Starting phenix.real_space_refine
on Sat Oct 11 11:30:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn7_40615/10_2025/8sn7_40615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn7_40615/10_2025/8sn7_40615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn7_40615/10_2025/8sn7_40615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn7_40615/10_2025/8sn7_40615.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn7_40615/10_2025/8sn7_40615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn7_40615/10_2025/8sn7_40615.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14600
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      33.174  72.290  48.380  1.00 72.35           S
  ATOM  12446  SG  CYS K  51      31.114  69.178  47.704  1.00 73.71           S
  ATOM  12470  SG  CYS K  54      32.901  70.989  44.890  1.00 79.16           S
  ATOM  12187  SG  CYS K  16      22.600  66.502  53.978  1.00 79.23           S
  ATOM  12205  SG  CYS K  19      20.009  64.339  55.691  1.00 76.33           S
  ATOM  12335  SG  CYS K  36      23.168  65.453  57.650  1.00 74.99           S
  ATOM  12357  SG  CYS K  39      23.514  62.918  55.146  1.00 76.41           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.75, per 1000 atoms: 0.26
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (110.224, 131.472, 127.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      33     16.00
     P     294     15.00
     O    3289      8.00
     N    2713      7.00
     C    8269      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
  Links applied
    TRANS
      " SER C 124 " - " SER D 123 "
      " SER G-102 " - " SER H 123 "
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 656.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      62.9% alpha, 4.5% beta
      136 base pairs and 244 stacking pairs defined.
    Time for finding SS restraints: 2.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.543A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.683A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.919A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 129 through 134
      removed outlier: 3.864A  pdb=" N   ALA C 134 " --> pdb=" O   ARG C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 150
    Processing helix  chain 'C' and resid 159 through 186
      removed outlier: 3.548A  pdb=" N   LEU C 178 " --> pdb=" O   GLU C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 202
    Processing helix  chain 'C' and resid 203 through 210
    Processing helix  chain 'C' and resid 225 through 229
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.795A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.602A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.697A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 4.006A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.833A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.635A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid -97 through -92
    Processing helix  chain 'G' and resid -86 through -76
    Processing helix  chain 'G' and resid -67 through -40
    Processing helix  chain 'G' and resid -34 through -23
      removed outlier: 3.658A  pdb=" N   ASP G -23 " --> pdb=" O   ALA G -27 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid -22 through -16
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.549A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.650A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.730A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.895A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.861A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 90
      removed outlier: 3.567A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.676A  pdb=" N   ARG L   5 " --> pdb=" O   MET L   1 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP L  16 " --> pdb=" O   ASP L  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 4.132A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.575A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 143
      removed outlier: 3.968A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 34
    Processing helix  chain 'M' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.099A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 156
      removed outlier: 8.078A  pdb=" N   ARG C 155 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 191
    Processing sheet with id=AA6, first strand: chain 'C' and resid 214 through 215
      removed outlier: 7.013A  pdb=" N   THR C 214 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.205A  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 -71 through -70
      removed outlier: 7.725A  pdb=" N   ARG G -71 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28
      removed outlier: 3.558A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB3, first strand: chain 'M' and resid 5 through 6

    491 hydrogen bonds defined for protein.
    1437 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      244 stacking parallelities
  Total time for adding SS restraints: 3.15

  Time building geometry restraints manager: 1.80 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: 3222
        1.33 -     1.45: 4431
        1.45 -     1.57: 7184
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" CG  LEU M  50 "
       pdb=" CD1 LEU M  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.08e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.33e+00
  bond pdb=" CB  GLU C 174 "
       pdb=" CG  GLU C 174 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.09e+00
  bond pdb=" CB  CYS E  96 "
       pdb=" SG  CYS E  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.775  0.033 3.30e-02 9.18e+02 1.02e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.452 -0.030 3.00e-02 1.11e+03 1.02e+00
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 21582
        1.56 -     3.12: 539
        3.12 -     4.68: 28
        4.68 -     6.24: 15
        6.24 -     7.80: 7
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" C   CYS K  31 "
        pdb=" N   ASN K  32 "
        pdb=" CA  ASN K  32 "
      ideal   model   delta    sigma   weight residual
     121.54  128.11   -6.57 1.91e+00 2.74e-01 1.18e+01
  angle pdb=" C3'  DG J -70 "
        pdb=" C2'  DG J -70 "
        pdb=" C1'  DG J -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.65   -4.05 1.50e+00 4.44e-01 7.31e+00
  angle pdb=" CB  MET L  38 "
        pdb=" CG  MET L  38 "
        pdb=" SD  MET L  38 "
      ideal   model   delta    sigma   weight residual
     112.70  120.02   -7.32 3.00e+00 1.11e-01 5.95e+00
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     122.46  125.89   -3.43 1.41e+00 5.03e-01 5.93e+00
  angle pdb=" CB  MET H  59 "
        pdb=" CG  MET H  59 "
        pdb=" SD  MET H  59 "
      ideal   model   delta    sigma   weight residual
     112.70  105.40    7.30 3.00e+00 1.11e-01 5.92e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 7274
       35.74 -    71.48: 1319
       71.48 -   107.22: 16
      107.22 -   142.96: 0
      142.96 -   178.70: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.30  178.70     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.18  149.82     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CB  GLU D 105 "
           pdb=" CG  GLU D 105 "
           pdb=" CD  GLU D 105 "
           pdb=" OE1 GLU D 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.83  -89.83     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1777
       0.032 -    0.065: 559
       0.065 -    0.097: 128
       0.097 -    0.129: 46
       0.129 -    0.162: 6
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CG  LEU F  62 "
            pdb=" CB  LEU F  62 "
            pdb=" CD1 LEU F  62 "
            pdb=" CD2 LEU F  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  ASN K  32 "
            pdb=" N   ASN K  32 "
            pdb=" C   ASN K  32 "
            pdb=" CB  ASN K  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "   -0.048 5.00e-02 4.00e+02   7.34e-02 8.63e+00
        pdb=" N   PRO L  61 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K  37 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO K  38 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO K  38 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO K  38 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.027 2.00e-02 2.50e+03   1.15e-02 3.66e+00
        pdb=" N9   DA I -35 "    0.024 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1637
        2.75 -     3.29: 13071
        3.29 -     3.82: 27060
        3.82 -     4.36: 31252
        4.36 -     4.90: 46874
  Nonbonded interactions: 119894
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.210 2.496
  nonbonded pdb=" OG  SER L 138 "
            pdb=" NH1 ARG L 139 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   PRO L  40 "
            pdb=" OG  SER L  43 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   TYR C 152 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ARG L 125 "
            pdb=" OG1 THR L 129 "
     model   vdw
     2.300 3.040
  ... (remaining 119889 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid -102 through 5)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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 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:             1.570
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     19.120
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
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   0.048  15482  Z= 0.165
  Angle     :  0.572   8.823  22186  Z= 0.329
  Chirality :  0.035   0.162   2516
  Planarity :  0.004   0.073   1794
  Dihedral  : 25.759 178.704   6577
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.26), residues: 1057
  helix:  2.34 (0.21), residues: 627
  sheet: -1.13 (0.72), residues: 41
  loop : -0.41 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 125 
 TYR   0.025   0.002   TYR M  59 
 PHE   0.008   0.001   PHE E  78 
 TRP   0.007   0.001   TRP K  77 
 HIS   0.004   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (15472)
  covalent geometry    : angle       0.56729 (22171)
  hydrogen bonds       : bond        0.10596 (  840)
  hydrogen bonds       : angle       4.21654 ( 2131)
  metal coordination   : bond        0.00765 (    8)
  metal coordination   : angle       3.87919 (    9)
  link_TRANS           : bond        0.00083 (    2)
  link_TRANS           : angle       0.23139 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  116 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8564 (ttmm)
REVERT: E   76 GLN cc_start: 0.8261 (pp30) cc_final: 0.8002 (pp30)
REVERT: H   34 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8899 (mtmm)
REVERT: H   86 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7804 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8569 (ttpp)
REVERT: L   63 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8253 (mttt)
REVERT: L  114 ASN cc_start: 0.7881 (t0) cc_final: 0.7667 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1550
  time to fit residues: 47.7196
Evaluate side-chains
  189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
F  25 ASN
G -29 GLN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.135522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.083173 restraints weight = 42406.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.085323 restraints weight = 23520.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.086077 restraints weight = 15801.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.086074 restraints weight = 14588.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.086289 restraints weight = 14371.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15482  Z= 0.181
  Angle     :  0.598  11.829  22186  Z= 0.338
  Chirality :  0.036   0.165   2516
  Planarity :  0.005   0.050   1794
  Dihedral  : 28.860 179.559   4413
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.61 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.27), residues: 1057
  helix:  2.37 (0.21), residues: 643
  sheet: -1.07 (0.80), residues: 34
  loop : -0.63 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  92 
 TYR   0.021   0.002   TYR D  83 
 PHE   0.011   0.001   PHE L  62 
 TRP   0.021   0.002   TRP L  33 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (15472)
  covalent geometry    : angle       0.59017 (22171)
  hydrogen bonds       : bond        0.04889 (  840)
  hydrogen bonds       : angle       3.65126 ( 2131)
  metal coordination   : bond        0.00508 (    8)
  metal coordination   : angle       4.92649 (    9)
  link_TRANS           : bond        0.00150 (    2)
  link_TRANS           : angle       0.49927 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 194
  time to evaluate  : 0.417 
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: D  116 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8451 (ttmm)
REVERT: E   76 GLN cc_start: 0.8310 (pp30) cc_final: 0.8013 (pp30)
REVERT: E  120 MET cc_start: 0.8352 (mtp) cc_final: 0.8112 (mtt)
REVERT: G  -38 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8803 (mmmm)
REVERT: H   34 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8928 (mtmm)
REVERT: H   86 ARG cc_start: 0.8203 (mmt90) cc_final: 0.7921 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8537 (ttpt)
REVERT: L    8 LYS cc_start: 0.9414 (mmtm) cc_final: 0.9164 (mmtt)
REVERT: L   63 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8270 (mttt)
REVERT: L  127 TYR cc_start: 0.8008 (t80) cc_final: 0.7327 (t80)
REVERT: L  135 ASN cc_start: 0.9116 (m-40) cc_final: 0.8866 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 197
  average time/residue: 0.1545
  time to fit residues: 42.2909
Evaluate side-chains
  193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 185
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain M residue   13 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   chunk 100 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9980
   chunk 101 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  92 GLN
M  40 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.136127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.099083 restraints weight = 37632.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.102372 restraints weight = 64763.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.103161 restraints weight = 26321.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.107685 restraints weight = 19408.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107432 restraints weight = 11945.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15482  Z= 0.161
  Angle     :  0.581  14.206  22186  Z= 0.328
  Chirality :  0.035   0.157   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 28.935 179.941   4413
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.58 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.27), residues: 1057
  helix:  2.36 (0.21), residues: 654
  sheet: -1.58 (0.73), residues: 33
  loop : -0.63 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  92 
 TYR   0.017   0.002   TYR L 134 
 PHE   0.008   0.001   PHE L  50 
 TRP   0.030   0.003   TRP L  33 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (15472)
  covalent geometry    : angle       0.56955 (22171)
  hydrogen bonds       : bond        0.04550 (  840)
  hydrogen bonds       : angle       3.50174 ( 2131)
  metal coordination   : bond        0.00896 (    8)
  metal coordination   : angle       5.75403 (    9)
  link_TRANS           : bond        0.00089 (    2)
  link_TRANS           : angle       0.42051 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 0.413 
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: symmetry clash
   revert: symmetry clash
REVERT: E   76 GLN cc_start: 0.8411 (pp30) cc_final: 0.7997 (pp30)
REVERT: E  120 MET cc_start: 0.8297 (mtp) cc_final: 0.8086 (mtt)
REVERT: H   34 LYS cc_start: 0.9134 (mtmm) cc_final: 0.8881 (mtmm)
REVERT: H   86 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7876 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8579 (ttpt)
REVERT: L   63 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8353 (mttt)
REVERT: L  135 ASN cc_start: 0.8478 (m-40) cc_final: 0.8159 (m-40)
REVERT: L  147 MET cc_start: 0.7075 (mpp) cc_final: 0.6779 (mpp)
  outliers start: 18
  outliers final: 13
  residues processed: 202
  average time/residue: 0.1462
  time to fit residues: 41.5165
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue  140 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0870
   chunk 45 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 128 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
G -29 GLN
L  32 HIS
L  41 ASN
L  92 GLN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.074962 restraints weight = 50065.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.077818 restraints weight = 22483.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.079725 restraints weight = 14333.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.080838 restraints weight = 11269.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.081345 restraints weight = 9984.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15482  Z= 0.154
  Angle     :  0.581  15.214  22186  Z= 0.327
  Chirality :  0.035   0.158   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 28.978 179.729   4413
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.31 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.27), residues: 1057
  helix:  2.48 (0.21), residues: 648
  sheet: -1.37 (0.74), residues: 33
  loop : -0.60 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L   5 
 TYR   0.022   0.001   TYR K  84 
 PHE   0.020   0.002   PHE L  62 
 TRP   0.032   0.003   TRP L  33 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (15472)
  covalent geometry    : angle       0.56808 (22171)
  hydrogen bonds       : bond        0.04413 (  840)
  hydrogen bonds       : angle       3.43165 ( 2131)
  metal coordination   : bond        0.00663 (    8)
  metal coordination   : angle       5.97416 (    9)
  link_TRANS           : bond        0.00084 (    2)
  link_TRANS           : angle       0.38527 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 192
  time to evaluate  : 0.447 
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   59 GLU cc_start: 0.8752 (pm20) cc_final: 0.8301 (pm20)
REVERT: E   76 GLN cc_start: 0.8503 (pp30) cc_final: 0.8106 (pp30)
REVERT: E  120 MET cc_start: 0.8324 (mtp) cc_final: 0.8113 (mtt)
REVERT: H   34 LYS cc_start: 0.9230 (mtmm) cc_final: 0.8915 (mtmm)
REVERT: H   86 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7999 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8436 (ttpt)
REVERT: L    0 HIS cc_start: 0.8535 (t-90) cc_final: 0.7922 (t-90)
REVERT: L    1 MET cc_start: 0.8323 (mmm) cc_final: 0.7996 (mmm)
REVERT: L   63 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8022 (mttt)
REVERT: L  135 ASN cc_start: 0.9092 (m-40) cc_final: 0.8821 (m-40)
REVERT: L  147 MET cc_start: 0.8689 (mpp) cc_final: 0.8383 (mpp)
  outliers start: 16
  outliers final: 12
  residues processed: 197
  average time/residue: 0.1436
  time to fit residues: 39.7135
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 188
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 126 optimal weight:   20.0000
   chunk 60 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
G -29 GLN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  92 GLN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.132628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.079920 restraints weight = 41560.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.081226 restraints weight = 23531.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.081958 restraints weight = 16106.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.081974 restraints weight = 14802.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.082332 restraints weight = 14311.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15482  Z= 0.182
  Angle     :  0.598  14.400  22186  Z= 0.335
  Chirality :  0.035   0.157   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 29.097 179.162   4413
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.50 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 647
  sheet: -1.37 (0.77), residues: 33
  loop : -0.58 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L   5 
 TYR   0.021   0.002   TYR D  83 
 PHE   0.019   0.002   PHE L  62 
 TRP   0.027   0.003   TRP L  33 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (15472)
  covalent geometry    : angle       0.58636 (22171)
  hydrogen bonds       : bond        0.04736 (  840)
  hydrogen bonds       : angle       3.51687 ( 2131)
  metal coordination   : bond        0.00734 (    8)
  metal coordination   : angle       5.78316 (    9)
  link_TRANS           : bond        0.00144 (    2)
  link_TRANS           : angle       0.45925 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 189
  time to evaluate  : 0.317 
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   59 GLU cc_start: 0.8777 (pm20) cc_final: 0.8353 (pm20)
REVERT: E   94 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8466 (mm-30)
REVERT: H   34 LYS cc_start: 0.9268 (mtmm) cc_final: 0.8952 (mtmm)
REVERT: H   86 ARG cc_start: 0.8271 (mmt90) cc_final: 0.8007 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8437 (ttpt)
REVERT: L    0 HIS cc_start: 0.8445 (t-90) cc_final: 0.7955 (t-90)
REVERT: L    1 MET cc_start: 0.8351 (mmm) cc_final: 0.8138 (mmm)
REVERT: L    5 ARG cc_start: 0.9253 (ttt-90) cc_final: 0.8864 (ttt-90)
REVERT: L   92 GLN cc_start: 0.8084 (mm110) cc_final: 0.7223 (mm-40)
REVERT: L  135 ASN cc_start: 0.9064 (m-40) cc_final: 0.8766 (m-40)
REVERT: L  147 MET cc_start: 0.8643 (mpp) cc_final: 0.8351 (mpp)
  outliers start: 19
  outliers final: 15
  residues processed: 193
  average time/residue: 0.1423
  time to fit residues: 38.5175
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 122 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
G -29 GLN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  46 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.078512 restraints weight = 41742.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.081161 restraints weight = 23874.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.082112 restraints weight = 16734.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.082609 restraints weight = 13451.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.082792 restraints weight = 13879.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2794
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2794
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15482  Z= 0.171
  Angle     :  0.593  13.673  22186  Z= 0.332
  Chirality :  0.035   0.274   2516
  Planarity :  0.004   0.051   1794
  Dihedral  : 29.133 179.310   4413
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.58 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.27), residues: 1057
  helix:  2.44 (0.21), residues: 648
  sheet: -1.24 (0.80), residues: 33
  loop : -0.53 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  92 
 TYR   0.017   0.002   TYR D  83 
 PHE   0.021   0.001   PHE L  62 
 TRP   0.021   0.002   TRP L 141 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (15472)
  covalent geometry    : angle       0.58295 (22171)
  hydrogen bonds       : bond        0.04622 (  840)
  hydrogen bonds       : angle       3.44220 ( 2131)
  metal coordination   : bond        0.00678 (    8)
  metal coordination   : angle       5.55873 (    9)
  link_TRANS           : bond        0.00101 (    2)
  link_TRANS           : angle       0.41729 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.413 
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: symmetry clash
REVERT: A   59 GLU cc_start: 0.8742 (pm20) cc_final: 0.8302 (pm20)
REVERT: E   94 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8459 (mm-30)
REVERT: F   25 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9062 (t0)
REVERT: H   34 LYS cc_start: 0.9249 (mtmm) cc_final: 0.8939 (mtmm)
REVERT: H   86 ARG cc_start: 0.8243 (mmt90) cc_final: 0.7991 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8451 (ttpt)
REVERT: L    0 HIS cc_start: 0.8464 (t-90) cc_final: 0.7875 (t-90)
REVERT: L    1 MET cc_start: 0.8443 (mmm) cc_final: 0.8188 (mmm)
REVERT: L    5 ARG cc_start: 0.9247 (ttt-90) cc_final: 0.8893 (ttt-90)
REVERT: L  135 ASN cc_start: 0.9088 (m-40) cc_final: 0.8718 (m-40)
REVERT: L  147 MET cc_start: 0.8727 (mpp) cc_final: 0.8453 (mpp)
  outliers start: 23
  outliers final: 19
  residues processed: 198
  average time/residue: 0.1463
  time to fit residues: 40.6214
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
L  32 HIS
L  46 GLN
L  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.133335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.080543 restraints weight = 43408.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.082037 restraints weight = 23647.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.083095 restraints weight = 16245.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.083040 restraints weight = 15036.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.083254 restraints weight = 13765.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15482  Z= 0.164
  Angle     :  0.590  13.187  22186  Z= 0.330
  Chirality :  0.035   0.324   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 29.145 179.390   4413
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.34 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.27), residues: 1057
  helix:  2.45 (0.21), residues: 647
  sheet: -1.11 (0.82), residues: 33
  loop : -0.53 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L   5 
 TYR   0.018   0.001   TYR L 134 
 PHE   0.024   0.002   PHE L  62 
 TRP   0.015   0.002   TRP L  33 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (15472)
  covalent geometry    : angle       0.58019 (22171)
  hydrogen bonds       : bond        0.04525 (  840)
  hydrogen bonds       : angle       3.40258 ( 2131)
  metal coordination   : bond        0.00710 (    8)
  metal coordination   : angle       5.37600 (    9)
  link_TRANS           : bond        0.00088 (    2)
  link_TRANS           : angle       0.37842 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 0.414 
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: symmetry clash
REVERT: A   59 GLU cc_start: 0.8717 (pm20) cc_final: 0.8284 (pm20)
REVERT: E   94 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8455 (mm-30)
REVERT: F   25 ASN cc_start: 0.9364 (OUTLIER) cc_final: 0.9103 (t0)
REVERT: H   34 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8962 (mtmm)
REVERT: H   86 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7987 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8439 (ttpt)
REVERT: L    5 ARG cc_start: 0.9230 (ttt-90) cc_final: 0.8912 (ttt-90)
REVERT: L  135 ASN cc_start: 0.9105 (m-40) cc_final: 0.8714 (m-40)
REVERT: L  140 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8523 (pm20)
REVERT: L  147 MET cc_start: 0.8708 (mpp) cc_final: 0.8452 (mpp)
  outliers start: 23
  outliers final: 17
  residues processed: 193
  average time/residue: 0.1280
  time to fit residues: 35.3040
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0970
   chunk 45 optimal weight:    0.8980
   chunk 120 optimal weight:    0.2980
   chunk 116 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 127 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:   20.0000
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
L  32 HIS
L  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.132375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.077125 restraints weight = 47721.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.079952 restraints weight = 21869.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.081816 restraints weight = 14078.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.082929 restraints weight = 11086.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.083484 restraints weight = 9822.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.144
  Angle     :  0.581  12.381  22186  Z= 0.325
  Chirality :  0.034   0.243   2516
  Planarity :  0.004   0.046   1794
  Dihedral  : 29.084 179.320   4413
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.75 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.27), residues: 1057
  helix:  2.53 (0.21), residues: 648
  sheet: -1.45 (0.64), residues: 48
  loop : -0.51 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  72 
 TYR   0.020   0.001   TYR L  45 
 PHE   0.020   0.001   PHE L  50 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (15472)
  covalent geometry    : angle       0.57249 (22171)
  hydrogen bonds       : bond        0.04147 (  840)
  hydrogen bonds       : angle       3.26774 ( 2131)
  metal coordination   : bond        0.00502 (    8)
  metal coordination   : angle       5.10387 (    9)
  link_TRANS           : bond        0.00068 (    2)
  link_TRANS           : angle       0.27806 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 185
  time to evaluate  : 0.421 
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   59 GLU cc_start: 0.8690 (pm20) cc_final: 0.8174 (pm20)
REVERT: B   84 MET cc_start: 0.8333 (tpp) cc_final: 0.8074 (tpt)
REVERT: G  -38 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8498 (mmmm)
REVERT: H   34 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8921 (mtmm)
REVERT: H   86 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7942 (mmt-90)
REVERT: H  120 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8405 (ttpt)
REVERT: L    5 ARG cc_start: 0.9133 (ttt-90) cc_final: 0.8849 (ttt-90)
REVERT: L  133 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8180 (pttt)
REVERT: L  135 ASN cc_start: 0.9177 (m-40) cc_final: 0.8816 (m-40)
REVERT: L  140 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8449 (pm20)
REVERT: L  147 MET cc_start: 0.8617 (mpp) cc_final: 0.8403 (mpp)
  outliers start: 15
  outliers final: 12
  residues processed: 193
  average time/residue: 0.1389
  time to fit residues: 37.7490
Evaluate side-chains
  194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue   -5 LEU
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  133 LYS
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
M  41 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.090332 restraints weight = 36572.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.090644 restraints weight = 30309.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.091695 restraints weight = 24084.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.092233 restraints weight = 18191.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.092591 restraints weight = 17795.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2982
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2982
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15482  Z= 0.165
  Angle     :  0.594  12.729  22186  Z= 0.330
  Chirality :  0.035   0.174   2516
  Planarity :  0.004   0.047   1794
  Dihedral  : 29.145 179.130   4413
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 18.18 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.26), residues: 1057
  helix:  2.50 (0.21), residues: 647
  sheet: -1.38 (0.65), residues: 48
  loop : -0.53 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  35 
 TYR   0.018   0.001   TYR L 134 
 PHE   0.020   0.001   PHE L  51 
 TRP   0.007   0.001   TRP L 141 
 HIS   0.004   0.001   HIS L   0 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (15472)
  covalent geometry    : angle       0.58445 (22171)
  hydrogen bonds       : bond        0.04486 (  840)
  hydrogen bonds       : angle       3.34899 ( 2131)
  metal coordination   : bond        0.00650 (    8)
  metal coordination   : angle       5.21871 (    9)
  link_TRANS           : bond        0.00102 (    2)
  link_TRANS           : angle       0.34542 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 182
  time to evaluate  : 0.407 
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   59 GLU cc_start: 0.8668 (pm20) cc_final: 0.8179 (pm20)
REVERT: E   94 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8429 (mm-30)
REVERT: G  -38 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8509 (mmmm)
REVERT: H   34 LYS cc_start: 0.9196 (mtmm) cc_final: 0.8912 (mtmm)
REVERT: H   86 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7936 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8514 (ttpt)
REVERT: K   42 SER cc_start: 0.7572 (p) cc_final: 0.7363 (p)
REVERT: L  135 ASN cc_start: 0.8656 (m-40) cc_final: 0.8414 (m-40)
REVERT: L  140 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7751 (pm20)
  outliers start: 15
  outliers final: 13
  residues processed: 187
  average time/residue: 0.1432
  time to fit residues: 37.8260
Evaluate side-chains
  194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0870
   chunk 42 optimal weight:    0.5980
   chunk 121 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    1.0360

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

Flipped N/Q/H residues before XYZ refinement:
L  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.133014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.079456 restraints weight = 49759.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.080771 restraints weight = 26769.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.081802 restraints weight = 20298.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.082603 restraints weight = 14675.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.083007 restraints weight = 13495.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15482  Z= 0.180
  Angle     :  0.615  13.541  22186  Z= 0.339
  Chirality :  0.035   0.180   2516
  Planarity :  0.004   0.054   1794
  Dihedral  : 29.195 179.176   4413
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 18.40 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.26), residues: 1057
  helix:  2.43 (0.21), residues: 648
  sheet: -1.31 (0.66), residues: 48
  loop : -0.56 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L   5 
 TYR   0.019   0.002   TYR L 134 
 PHE   0.020   0.001   PHE L  62 
 TRP   0.006   0.001   TRP L 141 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (15472)
  covalent geometry    : angle       0.60471 (22171)
  hydrogen bonds       : bond        0.04720 (  840)
  hydrogen bonds       : angle       3.40395 ( 2131)
  metal coordination   : bond        0.00731 (    8)
  metal coordination   : angle       5.51474 (    9)
  link_TRANS           : bond        0.00126 (    2)
  link_TRANS           : angle       0.36870 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 182
  time to evaluate  : 0.422 
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   59 GLU cc_start: 0.8693 (pm20) cc_final: 0.8223 (pm20)
REVERT: E   94 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8477 (mm-30)
REVERT: G  -38 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8516 (mmmm)
REVERT: H   34 LYS cc_start: 0.9244 (mtmm) cc_final: 0.8964 (mtmm)
REVERT: H   86 ARG cc_start: 0.8216 (mmt90) cc_final: 0.7971 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8448 (ttpt)
REVERT: L    8 LYS cc_start: 0.9335 (mmtm) cc_final: 0.9134 (mmtm)
REVERT: L  135 ASN cc_start: 0.9186 (m-40) cc_final: 0.8969 (m-40)
REVERT: L  140 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8456 (pm20)
  outliers start: 15
  outliers final: 13
  residues processed: 188
  average time/residue: 0.1475
  time to fit residues: 38.9723
Evaluate side-chains
  195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 128 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   chunk 87 optimal weight:    6.9990
   chunk 123 optimal weight:   30.0000
   chunk 127 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
L  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.134139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.080636 restraints weight = 43196.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.082993 restraints weight = 26015.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.083602 restraints weight = 17101.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.084152 restraints weight = 14151.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.084272 restraints weight = 14042.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.153
  Angle     :  0.600  12.500  22186  Z= 0.332
  Chirality :  0.034   0.160   2516
  Planarity :  0.005   0.096   1794
  Dihedral  : 29.140 179.313   4413
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.40 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.26), residues: 1057
  helix:  2.49 (0.21), residues: 651
  sheet: -1.32 (0.66), residues: 48
  loop : -0.55 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG L   5 
 TYR   0.018   0.001   TYR L 134 
 PHE   0.029   0.001   PHE L  62 
 TRP   0.008   0.001   TRP L  33 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (15472)
  covalent geometry    : angle       0.59107 (22171)
  hydrogen bonds       : bond        0.04407 (  840)
  hydrogen bonds       : angle       3.27951 ( 2131)
  metal coordination   : bond        0.00671 (    8)
  metal coordination   : angle       5.27801 (    9)
  link_TRANS           : bond        0.00074 (    2)
  link_TRANS           : angle       0.27118 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2677.77 seconds
wall clock time: 46 minutes 45.11 seconds (2805.11 seconds total)