Starting phenix.real_space_refine
on Tue Sep 24 04:43:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj4_16904/09_2024/8oj4_16904.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj4_16904/09_2024/8oj4_16904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj4_16904/09_2024/8oj4_16904.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj4_16904/09_2024/8oj4_16904.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj4_16904/09_2024/8oj4_16904.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj4_16904/09_2024/8oj4_16904.cif"
  }
  resolution = 4.35
  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=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    4442      2.51       5
     N    1155      2.21       5
     O    1376      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6983
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 1523
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 185, 1489
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 173}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 185, 1489
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 173}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 1484
    Chain: "A"
      Number of atoms: 899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 899
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 6, 'TRANS': 110}
    Chain: "B"
      Number of atoms: 899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 899
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 6, 'TRANS': 110}
    Chain: "C"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 918
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 6, 'TRANS': 112}
    Chain: "D"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 924
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 6, 'TRANS': 113}
    Chain: "E"
      Number of atoms: 910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 910
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 6, 'TRANS': 111}
    Chain: "F"
      Number of atoms: 910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 910
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 6, 'TRANS': 111}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  ALEU H  65 " occ=0.45
      ... (14 atoms not shown)
      pdb=" CD2BLEU H  65 " occ=0.55
    residue:
      pdb=" N  AARG H 153 " occ=0.48
      ... (20 atoms not shown)
      pdb=" NH2BARG H 153 " occ=0.52
    residue:
      pdb=" N  AILE H 167 " occ=0.44
      ... (14 atoms not shown)
      pdb=" CD1BILE H 167 " occ=0.56
    residue:
      pdb=" N  ATHR H 176 " occ=0.53
      ... (12 atoms not shown)
      pdb=" CG2BTHR H 176 " occ=0.47
  Time building chain proxies: 5.78, per 1000 atoms: 0.83
  Number of scatterers: 6983
  At special positions: 0
  Unit cell: (112.18, 107.21, 92.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O    1376      8.00
     N    1155      7.00
     C    4442      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: 1.86
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 9 sheets defined
      16.8% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'H' and resid 26 through 44
      removed outlier: 3.685A  pdb=" N   LEU H  30 " --> pdb=" O   ASN H  26 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN H  44 " --> pdb=" O   ASP H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 46 through 52
      removed outlier: 4.110A  pdb=" N   ARG H  50 " --> pdb=" O   GLN H  46 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 63
      removed outlier: 4.047A  pdb=" N   ASP H  61 " --> pdb=" O   ARG H  57 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 64 through 68
    Processing helix  chain 'H' and resid 70 through 75
    Processing helix  chain 'H' and resid 79 through 85
    Processing helix  chain 'H' and resid 86 through 109
      removed outlier: 4.610A  pdb=" N   GLU H  91 " --> pdb=" O   PRO H  87 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   ALA H  92 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ARG H  98 " --> pdb=" O   PHE H  94 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU H  99 " --> pdb=" O   ALA H  95 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLN H 103 " --> pdb=" O   GLU H  99 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ALA H 104 " --> pdb=" O   TYR H 100 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR H 105 " --> pdb=" O   LEU H 101 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 174 through 181
      removed outlier: 4.024A  pdb=" N   ASN H 179 " --> pdb=" O   THR H 175 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU H 180 " --> pdb=" O  ATHR H 176 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TRP H 181 " --> pdb=" O   LYS H 177 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 182 through 188
      removed outlier: 3.664A  pdb=" N   ARG H 186 " --> pdb=" O   GLY H 182 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 189 through 197
      removed outlier: 4.933A  pdb=" N   ALA H 195 " --> pdb=" O   ASP H 191 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN H 196 " --> pdb=" O   GLY H 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 150
      removed outlier: 4.291A  pdb=" N   LEU A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 151
      removed outlier: 4.069A  pdb=" N   LEU B 146 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 150
      removed outlier: 4.463A  pdb=" N   LEU C 146 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ILE C 147 " --> pdb=" O   LEU C 143 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY C 148 " --> pdb=" O   GLU C 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 150
    Processing helix  chain 'E' and resid 144 through 150
    Processing helix  chain 'F' and resid 144 through 150
    Processing sheet with id=AA1, first strand: chain 'H' and resid 130 through 135
      removed outlier: 3.854A  pdb=" N   VAL H 135 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU H 148 " --> pdb=" O   VAL H 135 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   GLN H 162 " --> pdb=" O  AARG H 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 45
      removed outlier: 4.279A  pdb=" N   ALA A  44 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL A  82 " --> pdb=" O   ALA A  44 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ASP A  70 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   GLU A  85 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   VAL A  68 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   GLU A  87 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   GLY A  66 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 103
      removed outlier: 3.656A  pdb=" N   ARG A 102 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 45
      removed outlier: 5.984A  pdb=" N   GLU B  85 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   VAL B  68 " --> pdb=" O   GLU B  85 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL B  58 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   LEU B 114 " --> pdb=" O   PRO B  57 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   SER B  59 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   VAL B 116 " --> pdb=" O   SER B  59 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 45
      removed outlier: 6.703A  pdb=" N   GLU C  85 " --> pdb=" O   VAL C  68 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   VAL C  68 " --> pdb=" O   GLU C  85 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   GLU C  87 " --> pdb=" O   GLY C  66 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   GLY C  66 " --> pdb=" O   GLU C  87 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 63 through 64
      removed outlier: 6.969A  pdb=" N   SER C  59 " --> pdb=" O   LEU C 114 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   VAL C 116 " --> pdb=" O   SER C  59 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR C 111 " --> pdb=" O   ARG C 102 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG C 102 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 103
      removed outlier: 8.389A  pdb=" N   LEU D 114 " --> pdb=" O   PRO D  57 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   SER D  59 " --> pdb=" O   LEU D 114 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL D  58 " --> pdb=" O   VAL D  65 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   GLY D  66 " --> pdb=" O   GLU D  87 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   GLU D  87 " --> pdb=" O   GLY D  66 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   VAL D  68 " --> pdb=" O   GLU D  85 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   GLU D  85 " --> pdb=" O   VAL D  68 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ASP D 132 " --> pdb=" O   THR D  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 40 through 45
      removed outlier: 6.176A  pdb=" N   GLU E  85 " --> pdb=" O   VAL E  68 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   VAL E  68 " --> pdb=" O   GLU E  85 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   VAL E  58 " --> pdb=" O   VAL E  65 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU E 112 " --> pdb=" O   PRO E  57 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU E 114 " --> pdb=" O   SER E  59 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 39 through 45
      removed outlier: 6.262A  pdb=" N   GLU F  85 " --> pdb=" O   VAL F  68 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   VAL F  68 " --> pdb=" O   GLU F  85 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   GLU F  87 " --> pdb=" O   GLY F  66 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   GLY F  66 " --> pdb=" O   GLU F  87 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL F  58 " --> pdb=" O   VAL F  65 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   LEU F 114 " --> pdb=" O   PRO F  57 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER F  59 " --> pdb=" O   LEU F 114 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   VAL F 116 " --> pdb=" O   SER F  59 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR F 111 " --> pdb=" O   ARG F 102 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG F 102 " --> pdb=" O   TYR F 111 " (cutoff:3.500A)

    177 hydrogen bonds defined for protein.
    468 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.56

  Time building geometry restraints manager: 2.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2306
        1.34 -     1.46: 1216
        1.46 -     1.57: 3568
        1.57 -     1.69: 0
        1.69 -     1.80: 20
  Bond restraints: 7110
  Sorted by residual:
  bond pdb=" CA  ILE C  93 "
       pdb=" CB  ILE C  93 "
    ideal  model  delta    sigma   weight residual
    1.539  1.526  0.013 7.50e-03 1.78e+04 3.14e+00
  bond pdb=" C   LEU F 143 "
       pdb=" N   GLU F 144 "
    ideal  model  delta    sigma   weight residual
    1.332  1.311  0.021 1.40e-02 5.10e+03 2.32e+00
  bond pdb=" N   ILE C  93 "
       pdb=" CA  ILE C  93 "
    ideal  model  delta    sigma   weight residual
    1.454  1.466 -0.011 7.70e-03 1.69e+04 2.22e+00
  bond pdb=" C   ASP D  74 "
       pdb=" O   ASP D  74 "
    ideal  model  delta    sigma   weight residual
    1.249  1.236  0.013 8.50e-03 1.38e+04 2.18e+00
  bond pdb=" N   GLY D 108 "
       pdb=" CA  GLY D 108 "
    ideal  model  delta    sigma   weight residual
    1.453  1.441  0.012 8.60e-03 1.35e+04 1.85e+00
  ... (remaining 7105 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 8906
        1.43 -     2.87: 664
        2.87 -     4.30: 96
        4.30 -     5.74: 14
        5.74 -     7.17: 1
  Bond angle restraints: 9681
  Sorted by residual:
  angle pdb=" N   TYR H  67 "
        pdb=" CA  TYR H  67 "
        pdb=" C   TYR H  67 "
      ideal   model   delta    sigma   weight residual
     113.38  109.47    3.91 1.23e+00 6.61e-01 1.01e+01
  angle pdb=" N   THR C  36 "
        pdb=" CA  THR C  36 "
        pdb=" C   THR C  36 "
      ideal   model   delta    sigma   weight residual
     108.38  112.56   -4.18 1.35e+00 5.49e-01 9.58e+00
  angle pdb=" C   LEU H  64 "
        pdb=" N  BLEU H  65 "
        pdb=" CA BLEU H  65 "
      ideal   model   delta    sigma   weight residual
     120.06  123.70   -3.64 1.19e+00 7.06e-01 9.34e+00
  angle pdb=" N   HIS D  92 "
        pdb=" CA  HIS D  92 "
        pdb=" C   HIS D  92 "
      ideal   model   delta    sigma   weight residual
     107.23  112.15   -4.92 1.67e+00 3.59e-01 8.68e+00
  angle pdb=" N   SER F 139 "
        pdb=" CA  SER F 139 "
        pdb=" C   SER F 139 "
      ideal   model   delta    sigma   weight residual
     108.38  112.17   -3.79 1.35e+00 5.49e-01 7.88e+00
  ... (remaining 9676 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.04: 3725
       15.04 -    30.09: 419
       30.09 -    45.13: 121
       45.13 -    60.18: 13
       60.18 -    75.22: 8
  Dihedral angle restraints: 4286
    sinusoidal: 1701
      harmonic: 2585
  Sorted by residual:
  dihedral pdb=" CA  PRO E  38 "
           pdb=" C   PRO E  38 "
           pdb=" N   THR E  39 "
           pdb=" CA  THR E  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.00  -19.00     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  GLU D  87 "
           pdb=" C   GLU D  87 "
           pdb=" N   GLN D  88 "
           pdb=" CA  GLN D  88 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.29  -18.71     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  GLU A  87 "
           pdb=" C   GLU A  87 "
           pdb=" N   GLN A  88 "
           pdb=" CA  GLN A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.47  -18.53     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 4283 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 673
       0.030 -    0.060: 293
       0.060 -    0.090: 80
       0.090 -    0.120: 76
       0.120 -    0.151: 18
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" CG  LEU E 107 "
            pdb=" CB  LEU E 107 "
            pdb=" CD1 LEU E 107 "
            pdb=" CD2 LEU E 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.67e-01
  chirality pdb=" CA  ILE E  86 "
            pdb=" N   ILE E  86 "
            pdb=" C   ILE E  86 "
            pdb=" CB  ILE E  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.07e-01
  chirality pdb=" CA  VAL F  58 "
            pdb=" N   VAL F  58 "
            pdb=" C   VAL F  58 "
            pdb=" CB  VAL F  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.05e-01
  ... (remaining 1137 not shown)

  Planarity restraints: 1250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  37 "   -0.043 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO C  38 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C  38 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  38 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C  BLEU H  65 "   -0.032 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO H  66 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO H  66 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO H  66 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C  ALEU H  65 "   -0.029 5.00e-02 4.00e+02   4.34e-02 3.02e+00
        pdb=" N   PRO H  66 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO H  66 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO H  66 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1247 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 588
        2.73 -     3.28: 7017
        3.28 -     3.82: 9685
        3.82 -     4.36: 10683
        4.36 -     4.90: 18296
  Nonbonded interactions: 46269
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  70 "
            pdb=" OG1 THR B  83 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   THR E 133 "
            pdb=" NE2 GLN E 135 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" NZ  LYS H 128 "
            pdb=" OG1 THR H 129 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG  SER D 139 "
            pdb=" N   ALA D 140 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OG1 THR B  39 "
            pdb=" OE1 GLU B  85 "
     model   vdw
     2.296 3.040
  ... (remaining 46264 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 'B'
  selection = (chain 'C' and resid 36 through 152)
  selection = (chain 'D' and resid 36 through 152)
  selection = (chain 'E' and resid 36 through 152)
  selection = (chain 'F' and resid 36 through 152)
}

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=0.44 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.160
  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:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.130
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
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   0.046   7110  Z= 0.237
  Angle     :  0.817   7.169   9681  Z= 0.496
  Chirality :  0.045   0.151   1140
  Planarity :  0.005   0.066   1250
  Dihedral  : 13.746  75.219   2644
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 15.91 %
    Favored  : 83.86 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  6.78 %
    Favored  : 92.96 %
  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: -4.77 (0.22), residues: 892
  helix: -3.04 (0.39), residues: 100
  sheet: -2.61 (0.31), residues: 188
  loop : -3.63 (0.20), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H 152 
 HIS   0.001   0.000   HIS B  92 
 PHE   0.010   0.001   PHE F  46 
 TYR   0.013   0.001   TYR D 111 
 ARG   0.002   0.000   ARG H 143 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  147 ARG cc_start: 0.8411 (mtt90) cc_final: 0.8109 (mtt-85)
REVERT: A   79 LEU cc_start: 0.9083 (mm) cc_final: 0.8804 (mp)
REVERT: A  109 GLU cc_start: 0.8059 (mp0) cc_final: 0.7806 (mp0)
REVERT: B  115 ASN cc_start: 0.8965 (t0) cc_final: 0.8549 (t0)
REVERT: C   76 LYS cc_start: 0.9233 (tppt) cc_final: 0.8925 (tppt)
REVERT: D   67 ARG cc_start: 0.7901 (ptt180) cc_final: 0.7680 (ptt90)
REVERT: D  115 ASN cc_start: 0.8279 (t0) cc_final: 0.8078 (t0)
REVERT: D  150 PHE cc_start: 0.7352 (m-10) cc_final: 0.6977 (m-10)
REVERT: E   67 ARG cc_start: 0.7627 (ptt90) cc_final: 0.7420 (ptt90)
REVERT: E  130 ASP cc_start: 0.8325 (t0) cc_final: 0.7889 (t0)
REVERT: E  132 ASP cc_start: 0.8208 (t0) cc_final: 0.7949 (t0)
REVERT: E  150 PHE cc_start: 0.8351 (t80) cc_final: 0.8090 (t80)
REVERT: F  129 LYS cc_start: 0.8801 (mppt) cc_final: 0.8312 (mtmm)
REVERT: F  132 ASP cc_start: 0.8448 (m-30) cc_final: 0.8206 (m-30)
REVERT: F  138 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8242 (mmtt)
REVERT: F  149 GLN cc_start: 0.7977 (mt0) cc_final: 0.7703 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2567
  time to fit residues: 62.7696
Evaluate side-chains
  146 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
H  46 GLN
** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7110  Z= 0.257
  Angle     :  0.706   8.293   9681  Z= 0.361
  Chirality :  0.047   0.174   1140
  Planarity :  0.005   0.063   1250
  Dihedral  :  5.070  20.701    988
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  7.69 %
    Favored  : 92.05 %
  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: -4.03 (0.23), residues: 892
  helix: -2.08 (0.40), residues: 106
  sheet: -2.11 (0.33), residues: 188
  loop : -3.19 (0.20), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 181 
 HIS   0.003   0.001   HIS H 113 
 PHE   0.011   0.001   PHE F  46 
 TYR   0.013   0.001   TYR D  40 
 ARG   0.008   0.000   ARG H  57 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   99 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7763 (tp30)
REVERT: A   79 LEU cc_start: 0.9123 (mm) cc_final: 0.8772 (mp)
REVERT: A  109 GLU cc_start: 0.7817 (mp0) cc_final: 0.7585 (mp0)
REVERT: A  139 SER cc_start: 0.9446 (t) cc_final: 0.9067 (m)
REVERT: B  119 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: B  127 ILE cc_start: 0.7660 (mm) cc_final: 0.7416 (mt)
REVERT: C   67 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7764 (ttm170)
REVERT: C   76 LYS cc_start: 0.9236 (tppt) cc_final: 0.8892 (tppt)
REVERT: D   37 GLU cc_start: 0.7917 (mp0) cc_final: 0.7672 (mp0)
REVERT: D   67 ARG cc_start: 0.8161 (ptt180) cc_final: 0.7931 (ptp90)
REVERT: D   88 GLN cc_start: 0.6569 (tp-100) cc_final: 0.6318 (tp-100)
REVERT: D  150 PHE cc_start: 0.7360 (m-10) cc_final: 0.6884 (m-10)
REVERT: E  130 ASP cc_start: 0.8476 (t0) cc_final: 0.7842 (t0)
REVERT: E  132 ASP cc_start: 0.8323 (t0) cc_final: 0.7969 (t0)
REVERT: E  135 GLN cc_start: 0.8102 (tp40) cc_final: 0.7800 (tp40)
REVERT: F   47 ASP cc_start: 0.8696 (p0) cc_final: 0.8044 (t0)
REVERT: F  129 LYS cc_start: 0.8770 (mppt) cc_final: 0.8451 (mtmm)
REVERT: F  132 ASP cc_start: 0.8563 (m-30) cc_final: 0.8284 (m-30)
REVERT: F  138 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8266 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2562
  time to fit residues: 54.4888
Evaluate side-chains
  143 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    0.4980
   chunk 64 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0470
   chunk 76 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.0682

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

Flipped N/Q/H residues before XYZ refinement:
** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 202 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7110  Z= 0.174
  Angle     :  0.661   8.279   9681  Z= 0.330
  Chirality :  0.045   0.179   1140
  Planarity :  0.005   0.062   1250
  Dihedral  :  4.694  18.246    988
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.77 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.82 %
    Favored  : 94.92 %
  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: -3.46 (0.24), residues: 892
  helix: -1.35 (0.43), residues: 112
  sheet: -1.80 (0.34), residues: 190
  loop : -2.84 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 181 
 HIS   0.002   0.000   HIS H 113 
 PHE   0.028   0.001   PHE E 150 
 TYR   0.015   0.001   TYR H 117 
 ARG   0.006   0.000   ARG H 147 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   99 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7745 (tp30)
REVERT: A   79 LEU cc_start: 0.8990 (mm) cc_final: 0.8726 (mp)
REVERT: A  109 GLU cc_start: 0.7840 (mp0) cc_final: 0.7535 (mp0)
REVERT: A  139 SER cc_start: 0.9424 (t) cc_final: 0.8991 (m)
REVERT: B  119 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: B  127 ILE cc_start: 0.7768 (mm) cc_final: 0.7409 (mt)
REVERT: C   76 LYS cc_start: 0.9194 (tppt) cc_final: 0.8892 (tppt)
REVERT: C  138 LYS cc_start: 0.8715 (tptt) cc_final: 0.8510 (tppp)
REVERT: D   34 ILE cc_start: 0.8315 (mt) cc_final: 0.8060 (mt)
REVERT: D   36 THR cc_start: 0.8518 (p) cc_final: 0.8298 (p)
REVERT: D   37 GLU cc_start: 0.7989 (mp0) cc_final: 0.7714 (mp0)
REVERT: D   67 ARG cc_start: 0.8136 (ptt180) cc_final: 0.7928 (ptp90)
REVERT: D   88 GLN cc_start: 0.6524 (tp-100) cc_final: 0.6210 (tp-100)
REVERT: D  150 PHE cc_start: 0.7432 (m-10) cc_final: 0.6896 (m-10)
REVERT: E   53 LYS cc_start: 0.8914 (ptmt) cc_final: 0.8707 (pttt)
REVERT: E  130 ASP cc_start: 0.8411 (t0) cc_final: 0.7733 (t0)
REVERT: E  132 ASP cc_start: 0.8349 (t0) cc_final: 0.7950 (t0)
REVERT: E  135 GLN cc_start: 0.8177 (tp40) cc_final: 0.7771 (tp40)
REVERT: F  129 LYS cc_start: 0.8838 (mppt) cc_final: 0.8418 (mtmm)
REVERT: F  132 ASP cc_start: 0.8608 (m-30) cc_final: 0.8341 (m-30)
REVERT: F  138 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8344 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2355
  time to fit residues: 52.8164
Evaluate side-chains
  142 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0000
   chunk 73 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
C  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7110  Z= 0.207
  Angle     :  0.668  12.023   9681  Z= 0.333
  Chirality :  0.045   0.198   1140
  Planarity :  0.005   0.062   1250
  Dihedral  :  4.651  17.653    988
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.86 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.48 %
    Favored  : 94.26 %
  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: -3.06 (0.25), residues: 892
  helix: -0.83 (0.46), residues: 112
  sheet: -1.31 (0.37), residues: 180
  loop : -2.69 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 152 
 HIS   0.003   0.001   HIS H 113 
 PHE   0.007   0.001   PHE F  46 
 TYR   0.013   0.001   TYR H 117 
 ARG   0.006   0.000   ARG H 147 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: 0.7946 (mp0) cc_final: 0.7540 (mp0)
REVERT: A  139 SER cc_start: 0.9446 (t) cc_final: 0.9016 (m)
REVERT: B  127 ILE cc_start: 0.7731 (mm) cc_final: 0.7502 (mt)
REVERT: C   67 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7723 (ttm170)
REVERT: C   76 LYS cc_start: 0.9211 (tppt) cc_final: 0.8914 (tppt)
REVERT: C  138 LYS cc_start: 0.8736 (tptt) cc_final: 0.8520 (tppp)
REVERT: D   37 GLU cc_start: 0.8029 (mp0) cc_final: 0.7783 (mp0)
REVERT: D   67 ARG cc_start: 0.8183 (ptt180) cc_final: 0.7944 (ptp90)
REVERT: D   88 GLN cc_start: 0.6695 (tp-100) cc_final: 0.6355 (tp-100)
REVERT: D  150 PHE cc_start: 0.7351 (m-10) cc_final: 0.6817 (m-10)
REVERT: E   53 LYS cc_start: 0.8966 (ptmt) cc_final: 0.8735 (pttt)
REVERT: E  130 ASP cc_start: 0.8395 (t0) cc_final: 0.7727 (t0)
REVERT: E  132 ASP cc_start: 0.8134 (t0) cc_final: 0.7710 (t0)
REVERT: E  150 PHE cc_start: 0.8409 (t80) cc_final: 0.8065 (t80)
REVERT: F   47 ASP cc_start: 0.8674 (p0) cc_final: 0.8064 (t0)
REVERT: F  129 LYS cc_start: 0.8839 (mppt) cc_final: 0.8467 (mtmm)
REVERT: F  132 ASP cc_start: 0.8671 (m-30) cc_final: 0.8362 (m-30)
REVERT: F  138 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8268 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2473
  time to fit residues: 51.5324
Evaluate side-chains
  140 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7110  Z= 0.267
  Angle     :  0.717  10.718   9681  Z= 0.359
  Chirality :  0.046   0.210   1140
  Planarity :  0.005   0.063   1250
  Dihedral  :  4.831  18.660    988
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.00 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.26 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.25), residues: 892
  helix: -0.61 (0.47), residues: 106
  sheet: -1.47 (0.36), residues: 188
  loop : -2.51 (0.22), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H 152 
 HIS   0.003   0.001   HIS B  92 
 PHE   0.020   0.001   PHE E 150 
 TYR   0.011   0.001   TYR H 117 
 ARG   0.005   0.000   ARG H 147 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LEU cc_start: 0.9101 (mm) cc_final: 0.8817 (mp)
REVERT: A  109 GLU cc_start: 0.7966 (mp0) cc_final: 0.7611 (mp0)
REVERT: B  127 ILE cc_start: 0.7727 (mm) cc_final: 0.7510 (mt)
REVERT: C   76 LYS cc_start: 0.9262 (tppt) cc_final: 0.8948 (tppt)
REVERT: C  138 LYS cc_start: 0.8760 (tptt) cc_final: 0.8542 (tppp)
REVERT: D   67 ARG cc_start: 0.8201 (ptt180) cc_final: 0.7852 (ptt-90)
REVERT: D   88 GLN cc_start: 0.6965 (tp-100) cc_final: 0.6579 (tp-100)
REVERT: D  150 PHE cc_start: 0.7323 (m-10) cc_final: 0.6886 (m-10)
REVERT: E   53 LYS cc_start: 0.9011 (ptmt) cc_final: 0.8725 (pttt)
REVERT: E  130 ASP cc_start: 0.8385 (t0) cc_final: 0.7735 (t0)
REVERT: E  132 ASP cc_start: 0.8279 (t0) cc_final: 0.7894 (t0)
REVERT: F   38 PRO cc_start: 0.8172 (Cg_exo) cc_final: 0.7934 (Cg_endo)
REVERT: F   47 ASP cc_start: 0.8703 (p0) cc_final: 0.8160 (t0)
REVERT: F  129 LYS cc_start: 0.8846 (mppt) cc_final: 0.8454 (mtmm)
REVERT: F  132 ASP cc_start: 0.8742 (m-30) cc_final: 0.8412 (m-30)
REVERT: F  138 LYS cc_start: 0.8662 (mmmm) cc_final: 0.8226 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2420
  time to fit residues: 50.2360
Evaluate side-chains
  142 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 82 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 38 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7110  Z= 0.166
  Angle     :  0.676  11.312   9681  Z= 0.331
  Chirality :  0.044   0.191   1140
  Planarity :  0.005   0.063   1250
  Dihedral  :  4.465  19.254    988
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.05 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.35 %
    Favored  : 97.39 %
  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: -2.67 (0.26), residues: 892
  helix: -0.34 (0.49), residues: 109
  sheet: -1.17 (0.37), residues: 184
  loop : -2.41 (0.23), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H 181 
 HIS   0.001   0.000   HIS E  92 
 PHE   0.006   0.001   PHE E 150 
 TYR   0.011   0.001   TYR H 117 
 ARG   0.005   0.000   ARG C  89 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: 0.7922 (mp0) cc_final: 0.7491 (mp0)
REVERT: A  139 SER cc_start: 0.9422 (t) cc_final: 0.8968 (m)
REVERT: C   67 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.8118 (ttp-170)
REVERT: C  138 LYS cc_start: 0.8717 (tptt) cc_final: 0.8506 (tppp)
REVERT: D   67 ARG cc_start: 0.8120 (ptt180) cc_final: 0.7836 (ptp90)
REVERT: D   88 GLN cc_start: 0.6852 (tp-100) cc_final: 0.6419 (tp-100)
REVERT: E   53 LYS cc_start: 0.8918 (ptmt) cc_final: 0.8638 (pttt)
REVERT: E  130 ASP cc_start: 0.8359 (t0) cc_final: 0.7568 (t0)
REVERT: E  132 ASP cc_start: 0.8279 (t0) cc_final: 0.7853 (t0)
REVERT: E  135 GLN cc_start: 0.7968 (tp40) cc_final: 0.7614 (tp40)
REVERT: E  150 PHE cc_start: 0.8020 (t80) cc_final: 0.7755 (t80)
REVERT: F   38 PRO cc_start: 0.8070 (Cg_exo) cc_final: 0.7868 (Cg_endo)
REVERT: F   47 ASP cc_start: 0.8658 (p0) cc_final: 0.8099 (t0)
REVERT: F  129 LYS cc_start: 0.8814 (mppt) cc_final: 0.8390 (mtmm)
REVERT: F  132 ASP cc_start: 0.8675 (m-30) cc_final: 0.8364 (m-30)
REVERT: F  138 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8234 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2325
  time to fit residues: 52.2582
Evaluate side-chains
  146 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
H  52 ASN
C  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7110  Z= 0.334
  Angle     :  0.742  10.529   9681  Z= 0.375
  Chirality :  0.046   0.200   1140
  Planarity :  0.005   0.063   1250
  Dihedral  :  5.033  20.142    988
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.36 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.78 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.25), residues: 892
  helix: -0.16 (0.49), residues: 103
  sheet: -1.02 (0.39), residues: 169
  loop : -2.52 (0.22), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H 161 
 HIS   0.004   0.001   HIS B  92 
 PHE   0.010   0.001   PHE F  46 
 TYR   0.012   0.001   TYR D  40 
 ARG   0.004   0.000   ARG H 147 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: 0.8066 (mp0) cc_final: 0.7648 (mp0)
REVERT: C   76 LYS cc_start: 0.9243 (tptp) cc_final: 0.9008 (tppt)
REVERT: C  138 LYS cc_start: 0.8728 (tptt) cc_final: 0.8527 (tppp)
REVERT: D   37 GLU cc_start: 0.8111 (mp0) cc_final: 0.7799 (mp0)
REVERT: D   67 ARG cc_start: 0.8204 (ptt180) cc_final: 0.7793 (ptp90)
REVERT: D  150 PHE cc_start: 0.7302 (m-10) cc_final: 0.6911 (m-10)
REVERT: E   85 GLU cc_start: 0.7957 (pp20) cc_final: 0.7722 (tm-30)
REVERT: E  130 ASP cc_start: 0.8328 (t0) cc_final: 0.7640 (t0)
REVERT: E  132 ASP cc_start: 0.8358 (t0) cc_final: 0.7980 (t0)
REVERT: F   38 PRO cc_start: 0.8154 (Cg_exo) cc_final: 0.7933 (Cg_endo)
REVERT: F   47 ASP cc_start: 0.8723 (p0) cc_final: 0.8202 (t0)
REVERT: F  129 LYS cc_start: 0.8860 (mppt) cc_final: 0.8424 (mtmm)
REVERT: F  132 ASP cc_start: 0.8807 (m-30) cc_final: 0.8474 (m-30)
REVERT: F  138 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8235 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2346
  time to fit residues: 48.8611
Evaluate side-chains
  140 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    0.1980
   chunk 64 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
E  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7110  Z= 0.218
  Angle     :  0.723  10.763   9681  Z= 0.356
  Chirality :  0.046   0.275   1140
  Planarity :  0.005   0.063   1250
  Dihedral  :  4.724  18.586    988
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.64 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.09 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.26), residues: 892
  helix: -0.12 (0.49), residues: 103
  sheet: -1.13 (0.37), residues: 185
  loop : -2.36 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H 152 
 HIS   0.002   0.001   HIS E  92 
 PHE   0.010   0.001   PHE E 150 
 TYR   0.013   0.001   TYR B 152 
 ARG   0.004   0.000   ARG C  89 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: 0.7994 (mp0) cc_final: 0.7665 (mp0)
REVERT: A  110 GLN cc_start: 0.8732 (mt0) cc_final: 0.8270 (mt0)
REVERT: C  139 SER cc_start: 0.8958 (t) cc_final: 0.8625 (t)
REVERT: D   37 GLU cc_start: 0.8219 (mp0) cc_final: 0.8017 (mp0)
REVERT: D   67 ARG cc_start: 0.8146 (ptt180) cc_final: 0.7813 (ptp90)
REVERT: D   97 SER cc_start: 0.9246 (m) cc_final: 0.9022 (t)
REVERT: D  150 PHE cc_start: 0.7314 (m-10) cc_final: 0.6838 (m-10)
REVERT: E   53 LYS cc_start: 0.8881 (ptmt) cc_final: 0.8634 (pttt)
REVERT: E   85 GLU cc_start: 0.7911 (pp20) cc_final: 0.7699 (tm-30)
REVERT: E   88 GLN cc_start: 0.7018 (tt0) cc_final: 0.6704 (tt0)
REVERT: E  130 ASP cc_start: 0.8290 (t0) cc_final: 0.7606 (t0)
REVERT: E  132 ASP cc_start: 0.8353 (t0) cc_final: 0.7943 (t0)
REVERT: E  150 PHE cc_start: 0.8473 (t80) cc_final: 0.8057 (t80)
REVERT: F   47 ASP cc_start: 0.8683 (p0) cc_final: 0.8079 (t0)
REVERT: F  129 LYS cc_start: 0.8830 (mppt) cc_final: 0.8399 (mtmm)
REVERT: F  132 ASP cc_start: 0.8720 (m-30) cc_final: 0.8389 (m-30)
REVERT: F  138 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8268 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2300
  time to fit residues: 49.6455
Evaluate side-chains
  145 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0050
   chunk 59 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.6002

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

Flipped N/Q/H residues before XYZ refinement:
C  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7110  Z= 0.224
  Angle     :  0.718  10.823   9681  Z= 0.354
  Chirality :  0.046   0.256   1140
  Planarity :  0.005   0.063   1250
  Dihedral  :  4.688  18.392    988
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.68 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.78 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.26), residues: 892
  helix: -0.02 (0.49), residues: 103
  sheet: -1.27 (0.36), residues: 194
  loop : -2.21 (0.23), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 152 
 HIS   0.001   0.001   HIS H 113 
 PHE   0.026   0.001   PHE E 150 
 TYR   0.012   0.001   TYR B 152 
 ARG   0.004   0.000   ARG H 147 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: 0.8022 (mp0) cc_final: 0.7622 (mp0)
REVERT: A  110 GLN cc_start: 0.8798 (mt0) cc_final: 0.8260 (mt0)
REVERT: C  138 LYS cc_start: 0.9306 (tppp) cc_final: 0.9097 (tptt)
REVERT: C  139 SER cc_start: 0.9132 (t) cc_final: 0.8915 (t)
REVERT: D   37 GLU cc_start: 0.8213 (mp0) cc_final: 0.7955 (mp0)
REVERT: D   67 ARG cc_start: 0.8135 (ptt180) cc_final: 0.7785 (ptp90)
REVERT: D  150 PHE cc_start: 0.7211 (m-10) cc_final: 0.6840 (m-10)
REVERT: E   53 LYS cc_start: 0.8853 (ptmt) cc_final: 0.8598 (pttt)
REVERT: E  130 ASP cc_start: 0.8275 (t0) cc_final: 0.7601 (t0)
REVERT: E  132 ASP cc_start: 0.8347 (t0) cc_final: 0.7938 (t0)
REVERT: F   47 ASP cc_start: 0.8687 (p0) cc_final: 0.8095 (t0)
REVERT: F  129 LYS cc_start: 0.8832 (mppt) cc_final: 0.8397 (mtmm)
REVERT: F  132 ASP cc_start: 0.8726 (m-30) cc_final: 0.8411 (m-30)
REVERT: F  138 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8237 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2681
  time to fit residues: 58.0859
Evaluate side-chains
  143 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.0670
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 84 optimal weight:    0.4980
   chunk 77 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.8722

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7110  Z= 0.184
  Angle     :  0.734  11.047   9681  Z= 0.359
  Chirality :  0.046   0.241   1140
  Planarity :  0.005   0.063   1250
  Dihedral  :  4.498  18.269    988
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.91 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.27), residues: 892
  helix: -0.11 (0.49), residues: 109
  sheet: -1.10 (0.37), residues: 195
  loop : -2.12 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 152 
 HIS   0.001   0.000   HIS H 113 
 PHE   0.022   0.001   PHE E 150 
 TYR   0.010   0.001   TYR B 152 
 ARG   0.008   0.000   ARG C  89 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: 0.7967 (mp0) cc_final: 0.7655 (mp0)
REVERT: A  110 GLN cc_start: 0.8655 (mt0) cc_final: 0.8311 (mt0)
REVERT: C   47 ASP cc_start: 0.8484 (p0) cc_final: 0.8025 (p0)
REVERT: C   67 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7727 (ttp-170)
REVERT: C  138 LYS cc_start: 0.9304 (tppp) cc_final: 0.9092 (tptt)
REVERT: C  139 SER cc_start: 0.9143 (t) cc_final: 0.8928 (m)
REVERT: D   67 ARG cc_start: 0.8115 (ptt180) cc_final: 0.7774 (ptp90)
REVERT: E   53 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8526 (pttt)
REVERT: E  130 ASP cc_start: 0.8230 (t0) cc_final: 0.7605 (t0)
REVERT: E  132 ASP cc_start: 0.8360 (t0) cc_final: 0.7956 (t0)
REVERT: F   47 ASP cc_start: 0.8672 (p0) cc_final: 0.8103 (t0)
REVERT: F  129 LYS cc_start: 0.8820 (mppt) cc_final: 0.8408 (mtmm)
REVERT: F  132 ASP cc_start: 0.8692 (m-30) cc_final: 0.8390 (m-30)
REVERT: F  138 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8272 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2292
  time to fit residues: 49.2547
Evaluate side-chains
  145 residues out of total 760 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0470
   chunk 12 optimal weight:    5.9990
   chunk 59 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.7882

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

Flipped N/Q/H residues before XYZ refinement:
H  46 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.103398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.081359 restraints weight = 86819.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.082943 restraints weight = 64077.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.086674 restraints weight = 24226.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7110  Z= 0.175
  Angle     :  0.705  11.081   9681  Z= 0.344
  Chirality :  0.045   0.225   1140
  Planarity :  0.005   0.062   1250
  Dihedral  :  4.335  18.095    988
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.17 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.27), residues: 892
  helix:  0.03 (0.49), residues: 108
  sheet: -1.01 (0.36), residues: 195
  loop : -2.04 (0.24), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 181 
 HIS   0.001   0.000   HIS H 113 
 PHE   0.021   0.001   PHE E 150 
 TYR   0.008   0.001   TYR B  40 
 ARG   0.005   0.000   ARG B  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2085.28 seconds
wall clock time: 37 minutes 46.49 seconds (2266.49 seconds total)