time/residue: 0.2885
  time to fit residues: 71.7750
Evaluate side-chains
  188 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 124
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   60 THR
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  105 ASP
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain G residue  110 ILE
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   91 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain H residue  130 ASP
Chi-restraints excluded: chain H residue  142 ILE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  164 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
G  83 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11971  Z= 0.191
  Angle     :  0.595   7.724  17250  Z= 0.341
  Chirality :  0.034   0.136   1991
  Planarity :  0.004   0.056   1272
  Dihedral  : 30.669 151.538   3663
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 10.24 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  9.49 %
    Allowed  : 32.75 %
    Favored  : 57.75 %
  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: -0.28 (0.33), residues: 762
  helix:  1.24 (0.25), residues: 485
  sheet:  None (None), residues: 0
  loop : -2.93 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS B  68 
 PHE   0.011   0.002   PHE B  47 
 TYR   0.010   0.001   TYR F  56 
 ARG   0.003   0.000   ARG D 132 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 130
  time to evaluate  : 1.142 
Fit side-chains
REVERT: B   80 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7120 (ttp-170)
REVERT: C   81 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8402 (tppt)
REVERT: C  109 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7716 (tm-30)
REVERT: C  146 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.5088 (pp)
REVERT: D  104 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6762 (mptt)
REVERT: D  124 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6675 (mt0)
REVERT: E   52 LYS cc_start: 0.8570 (mmtp) cc_final: 0.8214 (mmmt)
REVERT: G  133 LYS cc_start: 0.8044 (tppt) cc_final: 0.7801 (tppt)
REVERT: G  140 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7557 (mt-10)
REVERT: G  153 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5745 (p-80)
REVERT: H  117 LEU cc_start: 0.7480 (tp) cc_final: 0.7226 (tp)
REVERT: H  124 GLN cc_start: 0.6658 (OUTLIER) cc_final: 0.6354 (pt0)
  outliers start: 60
  outliers final: 46
  residues processed: 173
  average time/residue: 0.2974
  time to fit residues: 68.3051
Evaluate side-chains
  179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 126
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  105 ASP
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   91 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain H residue  130 ASP
Chi-restraints excluded: chain H residue  142 ILE
Chi-restraints excluded: chain H residue  164 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 75 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
G  83 ASN
** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  11971  Z= 0.362
  Angle     :  0.700   7.398  17250  Z= 0.398
  Chirality :  0.040   0.170   1991
  Planarity :  0.005   0.054   1272
  Dihedral  : 31.016 148.330   3658
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 10.89 %
    Favored  : 88.58 %
  Rotamer:
    Outliers : 11.08 %
    Allowed  : 31.33 %
    Favored  : 57.59 %
  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: -0.79 (0.31), residues: 762
  helix:  0.75 (0.24), residues: 488
  sheet:  None (None), residues: 0
  loop : -3.00 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 120 
 PHE   0.020   0.003   PHE B  47 
 TYR   0.012   0.002   TYR B  56 
 ARG   0.007   0.000   ARG D 132 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 121
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 GLU cc_start: 0.7756 (pp20) cc_final: 0.7211 (pp20)
REVERT: B   60 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7841 (m-40)
REVERT: C   81 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8232 (tppt)
REVERT: C  109 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7577 (tm-30)
REVERT: D  104 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6891 (mptt)
REVERT: D  123 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7527 (ttp-170)
REVERT: D  124 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.6822 (mt0)
REVERT: E   52 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8232 (mmmt)
REVERT: E  123 MET cc_start: 0.7608 (mtp) cc_final: 0.7328 (mtp)
REVERT: G  140 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7781 (mt-10)
REVERT: G  153 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.6146 (p-80)
REVERT: H   96 MET cc_start: 0.8436 (mmm) cc_final: 0.8217 (tpp)
REVERT: H  124 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6557 (pm20)
  outliers start: 70
  outliers final: 51
  residues processed: 177
  average time/residue: 0.3051
  time to fit residues: 71.4190
Evaluate side-chains
  179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 121
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  123 ARG
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  163 TYR
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   91 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  108 THR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain H residue  140 SER
Chi-restraints excluded: chain H residue  142 ILE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  164 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
G  83 ASN
** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11971  Z= 0.217
  Angle     :  0.631   8.048  17250  Z= 0.360
  Chirality :  0.035   0.167   1991
  Planarity :  0.004   0.052   1272
  Dihedral  : 30.824 148.572   3658
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.10 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  9.02 %
    Allowed  : 33.39 %
    Favored  : 57.59 %
  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: -0.50 (0.32), residues: 762
  helix:  1.05 (0.25), residues: 487
  sheet:  None (None), residues: 0
  loop : -3.02 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  68 
 PHE   0.015   0.002   PHE H  91 
 TYR   0.010   0.001   TYR B  56 
 ARG   0.003   0.000   ARG H 132 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 129
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.7485 (mp10) cc_final: 0.7280 (mm-40)
REVERT: B   19 GLU cc_start: 0.7430 (pp20) cc_final: 0.6999 (pp20)
REVERT: B   60 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7788 (m-40)
REVERT: C   81 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8351 (tppt)
REVERT: C  109 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7665 (tm-30)
REVERT: D  104 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6773 (mptt)
REVERT: D  124 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6771 (mt0)
REVERT: D  158 LYS cc_start: 0.8238 (tppt) cc_final: 0.7983 (tppt)
REVERT: E   52 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8149 (mmmt)
REVERT: G  140 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7626 (mt-10)
REVERT: G  153 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.6055 (p-80)
REVERT: H  124 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6309 (pm20)
  outliers start: 57
  outliers final: 48
  residues processed: 170
  average time/residue: 0.2786
  time to fit residues: 62.8001
Evaluate side-chains
  177 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 123
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain G residue  153 HIS
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   91 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain H residue  142 ILE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  164 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0970
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
G  83 ASN
H 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11971  Z= 0.201
  Angle     :  0.630  10.932  17250  Z= 0.356
  Chirality :  0.034   0.167   1991
  Planarity :  0.004   0.055   1272
  Dihedral  : 30.715 146.792   3658
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.10 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  8.39 %
    Allowed  : 34.02 %
    Favored  : 57.59 %
  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: -0.38 (0.32), residues: 762
  helix:  1.12 (0.25), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.94 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  48 
 PHE   0.012   0.002   PHE H  91 
 TYR   0.010   0.001   TYR F  56 
 ARG   0.003   0.000   ARG H 132 

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 130
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7805 (m-40)
REVERT: C   81 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8351 (tppt)
REVERT: C  109 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7657 (tm-30)
REVERT: D  104 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6760 (mptt)
REVERT: D  124 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6756 (mt0)
REVERT: D  158 LYS cc_start: 0.8227 (tppt) cc_final: 0.7958 (tppt)
REVERT: E   52 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8196 (mmmt)
REVERT: E  123 MET cc_start: 0.7463 (mtp) cc_final: 0.7234 (mtp)
REVERT: G  140 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: H  157 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7816 (mp0)
  outliers start: 53
  outliers final: 48
  residues processed: 169
  average time/residue: 0.2851
  time to fit residues: 64.5538
Evaluate side-chains
  177 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 125
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  104 LYS
Chi-restraints excluded: chain D residue  115 ASN
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  164 GLN
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   54 GLU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue   76 ILE
Chi-restraints excluded: chain E residue   92 VAL
Chi-restraints excluded: chain E residue  105 ASP
Chi-restraints excluded: chain E residue  121 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  136 GLU
Chi-restraints excluded: chain F residue   15 LYS
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   36 VAL
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   60 ASN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain G residue   83 ASN
Chi-restraints excluded: chain G residue  119 GLU
Chi-restraints excluded: chain G residue  135 LEU
Chi-restraints excluded: chain G residue  138 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   91 PHE
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  102 ILE
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  120 HIS
Chi-restraints excluded: chain H residue  124 GLN
Chi-restraints excluded: chain H residue  142 ILE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain H residue  164 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 81 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0670
   chunk 57 optimal weight:    0.0980
   overall best weight:    0.3518

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

Flipped N/Q/H residues before XYZ refinement:
G  83 ASN
H 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.137558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.110578 restraints weight = 23406.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.03
r_work: 0.3685 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.143  11971  Z= 0.232
  Angle     :  0.871  59.187  17250  Z= 0.514
  Chirality :  0.044   1.260   1991
  Planarity :  0.005   0.092   1272
  Dihedral  : 30.727 146.806   3654
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 10.37 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  8.07 %
    Allowed  : 34.34 %
    Favored  : 57.59 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.32), residues: 762
  helix:  1.12 (0.25), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.96 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  48 
 PHE   0.011   0.002   PHE H  91 
 TYR   0.010   0.001   TYR F  56 
 ARG   0.007   0.000   ARG B  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2315.68 seconds
wall clock time: 42 minutes 49.83 seconds (2569.83 seconds total)