Starting phenix.real_space_refine
on Thu May 15 13:58:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pc6_17595/05_2025/8pc6_17595.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pc6_17595/05_2025/8pc6_17595.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pc6_17595/05_2025/8pc6_17595.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pc6_17595/05_2025/8pc6_17595.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pc6_17595/05_2025/8pc6_17595.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pc6_17595/05_2025/8pc6_17595.cif"
  }
  resolution = 3.04
  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: 5
    Type Number    sf(0)   Gaussians
     P     293      5.49       5
     S      15      5.16       5
     C    7600      2.51       5
     N    2518      2.21       5
     O    3067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13493
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "I"
      Number of atoms: 2971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2971
          Inner-chain residues flagged as termini: ['pdbres=" DT I -72 "']
          Classifications: {'DNA': 147}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 146}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 828
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Planarities with less than four sites: {'ML3:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 656
          Classifications: {'peptide': 82}
          Incomplete info: {'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 822
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "F"
      Number of atoms: 692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 692
          Classifications: {'peptide': 86}
          Incomplete info: {'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "G"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 822
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "K"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 708
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 11, 'TRANS': 74}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
    Chain: "J"
      Number of atoms: 3014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3014
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen planarities: 17
    Chain: "L"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 710
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 11, 'TRANS': 74}
          Chain breaks: 1
  Time building chain proxies: 8.62, per 1000 atoms: 0.64
  Number of scatterers: 13493
  At special positions: 0
  Unit cell: (104.2, 140.045, 120.872, 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      15     16.00
     P     293     15.00
     O    3067      8.00
     N    2518      7.00
     C    7600      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: 3.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1756

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 12 sheets defined
      59.5% alpha, 6.2% beta
      129 base pairs and 267 stacking pairs defined.
    Time for finding SS restraints: 6.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.602A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.583A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.882A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.566A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.826A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.556A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.501A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 3.899A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 4.251A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.666A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.546A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.377A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 4.234A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 76 through 83
    Processing helix  chain 'L' and resid 76 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.649A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.464A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.155A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.424A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.223A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53
      removed outlier: 3.950A  pdb=" N   GLU K  49 " --> pdb=" O   PHE K  44 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA K  51 " --> pdb=" O   ILE K  42 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE K  42 " --> pdb=" O   ALA K  51 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 49 through 53
      removed outlier: 3.967A  pdb=" N   GLU L  49 " --> pdb=" O   PHE L  44 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA L  51 " --> pdb=" O   ILE L  42 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE L  42 " --> pdb=" O   ALA L  51 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      329 hydrogen bonds
      654 hydrogen bond angles
      0 basepair planarities
      129 basepair parallelities
      267 stacking parallelities
  Total time for adding SS restraints: 4.99

  Time building geometry restraints manager: 3.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2773
        1.33 -     1.45: 4380
        1.45 -     1.57: 6591
        1.57 -     1.69: 584
        1.69 -     1.81: 30
  Bond restraints: 14358
  Sorted by residual:
  bond pdb=" SG  ML3 A  36 "
       pdb=" CD  ML3 A  36 "
    ideal  model  delta    sigma   weight residual
    1.815  1.757  0.058 2.00e-02 2.50e+03 8.35e+00
  bond pdb=" CB  ML3 A  36 "
       pdb=" SG  ML3 A  36 "
    ideal  model  delta    sigma   weight residual
    1.817  1.766  0.051 2.00e-02 2.50e+03 6.52e+00
  bond pdb=" N   LEU L  53 "
       pdb=" CA  LEU L  53 "
    ideal  model  delta    sigma   weight residual
    1.454  1.483 -0.029 1.29e-02 6.01e+03 4.99e+00
  bond pdb=" C3'  DG J  64 "
       pdb=" O3'  DG J  64 "
    ideal  model  delta    sigma   weight residual
    1.422  1.474 -0.052 3.00e-02 1.11e+03 2.98e+00
  bond pdb=" C3'  DT J -72 "
       pdb=" O3'  DT J -72 "
    ideal  model  delta    sigma   weight residual
    1.422  1.469 -0.047 3.00e-02 1.11e+03 2.44e+00
  ... (remaining 14353 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 20408
        2.54 -     5.09: 194
        5.09 -     7.63: 15
        7.63 -    10.18: 4
       10.18 -    12.72: 1
  Bond angle restraints: 20622
  Sorted by residual:
  angle pdb=" CB  MET L   1 "
        pdb=" CG  MET L   1 "
        pdb=" SD  MET L   1 "
      ideal   model   delta    sigma   weight residual
     112.70  125.42  -12.72 3.00e+00 1.11e-01 1.80e+01
  angle pdb=" C3'  DC I  49 "
        pdb=" O3'  DC I  49 "
        pdb=" P    DA I  50 "
      ideal   model   delta    sigma   weight residual
     120.20  125.88   -5.68 1.50e+00 4.44e-01 1.43e+01
  angle pdb=" N   LEU L  53 "
        pdb=" CA  LEU L  53 "
        pdb=" CB  LEU L  53 "
      ideal   model   delta    sigma   weight residual
     111.55  105.15    6.40 1.74e+00 3.30e-01 1.35e+01
  angle pdb=" CA  TYR L  61 "
        pdb=" CB  TYR L  61 "
        pdb=" CG  TYR L  61 "
      ideal   model   delta    sigma   weight residual
     113.90  120.41   -6.51 1.80e+00 3.09e-01 1.31e+01
  angle pdb=" N   MET L   1 "
        pdb=" CA  MET L   1 "
        pdb=" C   MET L   1 "
      ideal   model   delta    sigma   weight residual
     111.00  101.39    9.61 2.80e+00 1.28e-01 1.18e+01
  ... (remaining 20617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.96: 6328
       35.96 -    71.91: 1552
       71.91 -   107.86: 27
      107.86 -   143.82: 3
      143.82 -   179.77: 3
  Dihedral angle restraints: 7913
    sinusoidal: 5194
      harmonic: 2719
  Sorted by residual:
  dihedral pdb=" C4'  DT J  69 "
           pdb=" C3'  DT J  69 "
           pdb=" O3'  DT J  69 "
           pdb=" P    DC J  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.23  179.77     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC J  68 "
           pdb=" C3'  DC J  68 "
           pdb=" O3'  DC J  68 "
           pdb=" P    DT J  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   25.50 -165.50     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DA J -73 "
           pdb=" C3'  DA J -73 "
           pdb=" O3'  DA J -73 "
           pdb=" P    DT J -72 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   18.32 -158.32     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 7910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 2023
       0.064 -    0.127: 278
       0.127 -    0.191: 14
       0.191 -    0.254: 5
       0.254 -    0.318: 2
  Chirality restraints: 2322
  Sorted by residual:
  chirality pdb=" CA  LEU L  53 "
            pdb=" N   LEU L  53 "
            pdb=" C   LEU L  53 "
            pdb=" CB  LEU L  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.53e+00
  chirality pdb=" CB  ILE L  58 "
            pdb=" CA  ILE L  58 "
            pdb=" CG1 ILE L  58 "
            pdb=" CG2 ILE L  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" C1'  DT J -72 "
            pdb=" O4'  DT J -72 "
            pdb=" C2'  DT J -72 "
            pdb=" N1   DT J -72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 2319 not shown)

  Planarity restraints: 1605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  59 "   -0.019 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        pdb=" C   LYS F  59 "    0.064 2.00e-02 2.50e+03
        pdb=" O   LYS F  59 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL F  60 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F  62 "    0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   LEU F  62 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   LEU F  62 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLU F  63 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 108 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   VAL D 108 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL D 108 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER D 109 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1602 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 454
        2.69 -     3.25: 11465
        3.25 -     3.80: 25026
        3.80 -     4.35: 31928
        4.35 -     4.90: 46216
  Nonbonded interactions: 115089
  Sorted by model distance:
  nonbonded pdb=" O   TYR L  61 "
            pdb=" NZ  LYS L  65 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   PHE G  25 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" N   THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" NH1 ARG A 129 "
            pdb=" OD1 ASP E 106 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" N4   DC I  51 "
            pdb=" O6   DG J -51 "
     model   vdw
     2.310 3.120
  ... (remaining 115084 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' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and (resid 20 through 100 or (resid 101 and (name N or name CA or nam \ 
e C ))))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = (chain 'L' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ 
 or name CB or name CG or name CD )) or resid 35 through 90 or (resid 91 and (na \ 
me N or name CA or name C or name CB or name CG or name CD or name CE or name NZ \ 
 ))))
}

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=0.00 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:             6.920
  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:          0.590
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     37.450
  Find NCS groups from input model:        0.350
  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:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
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   0.058  14358  Z= 0.173
  Angle     :  0.682  12.723  20622  Z= 0.402
  Chirality :  0.044   0.318   2322
  Planarity :  0.007   0.074   1605
  Dihedral  : 28.540 179.771   6157
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.15 %
    Favored  : 97.72 %
  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:  0.83 (0.27), residues: 913
  helix:  1.72 (0.22), residues: 556
  sheet: -3.79 (0.60), residues: 23
  loop : -1.15 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K  21 
 HIS   0.004   0.001   HIS K  20 
 PHE   0.041   0.002   PHE C  25 
 TYR   0.030   0.001   TYR L  61 
 ARG   0.018   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19305 (  753)
  hydrogen bonds       : angle       6.21305 ( 1899)
  covalent geometry    : bond        0.00373 (14358)
  covalent geometry    : angle       0.68243 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 1.064 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 182
  average time/residue: 0.3900
  time to fit residues: 91.4486
Evaluate side-chains
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   53 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0570
   chunk 91 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.1702

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  46 HIS
E  93 GLN
K  20 HIS
K  72 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.082687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.054286 restraints weight = 42148.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.90
r_work: 0.2793 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14358  Z= 0.198
  Angle     :  0.581   8.442  20622  Z= 0.342
  Chirality :  0.038   0.184   2322
  Planarity :  0.005   0.048   1605
  Dihedral  : 31.110 163.485   4252
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.10 %
    Favored  : 92.14 %
  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:  1.54 (0.28), residues: 913
  helix:  2.29 (0.22), residues: 567
  sheet: -3.55 (0.64), residues: 23
  loop : -1.00 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L  21 
 HIS   0.004   0.001   HIS D  46 
 PHE   0.021   0.002   PHE C  25 
 TYR   0.010   0.001   TYR G  50 
 ARG   0.011   0.001   ARG K  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04996 (  753)
  hydrogen bonds       : angle       3.22171 ( 1899)
  covalent geometry    : bond        0.00451 (14358)
  covalent geometry    : angle       0.58145 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 1.171 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   91 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8064 (tm-30)
REVERT: K   45 PHE cc_start: 0.6404 (m-10) cc_final: 0.6098 (m-10)
REVERT: L   53 LEU cc_start: 0.5027 (OUTLIER) cc_final: 0.4535 (mp)
  outliers start: 6
  outliers final: 3
  residues processed: 118
  average time/residue: 0.3126
  time to fit residues: 50.7306
Evaluate side-chains
  105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   68 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0470
   chunk 78 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.081503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.053242 restraints weight = 42590.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.90
r_work: 0.2768 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14358  Z= 0.187
  Angle     :  0.549   6.649  20622  Z= 0.323
  Chirality :  0.036   0.166   2322
  Planarity :  0.004   0.040   1605
  Dihedral  : 30.611 165.701   4252
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  8.37 %
    Favored  : 90.24 %
  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:  1.77 (0.28), residues: 913
  helix:  2.49 (0.22), residues: 573
  sheet: -3.21 (0.68), residues: 29
  loop : -0.98 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP K  21 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.021   0.002   PHE C  25 
 TYR   0.015   0.001   TYR L  61 
 ARG   0.004   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04718 (  753)
  hydrogen bonds       : angle       3.01849 ( 1899)
  covalent geometry    : bond        0.00424 (14358)
  covalent geometry    : angle       0.54922 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 1.165 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   91 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: D   30 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8472 (ttm170)
REVERT: K   15 MET cc_start: 0.6980 (ppp) cc_final: 0.6751 (ppp)
REVERT: K   45 PHE cc_start: 0.6585 (m-10) cc_final: 0.5725 (m-10)
REVERT: L   53 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4800 (mp)
  outliers start: 11
  outliers final: 3
  residues processed: 115
  average time/residue: 0.3310
  time to fit residues: 52.1620
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   68 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.082002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.054012 restraints weight = 42020.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.88
r_work: 0.2794 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14358  Z= 0.161
  Angle     :  0.517   8.324  20622  Z= 0.305
  Chirality :  0.034   0.158   2322
  Planarity :  0.004   0.078   1605
  Dihedral  : 30.358 172.318   4252
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.00 %
    Favored  : 89.73 %
  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:  2.08 (0.28), residues: 913
  helix:  2.71 (0.22), residues: 575
  sheet: -2.76 (0.64), residues: 37
  loop : -0.79 (0.32), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K  21 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.012   0.001   PHE C  25 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.004   0.000   ARG L  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  753)
  hydrogen bonds       : angle       2.86634 ( 1899)
  covalent geometry    : bond        0.00359 (14358)
  covalent geometry    : angle       0.51712 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 1.110 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8778 (mptp)
REVERT: C   56 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8588 (tt0)
REVERT: D   30 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8438 (ttm170)
REVERT: K   15 MET cc_start: 0.7070 (ppp) cc_final: 0.6650 (ppp)
REVERT: L   53 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4729 (mp)
  outliers start: 10
  outliers final: 5
  residues processed: 111
  average time/residue: 0.3248
  time to fit residues: 48.6070
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain L residue   10 LEU
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   68 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0870
   chunk 86 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
L  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.081399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.053421 restraints weight = 41852.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 1.86
r_work: 0.2778 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.2658 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14358  Z= 0.167
  Angle     :  0.520   6.687  20622  Z= 0.307
  Chirality :  0.035   0.147   2322
  Planarity :  0.004   0.040   1605
  Dihedral  : 30.281 178.809   4252
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.01 %
    Favored  : 88.97 %
  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:  2.15 (0.28), residues: 913
  helix:  2.77 (0.22), residues: 575
  sheet: -2.92 (0.59), residues: 37
  loop : -0.74 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  21 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.015   0.001   PHE C  25 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.003   0.000   ARG L   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  753)
  hydrogen bonds       : angle       2.88465 ( 1899)
  covalent geometry    : bond        0.00375 (14358)
  covalent geometry    : angle       0.52002 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 1.193 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8818 (mptp)
REVERT: C   56 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8802 (tt0)
REVERT: C   91 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8452 (tm-30)
REVERT: D   30 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.8491 (ttm170)
REVERT: K   15 MET cc_start: 0.7250 (ppp) cc_final: 0.6807 (ppp)
REVERT: L    1 MET cc_start: 0.6055 (tpt) cc_final: 0.5449 (tpp)
REVERT: L   53 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.4976 (mp)
  outliers start: 8
  outliers final: 3
  residues processed: 109
  average time/residue: 0.3415
  time to fit residues: 50.6383
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   68 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    0.0020
   chunk 77 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.082077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.054182 restraints weight = 42445.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.87
r_work: 0.2798 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14358  Z= 0.152
  Angle     :  0.503   6.921  20622  Z= 0.298
  Chirality :  0.034   0.148   2322
  Planarity :  0.004   0.046   1605
  Dihedral  : 30.126 178.351   4252
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.65 %
    Favored  : 88.72 %
  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:  2.25 (0.28), residues: 913
  helix:  2.84 (0.22), residues: 577
  sheet: -2.95 (0.55), residues: 37
  loop : -0.67 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP K  21 
 HIS   0.003   0.001   HIS K  20 
 PHE   0.010   0.001   PHE K  59 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.002   0.000   ARG L   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  753)
  hydrogen bonds       : angle       2.78200 ( 1899)
  covalent geometry    : bond        0.00337 (14358)
  covalent geometry    : angle       0.50348 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 1.166 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8733 (mptp)
REVERT: C   56 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8568 (tt0)
REVERT: D   30 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8419 (ttm170)
REVERT: E   73 GLU cc_start: 0.8933 (tt0) cc_final: 0.8717 (tt0)
REVERT: K   15 MET cc_start: 0.7355 (ppp) cc_final: 0.6996 (ppp)
REVERT: K   49 GLU cc_start: 0.6483 (mm-30) cc_final: 0.6141 (mm-30)
REVERT: L    1 MET cc_start: 0.5997 (tpt) cc_final: 0.5386 (tpp)
REVERT: L   53 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.4677 (mp)
  outliers start: 5
  outliers final: 2
  residues processed: 106
  average time/residue: 0.3327
  time to fit residues: 48.4544
Evaluate side-chains
  97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   68 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.080051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.052034 restraints weight = 42190.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 1.85
r_work: 0.2741 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14358  Z= 0.192
  Angle     :  0.534   8.036  20622  Z= 0.314
  Chirality :  0.036   0.150   2322
  Planarity :  0.004   0.042   1605
  Dihedral  : 30.251 174.024   4252
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.90 %
    Favored  : 88.47 %
  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:  2.07 (0.28), residues: 913
  helix:  2.72 (0.22), residues: 574
  sheet: -3.06 (0.54), residues: 37
  loop : -0.76 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP K  21 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.017   0.001   PHE C  25 
 TYR   0.011   0.001   TYR F  51 
 ARG   0.005   0.000   ARG L   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  753)
  hydrogen bonds       : angle       2.93104 ( 1899)
  covalent geometry    : bond        0.00437 (14358)
  covalent geometry    : angle       0.53401 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 1.051 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8818 (mptp)
REVERT: C   56 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8804 (tt0)
REVERT: C   91 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8565 (tm-30)
REVERT: D   30 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8481 (ttm170)
REVERT: K   72 ASN cc_start: 0.7498 (m110) cc_final: 0.7230 (m110)
REVERT: L   53 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5040 (mp)
  outliers start: 5
  outliers final: 1
  residues processed: 101
  average time/residue: 0.3433
  time to fit residues: 46.9887
Evaluate side-chains
  95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain L residue   53 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 111 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
F  18 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.078664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.050703 restraints weight = 42291.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 1.85
r_work: 0.2706 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2586 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8993
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14358  Z= 0.236
  Angle     :  0.566   8.961  20622  Z= 0.330
  Chirality :  0.037   0.137   2322
  Planarity :  0.004   0.043   1605
  Dihedral  : 30.400 171.954   4252
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.90 %
    Favored  : 88.34 %
  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:  1.91 (0.28), residues: 913
  helix:  2.55 (0.22), residues: 576
  sheet: -3.28 (0.52), residues: 38
  loop : -0.71 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.004   TRP K  21 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.021   0.002   PHE L  52 
 TYR   0.011   0.001   TYR B  51 
 ARG   0.013   0.001   ARG L  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04967 (  753)
  hydrogen bonds       : angle       3.04301 ( 1899)
  covalent geometry    : bond        0.00543 (14358)
  covalent geometry    : angle       0.56563 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.205 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8812 (mptp)
REVERT: B   24 ASP cc_start: 0.7714 (p0) cc_final: 0.7496 (p0)
REVERT: C   91 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8522 (tm-30)
REVERT: K   11 ILE cc_start: 0.4484 (OUTLIER) cc_final: 0.4071 (mt)
REVERT: K   72 ASN cc_start: 0.7675 (m110) cc_final: 0.7274 (m110)
REVERT: L   53 LEU cc_start: 0.5614 (OUTLIER) cc_final: 0.5138 (mp)
  outliers start: 6
  outliers final: 1
  residues processed: 99
  average time/residue: 0.3522
  time to fit residues: 47.5201
Evaluate side-chains
  92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain K residue   11 ILE
Chi-restraints excluded: chain L residue   53 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    1.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.078788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.050902 restraints weight = 41783.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 1.84
r_work: 0.2715 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8986
moved from start:          0.4103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14358  Z= 0.220
  Angle     :  0.558  11.566  20622  Z= 0.325
  Chirality :  0.036   0.135   2322
  Planarity :  0.005   0.070   1605
  Dihedral  : 30.353 171.967   4252
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.77 %
    Favored  : 88.34 %
  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:  1.90 (0.28), residues: 913
  helix:  2.62 (0.22), residues: 572
  sheet: -3.35 (0.50), residues: 38
  loop : -0.84 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP K  21 
 HIS   0.005   0.001   HIS L  20 
 PHE   0.017   0.002   PHE C  25 
 TYR   0.011   0.001   TYR F  51 
 ARG   0.005   0.000   ARG L  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04785 (  753)
  hydrogen bonds       : angle       2.98702 ( 1899)
  covalent geometry    : bond        0.00504 (14358)
  covalent geometry    : angle       0.55751 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.240 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8815 (mptp)
REVERT: B   24 ASP cc_start: 0.7628 (p0) cc_final: 0.7423 (p0)
REVERT: C   91 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: K   11 ILE cc_start: 0.4407 (OUTLIER) cc_final: 0.4006 (mt)
REVERT: K   15 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7568 (ppp)
REVERT: K   72 ASN cc_start: 0.7679 (m110) cc_final: 0.7277 (m110)
REVERT: L   53 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5138 (mp)
  outliers start: 7
  outliers final: 1
  residues processed: 99
  average time/residue: 0.3167
  time to fit residues: 43.0004
Evaluate side-chains
  98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain K residue   11 ILE
Chi-restraints excluded: chain K residue   15 MET
Chi-restraints excluded: chain L residue   53 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.079381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.051628 restraints weight = 41813.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 1.84
r_work: 0.2737 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14358  Z= 0.154
  Angle     :  0.538  13.810  20622  Z= 0.315
  Chirality :  0.035   0.135   2322
  Planarity :  0.004   0.060   1605
  Dihedral  : 30.353 172.341   4252
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 11.53 %
    Favored  : 87.96 %
  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:  2.00 (0.28), residues: 913
  helix:  2.71 (0.22), residues: 572
  sheet: -3.36 (0.50), residues: 38
  loop : -0.80 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP K  21 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.020   0.001   PHE L  44 
 TYR   0.021   0.001   TYR L  61 
 ARG   0.004   0.000   ARG L   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04436 (  753)
  hydrogen bonds       : angle       2.92346 ( 1899)
  covalent geometry    : bond        0.00339 (14358)
  covalent geometry    : angle       0.53759 (20622)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 1.043 
Fit side-chains
TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8780 (mptp)
REVERT: C   91 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8485 (tm-30)
REVERT: K   72 ASN cc_start: 0.7668 (m110) cc_final: 0.7269 (m110)
REVERT: K   89 LYS cc_start: 0.7121 (mmmt) cc_final: 0.6550 (mmmt)
REVERT: L   53 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5095 (mp)
  outliers start: 4
  outliers final: 2
  residues processed: 99
  average time/residue: 0.3234
  time to fit residues: 43.6725
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain L residue   53 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.077996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050092 restraints weight = 42169.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 1.85
r_work: 0.2693 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2573 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9003
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  14358  Z= 0.253
  Angle     :  0.582  11.996  20622  Z= 0.337
  Chirality :  0.038   0.135   2322
  Planarity :  0.005   0.063   1605
  Dihedral  : 30.471 169.855   4252
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 11.66 %
    Favored  : 87.83 %
  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:  1.76 (0.28), residues: 913
  helix:  2.48 (0.22), residues: 575
  sheet: -3.40 (0.50), residues: 38
  loop : -0.87 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP K  21 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.019   0.002   PHE C  25 
 TYR   0.011   0.001   TYR G  50 
 ARG   0.025   0.001   ARG L  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05156 (  753)
  hydrogen bonds       : angle       3.07625 ( 1899)
  covalent geometry    : bond        0.00583 (14358)
  covalent geometry    : angle       0.58171 (20622)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7572.87 seconds
wall clock time: 131 minutes 13.77 seconds (7873.77 seconds total)