Starting phenix.real_space_refine
on Sun Nov 17 11:35:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/11_2024/8of4_16845.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/11_2024/8of4_16845.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/11_2024/8of4_16845.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/11_2024/8of4_16845.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/11_2024/8of4_16845.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8of4_16845/11_2024/8of4_16845.cif"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.010 sd=   0.087
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      1      6.06       5
     P     288      5.49       5
     S      21      5.16       5
     C    7933      2.51       5
     N    2664      2.21       5
     O    3180      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 116 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 14087
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 916
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
    Chain: "D"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 785
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 703
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    Chain: "G"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 832
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 785
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "L"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1850
          Classifications: {'peptide': 237}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 226}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12968  SG  CYS L 141      43.940  64.998  46.759  1.00 66.29           S
  ATOM  12988  SG  CYS L 144      43.083  62.071  45.610  1.00 61.78           S
  ATOM  13153  SG  CYS L 166      41.246  63.788  49.455  1.00 72.90           S
  ATOM  13231  SG  CYS L 177      44.562  61.755  48.746  1.00 71.13           S

  Time building chain proxies: 8.47, per 1000 atoms: 0.60
  Number of scatterers: 14087
  At special positions: 0
  Unit cell: (110.836, 118.164, 121.828, 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      1     29.99
     S      21     16.00
     P     288     15.00
     O    3180      8.00
     N    2664      7.00
     C    7933      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.62
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L 401 "
        pdb="ZN    ZN L 401 " - pdb=" SG  CYS L 144 "
        pdb="ZN    ZN L 401 " - pdb=" SG  CYS L 177 "
        pdb="ZN    ZN L 401 " - pdb=" SG  CYS L 141 "
        pdb="ZN    ZN L 401 " - pdb=" SG  CYS L 166 "
      Number of angles added : 6


  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      63.1% alpha, 4.2% beta
      141 base pairs and 258 stacking pairs defined.
    Time for finding SS restraints: 6.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.521A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.786A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 5 through 11
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.293A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.663A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.595A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.588A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   THR D  93 " --> pdb=" O   ARG D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 120
      removed outlier: 3.985A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.578A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.509A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.535A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.311A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.637A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 120
      removed outlier: 3.738A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 27 through 44
    Processing helix  chain 'L' and resid 52 through 58
      removed outlier: 4.444A  pdb=" N   SER L  56 " --> pdb=" O   GLY L  52 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 92 through 104
    Processing helix  chain 'L' and resid 117 through 122
    Processing helix  chain 'L' and resid 125 through 127
      No H-bonds generated for 'chain 'L' and resid 125 through 127'
    Processing helix  chain 'L' and resid 193 through 206
    Processing helix  chain 'L' and resid 221 through 223
      No H-bonds generated for 'chain 'L' and resid 221 through 223'
    Processing helix  chain 'L' and resid 224 through 232
      removed outlier: 3.745A  pdb=" N   ALA L 228 " --> pdb=" O   ASN L 224 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   THR L 229 " --> pdb=" O   LEU L 225 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS L 230 " --> pdb=" O   PRO L 226 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 246 through 250
      removed outlier: 4.150A  pdb=" N   ALA L 250 " --> pdb=" O   ASP L 247 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 257 through 269
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.840A  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 42 through 43
      removed outlier: 6.733A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.737A  pdb=" N   THR C 101 " --> 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: 6.898A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.060A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'L' and resid 129 through 131
      removed outlier: 6.728A  pdb=" N   VAL L  47 " --> pdb=" O   PHE L 109 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   VAL L 111 " --> pdb=" O   VAL L  47 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   PHE L  49 " --> pdb=" O   VAL L 111 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   VAL L  48 " --> pdb=" O   ILE L 211 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   LEU L 213 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   HIS L  50 " --> pdb=" O   LEU L 213 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   SER L 210 " --> pdb=" O   VAL L 237 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   VAL L 239 " --> pdb=" O   SER L 210 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   THR L 212 " --> pdb=" O   VAL L 239 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LEU L 236 " --> pdb=" O   LEU L 252 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   ILE L 254 " --> pdb=" O   LEU L 236 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE L 238 " --> pdb=" O   ILE L 254 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 139 through 141

    455 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      354 hydrogen bonds
      708 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      258 stacking parallelities
  Total time for adding SS restraints: 5.85

  Time building geometry restraints manager: 4.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3203
        1.33 -     1.46: 4238
        1.46 -     1.58: 6863
        1.58 -     1.70: 580
        1.70 -     1.82: 37
  Bond restraints: 14921
  Sorted by residual:
  bond pdb=" C5   DT I -65 "
       pdb=" C7   DT I -65 "
    ideal  model  delta    sigma   weight residual
    1.500  1.817 -0.317 2.00e-02 2.50e+03 2.52e+02
  bond pdb=" C5   DT I -59 "
       pdb=" C7   DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.500  1.662 -0.162 2.00e-02 2.50e+03 6.54e+01
  bond pdb=" N   LYS C 119 "
       pdb=" CA  LYS C 119 "
    ideal  model  delta    sigma   weight residual
    1.454  1.517 -0.063 1.27e-02 6.20e+03 2.45e+01
  bond pdb=" CZ  ARG H  96 "
       pdb=" NH2 ARG H  96 "
    ideal  model  delta    sigma   weight residual
    1.330  1.283  0.047 1.30e-02 5.92e+03 1.29e+01
  bond pdb=" CZ  ARG A  72 "
       pdb=" NH2 ARG A  72 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.17e+01
  ... (remaining 14916 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.50: 21376
       12.50 -    25.01: 1
       25.01 -    37.51: 1
       37.51 -    50.01: 0
       50.01 -    62.52: 1
  Bond angle restraints: 21379
  Sorted by residual:
  angle pdb=" O   LYS C 118 "
        pdb=" C   LYS C 118 "
        pdb=" N   LYS C 119 "
      ideal   model   delta    sigma   weight residual
     122.96   60.44   62.52 1.26e+00 6.30e-01 2.46e+03
  angle pdb=" O   SER C 122 "
        pdb=" C   SER C 122 "
        pdb=" N   ALA C 123 "
      ideal   model   delta    sigma   weight residual
     122.04   95.03   27.01 1.35e+00 5.49e-01 4.00e+02
  angle pdb=" CA  PRO E  38 "
        pdb=" N   PRO E  38 "
        pdb=" CD  PRO E  38 "
      ideal   model   delta    sigma   weight residual
     112.00  100.79   11.21 1.40e+00 5.10e-01 6.41e+01
  angle pdb=" CA  LYS C 118 "
        pdb=" C   LYS C 118 "
        pdb=" O   LYS C 118 "
      ideal   model   delta    sigma   weight residual
     121.51  112.88    8.63 1.12e+00 7.97e-01 5.94e+01
  angle pdb=" C   SER C 122 "
        pdb=" N   ALA C 123 "
        pdb=" CA  ALA C 123 "
      ideal   model   delta    sigma   weight residual
     121.70  134.68  -12.98 1.80e+00 3.09e-01 5.20e+01
  ... (remaining 21374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.84: 6991
       33.84 -    67.68: 1230
       67.68 -   101.51: 49
      101.51 -   135.35: 1
      135.35 -   169.19: 3
  Dihedral angle restraints: 8274
    sinusoidal: 5309
      harmonic: 2965
  Sorted by residual:
  dihedral pdb=" CA  LYS C 118 "
           pdb=" C   LYS C 118 "
           pdb=" N   LYS C 119 "
           pdb=" CA  LYS C 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.20  -28.80     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  THR L 215 "
           pdb=" C   THR L 215 "
           pdb=" N   SER L 216 "
           pdb=" CA  SER L 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.22   28.78     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  LEU L 186 "
           pdb=" C   LEU L 186 "
           pdb=" N   ASP L 187 "
           pdb=" CA  ASP L 187 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.26  -28.74     0      5.00e+00 4.00e-02 3.30e+01
  ... (remaining 8271 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 1880
       0.101 -    0.202: 457
       0.202 -    0.303: 62
       0.303 -    0.404: 28
       0.404 -    0.505: 2
  Chirality restraints: 2429
  Sorted by residual:
  chirality pdb=" C3'  DT J -17 "
            pdb=" C4'  DT J -17 "
            pdb=" O3'  DT J -17 "
            pdb=" C2'  DT J -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.16   -0.50 2.00e-01 2.50e+01 6.38e+00
  chirality pdb=" C3'  DG J  20 "
            pdb=" C4'  DG J  20 "
            pdb=" O3'  DG J  20 "
            pdb=" C2'  DG J  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.22   -0.44 2.00e-01 2.50e+01 4.87e+00
  chirality pdb=" CA  ASP A  81 "
            pdb=" N   ASP A  81 "
            pdb=" C   ASP A  81 "
            pdb=" CB  ASP A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.78e+00
  ... (remaining 2426 not shown)

  Planarity restraints: 1708
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  70 "   -0.449 2.00e-02 2.50e+03   1.88e-01 1.05e+03
        pdb=" N9   DG J  70 "    0.082 2.00e-02 2.50e+03
        pdb=" C8   DG J  70 "    0.228 2.00e-02 2.50e+03
        pdb=" N7   DG J  70 "    0.178 2.00e-02 2.50e+03
        pdb=" C5   DG J  70 "    0.064 2.00e-02 2.50e+03
        pdb=" C6   DG J  70 "   -0.085 2.00e-02 2.50e+03
        pdb=" O6   DG J  70 "   -0.276 2.00e-02 2.50e+03
        pdb=" N1   DG J  70 "   -0.052 2.00e-02 2.50e+03
        pdb=" C2   DG J  70 "    0.013 2.00e-02 2.50e+03
        pdb=" N2   DG J  70 "    0.178 2.00e-02 2.50e+03
        pdb=" N3   DG J  70 "    0.039 2.00e-02 2.50e+03
        pdb=" C4   DG J  70 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 118 "    0.193 2.00e-02 2.50e+03   2.79e-01 7.76e+02
        pdb=" C   LYS C 118 "   -0.481 2.00e-02 2.50e+03
        pdb=" O   LYS C 118 "    0.136 2.00e-02 2.50e+03
        pdb=" N   LYS C 119 "    0.151 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  -6 "    0.314 2.00e-02 2.50e+03   1.54e-01 5.93e+02
        pdb=" N1   DT I  -6 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2   DT I  -6 "   -0.089 2.00e-02 2.50e+03
        pdb=" O2   DT I  -6 "   -0.187 2.00e-02 2.50e+03
        pdb=" N3   DT I  -6 "   -0.025 2.00e-02 2.50e+03
        pdb=" C4   DT I  -6 "    0.059 2.00e-02 2.50e+03
        pdb=" O4   DT I  -6 "    0.246 2.00e-02 2.50e+03
        pdb=" C5   DT I  -6 "   -0.063 2.00e-02 2.50e+03
        pdb=" C7   DT I  -6 "   -0.133 2.00e-02 2.50e+03
        pdb=" C6   DT I  -6 "   -0.089 2.00e-02 2.50e+03
  ... (remaining 1705 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 5401
        2.97 -     3.45: 14075
        3.45 -     3.93: 26652
        3.93 -     4.42: 29933
        4.42 -     4.90: 41949
  Nonbonded interactions: 118010
  Sorted by model distance:
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  75 "
     model   vdw
     2.486 3.040
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  75 "
     model   vdw
     2.490 3.040
  nonbonded pdb=" O   LYS C 118 "
            pdb=" CA  LYS C 119 "
     model   vdw
     2.511 2.776
  nonbonded pdb=" OG  SER E  57 "
            pdb=" OE1 GLU E  59 "
     model   vdw
     2.550 3.040
  nonbonded pdb=" OG  SER B  47 "
            pdb=" OP1  DC J   7 "
     model   vdw
     2.572 3.040
  ... (remaining 118005 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 12 through 119)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     40.480
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
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      :  0.014   0.317  14921  Z= 0.767
  Angle     :  1.972  62.518  21379  Z= 1.325
  Chirality :  0.093   0.505   2429
  Planarity :  0.031   0.279   1708
  Dihedral  : 25.752 169.188   6360
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 0.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  2.80 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.42 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.24), residues: 1009
  helix:  0.25 (0.19), residues: 610
  sheet: -1.00 (0.95), residues: 35
  loop : -0.79 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.250   0.042   TRP L 276 
 HIS   0.013   0.003   HIS H  46 
 PHE   0.048   0.013   PHE D  67 
 TYR   0.143   0.017   TYR C  57 
 ARG   0.016   0.002   ARG D  27 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 269
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.7937 (tt0) cc_final: 0.7675 (tt0)
REVERT: A   90 MET cc_start: 0.7478 (mmp) cc_final: 0.7257 (mmp)
REVERT: A  105 GLU cc_start: 0.7502 (tt0) cc_final: 0.7300 (mt-10)
REVERT: B   84 MET cc_start: 0.8093 (mmp) cc_final: 0.7850 (mmp)
REVERT: D   59 MET cc_start: 0.8475 (mmm) cc_final: 0.8210 (mmp)
REVERT: F   35 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7307 (mtp85)
REVERT: H   75 SER cc_start: 0.8778 (t) cc_final: 0.8545 (t)
REVERT: H   96 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7954 (ttt-90)
REVERT: H  112 THR cc_start: 0.8798 (t) cc_final: 0.8454 (p)
REVERT: L   49 PHE cc_start: 0.6716 (m-80) cc_final: 0.6323 (m-80)
REVERT: L   55 ILE cc_start: 0.3933 (OUTLIER) cc_final: 0.3582 (pt)
REVERT: L  129 LEU cc_start: 0.7845 (tp) cc_final: 0.7430 (tm)
REVERT: L  185 ILE cc_start: 0.7343 (mm) cc_final: 0.6997 (mt)
REVERT: L  194 ASP cc_start: 0.7764 (p0) cc_final: 0.7270 (p0)
REVERT: L  205 ARG cc_start: 0.7761 (tpt170) cc_final: 0.7487 (mmm160)
REVERT: L  262 MET cc_start: 0.6270 (mmm) cc_final: 0.5697 (mmm)
  outliers start: 5
  outliers final: 1
  residues processed: 272
  average time/residue: 1.6688
  time to fit residues: 485.8158
Evaluate side-chains
  225 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 223
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain L residue   55 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 94 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
D 106 HIS
F  93 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  89 ASN
L  95 HIS
L 113 GLN
** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14921  Z= 0.208
  Angle     :  0.674   8.284  21379  Z= 0.400
  Chirality :  0.039   0.151   2429
  Planarity :  0.005   0.039   1708
  Dihedral  : 30.578 179.459   4323
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.02 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1009
  helix:  1.93 (0.20), residues: 631
  sheet: -0.58 (0.86), residues: 30
  loop : -1.01 (0.29), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP L 276 
 HIS   0.007   0.001   HIS L 268 
 PHE   0.007   0.001   PHE F 100 
 TYR   0.011   0.001   TYR F  72 
 ARG   0.009   0.001   ARG L  39 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7550 (mmp) cc_final: 0.7283 (mmp)
REVERT: C   73 ASN cc_start: 0.8009 (t0) cc_final: 0.7790 (t0)
REVERT: E  129 ARG cc_start: 0.8039 (tpt90) cc_final: 0.7832 (tmt170)
REVERT: F   35 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7270 (mtp85)
REVERT: F   85 ASP cc_start: 0.8031 (m-30) cc_final: 0.7731 (m-30)
REVERT: F   92 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8610 (ttp80)
REVERT: G   73 ASN cc_start: 0.8143 (t0) cc_final: 0.7911 (t0)
REVERT: H   75 SER cc_start: 0.8784 (t) cc_final: 0.8563 (t)
REVERT: H   76 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7297 (mtp85)
REVERT: L  100 GLN cc_start: 0.7404 (tp-100) cc_final: 0.6900 (tp-100)
REVERT: L  109 PHE cc_start: 0.5649 (t80) cc_final: 0.5274 (t80)
REVERT: L  114 ASN cc_start: 0.7016 (t0) cc_final: 0.6412 (m-40)
REVERT: L  262 MET cc_start: 0.6282 (mmm) cc_final: 0.5680 (mmm)
  outliers start: 26
  outliers final: 11
  residues processed: 247
  average time/residue: 1.6574
  time to fit residues: 440.3491
Evaluate side-chains
  235 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 222
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain L residue   51 THR
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  212 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 94 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 113 optimal weight:   20.0000
   chunk 122 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 112 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS
E  76 GLN
** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.101  14921  Z= 0.448
  Angle     :  0.739   7.718  21379  Z= 0.431
  Chirality :  0.044   0.168   2429
  Planarity :  0.006   0.057   1708
  Dihedral  : 30.296 173.717   4320
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 15.87 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1009
  helix:  1.67 (0.20), residues: 634
  sheet: -0.97 (0.72), residues: 42
  loop : -1.29 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP L  42 
 HIS   0.007   0.001   HIS L 268 
 PHE   0.017   0.002   PHE L 109 
 TYR   0.013   0.002   TYR H  34 
 ARG   0.010   0.001   ARG E  40 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 219
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7857 (mmp) cc_final: 0.7578 (mmp)
REVERT: B   93 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7910 (mp10)
REVERT: C   29 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8453 (ttm170)
REVERT: C   56 GLU cc_start: 0.8425 (tt0) cc_final: 0.8070 (tt0)
REVERT: C   73 ASN cc_start: 0.8407 (t0) cc_final: 0.7951 (t0)
REVERT: E   56 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8883 (ttmp)
REVERT: E  129 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7911 (tmt170)
REVERT: F   35 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7613 (mtp85)
REVERT: F   77 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8718 (mtmp)
REVERT: F   85 ASP cc_start: 0.8023 (m-30) cc_final: 0.7731 (m-30)
REVERT: F   92 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8381 (ttp80)
REVERT: G   73 ASN cc_start: 0.8572 (t0) cc_final: 0.8119 (t0)
REVERT: H   75 SER cc_start: 0.8802 (t) cc_final: 0.8548 (t)
REVERT: H   76 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7369 (mtp85)
REVERT: L   49 PHE cc_start: 0.6955 (m-80) cc_final: 0.6591 (m-80)
REVERT: L  153 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8084 (t)
REVERT: L  189 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8068 (tp30)
  outliers start: 37
  outliers final: 19
  residues processed: 233
  average time/residue: 1.6597
  time to fit residues: 414.6504
Evaluate side-chains
  234 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 207
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   29 ARG
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue   98 LEU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  127 ASP
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  153 VAL
Chi-restraints excluded: chain L residue  180 GLU
Chi-restraints excluded: chain L residue  189 GLU
Chi-restraints excluded: chain L residue  282 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 114 optimal weight:    0.0020
   chunk 120 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   overall best weight:    1.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  39 HIS
E  76 GLN
L 246 HIS
** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14921  Z= 0.235
  Angle     :  0.642  11.658  21379  Z= 0.374
  Chirality :  0.038   0.150   2429
  Planarity :  0.005   0.049   1708
  Dihedral  : 29.697 173.905   4320
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.02 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.26), residues: 1009
  helix:  2.05 (0.21), residues: 627
  sheet: -0.28 (0.93), residues: 30
  loop : -1.24 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L  42 
 HIS   0.005   0.001   HIS L 268 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.008   0.001   TYR H  37 
 ARG   0.008   0.001   ARG H  30 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 218
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7656 (mmp) cc_final: 0.7395 (mmp)
REVERT: B   93 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7913 (mp10)
REVERT: C   73 ASN cc_start: 0.8390 (t0) cc_final: 0.7962 (t0)
REVERT: E  129 ARG cc_start: 0.8117 (tpt90) cc_final: 0.7883 (tmt170)
REVERT: F   35 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7361 (mtp85)
REVERT: F   85 ASP cc_start: 0.7961 (m-30) cc_final: 0.7654 (m-30)
REVERT: G   73 ASN cc_start: 0.8564 (t0) cc_final: 0.8089 (t0)
REVERT: H   39 TYR cc_start: 0.8522 (t80) cc_final: 0.8306 (t80)
REVERT: H   75 SER cc_start: 0.8773 (t) cc_final: 0.8519 (t)
REVERT: H   76 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7312 (mtp85)
REVERT: L   49 PHE cc_start: 0.6659 (m-80) cc_final: 0.6390 (t80)
REVERT: L  153 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7831 (t)
REVERT: L  180 GLU cc_start: 0.5751 (tt0) cc_final: 0.5437 (tt0)
REVERT: L  282 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7596 (tp)
  outliers start: 35
  outliers final: 16
  residues processed: 228
  average time/residue: 1.7273
  time to fit residues: 421.0930
Evaluate side-chains
  226 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   55 GLN
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue   98 LEU
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  153 VAL
Chi-restraints excluded: chain L residue  215 THR
Chi-restraints excluded: chain L residue  282 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 89 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 108 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
E  76 GLN
L 268 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14921  Z= 0.200
  Angle     :  0.618  11.354  21379  Z= 0.358
  Chirality :  0.036   0.162   2429
  Planarity :  0.005   0.050   1708
  Dihedral  : 29.378 173.563   4320
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.65 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.27), residues: 1009
  helix:  2.26 (0.21), residues: 628
  sheet: -0.29 (0.93), residues: 32
  loop : -1.20 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP L  42 
 HIS   0.006   0.001   HIS L 268 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.013   0.001   TYR D  37 
 ARG   0.011   0.001   ARG C  20 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 216
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7595 (mmp) cc_final: 0.7275 (mmp)
REVERT: B   93 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7855 (mp10)
REVERT: C   73 ASN cc_start: 0.8377 (t0) cc_final: 0.7977 (t0)
REVERT: C  110 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8099 (p0)
REVERT: E  129 ARG cc_start: 0.8071 (tpt90) cc_final: 0.7851 (tmt170)
REVERT: F   85 ASP cc_start: 0.7858 (m-30) cc_final: 0.7498 (m-30)
REVERT: G   73 ASN cc_start: 0.8585 (t0) cc_final: 0.8087 (t0)
REVERT: H   39 TYR cc_start: 0.8492 (t80) cc_final: 0.8099 (t80)
REVERT: H   43 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8314 (mmtm)
REVERT: H   75 SER cc_start: 0.8774 (t) cc_final: 0.8525 (t)
REVERT: H   76 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7303 (mtp85)
REVERT: L   49 PHE cc_start: 0.6769 (m-80) cc_final: 0.6433 (t80)
REVERT: L  109 PHE cc_start: 0.5931 (t80) cc_final: 0.5547 (t80)
REVERT: L  174 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8639 (mp)
REVERT: L  180 GLU cc_start: 0.5688 (tt0) cc_final: 0.5324 (tt0)
REVERT: L  277 ASP cc_start: 0.8011 (p0) cc_final: 0.7794 (p0)
  outliers start: 29
  outliers final: 15
  residues processed: 226
  average time/residue: 1.6499
  time to fit residues: 400.6987
Evaluate side-chains
  229 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 210
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  174 LEU
Chi-restraints excluded: chain L residue  215 THR
Chi-restraints excluded: chain L residue  249 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14921  Z= 0.207
  Angle     :  0.622  12.320  21379  Z= 0.359
  Chirality :  0.036   0.144   2429
  Planarity :  0.005   0.048   1708
  Dihedral  : 29.185 173.367   4320
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.05 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.27), residues: 1009
  helix:  2.31 (0.21), residues: 628
  sheet: -0.08 (0.95), residues: 31
  loop : -1.16 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP L  42 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.010   0.001   PHE L  49 
 TYR   0.016   0.001   TYR D  37 
 ARG   0.011   0.001   ARG C  20 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 215
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7788 (mp10)
REVERT: C   73 ASN cc_start: 0.8390 (t0) cc_final: 0.8011 (t0)
REVERT: C  110 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8123 (p0)
REVERT: E  129 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7873 (tmt170)
REVERT: F   85 ASP cc_start: 0.7851 (m-30) cc_final: 0.7497 (m-30)
REVERT: G   73 ASN cc_start: 0.8604 (t0) cc_final: 0.8112 (t0)
REVERT: H   75 SER cc_start: 0.8782 (t) cc_final: 0.8534 (t)
REVERT: H   76 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7298 (mtp85)
REVERT: L   49 PHE cc_start: 0.6777 (m-80) cc_final: 0.6543 (t80)
REVERT: L  109 PHE cc_start: 0.5962 (t80) cc_final: 0.5629 (t80)
REVERT: L  180 GLU cc_start: 0.5664 (tt0) cc_final: 0.5285 (tt0)
REVERT: L  277 ASP cc_start: 0.7995 (p0) cc_final: 0.7663 (p0)
  outliers start: 27
  outliers final: 16
  residues processed: 226
  average time/residue: 1.6853
  time to fit residues: 408.4779
Evaluate side-chains
  225 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 206
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  213 LEU
Chi-restraints excluded: chain L residue  215 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9990
   chunk 75 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   chunk 48 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  14921  Z= 0.308
  Angle     :  0.675  12.002  21379  Z= 0.386
  Chirality :  0.039   0.144   2429
  Planarity :  0.005   0.053   1708
  Dihedral  : 29.289 172.493   4320
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 21.59 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.27), residues: 1009
  helix:  2.10 (0.21), residues: 627
  sheet: -1.08 (0.84), residues: 38
  loop : -1.18 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  42 
 HIS   0.005   0.001   HIS L  95 
 PHE   0.011   0.001   PHE L  49 
 TYR   0.019   0.002   TYR D  37 
 ARG   0.013   0.001   ARG L 205 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7818 (mp10)
REVERT: C   73 ASN cc_start: 0.8504 (t0) cc_final: 0.8118 (t0)
REVERT: C  110 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8143 (p0)
REVERT: F   85 ASP cc_start: 0.7957 (m-30) cc_final: 0.7614 (m-30)
REVERT: G   73 ASN cc_start: 0.8636 (t0) cc_final: 0.8070 (t0)
REVERT: H   75 SER cc_start: 0.8809 (t) cc_final: 0.8545 (t)
REVERT: H   76 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7310 (mtp85)
REVERT: L   49 PHE cc_start: 0.7003 (m-80) cc_final: 0.6680 (t80)
REVERT: L  109 PHE cc_start: 0.6226 (t80) cc_final: 0.5864 (t80)
REVERT: L  205 ARG cc_start: 0.7592 (mmm160) cc_final: 0.7246 (tpp-160)
REVERT: L  277 ASP cc_start: 0.8152 (p0) cc_final: 0.7819 (p0)
  outliers start: 30
  outliers final: 21
  residues processed: 218
  average time/residue: 1.6806
  time to fit residues: 393.7721
Evaluate side-chains
  227 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 203
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   35 ARG
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain L residue  213 LEU
Chi-restraints excluded: chain L residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14921  Z= 0.218
  Angle     :  0.636  11.204  21379  Z= 0.365
  Chirality :  0.037   0.161   2429
  Planarity :  0.005   0.047   1708
  Dihedral  : 29.221 173.251   4320
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.29 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.27), residues: 1009
  helix:  2.23 (0.21), residues: 626
  sheet: -0.62 (0.91), residues: 31
  loop : -1.18 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP L  42 
 HIS   0.003   0.001   HIS L  95 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.020   0.002   TYR D  37 
 ARG   0.011   0.001   ARG L 205 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 206
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7792 (mp10)
REVERT: C   73 ASN cc_start: 0.8520 (t0) cc_final: 0.8172 (t0)
REVERT: C  110 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8088 (p0)
REVERT: D   83 ARG cc_start: 0.8331 (mmt90) cc_final: 0.8116 (mpt180)
REVERT: E   56 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8909 (ttmp)
REVERT: F   85 ASP cc_start: 0.7884 (m-30) cc_final: 0.7530 (m-30)
REVERT: G   73 ASN cc_start: 0.8631 (t0) cc_final: 0.8097 (t0)
REVERT: H   75 SER cc_start: 0.8796 (t) cc_final: 0.8542 (t)
REVERT: H   76 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7287 (mtp85)
REVERT: L   49 PHE cc_start: 0.6912 (m-80) cc_final: 0.6647 (t80)
REVERT: L  109 PHE cc_start: 0.5941 (t80) cc_final: 0.5551 (t80)
REVERT: L  277 ASP cc_start: 0.8057 (p0) cc_final: 0.7682 (p0)
  outliers start: 31
  outliers final: 19
  residues processed: 218
  average time/residue: 1.6943
  time to fit residues: 395.9871
Evaluate side-chains
  222 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  154 VAL
Chi-restraints excluded: chain L residue  213 LEU
Chi-restraints excluded: chain L residue  215 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0270
   chunk 88 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 118 optimal weight:    8.9990
   overall best weight:    1.4042

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

Flipped N/Q/H residues before XYZ refinement:
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14921  Z= 0.223
  Angle     :  0.642  10.921  21379  Z= 0.366
  Chirality :  0.037   0.130   2429
  Planarity :  0.005   0.066   1708
  Dihedral  : 29.192 173.405   4320
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.45 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.27), residues: 1009
  helix:  2.28 (0.21), residues: 627
  sheet: -2.10 (0.71), residues: 50
  loop : -1.08 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP L  42 
 HIS   0.004   0.001   HIS L  95 
 PHE   0.010   0.001   PHE L  49 
 TYR   0.022   0.002   TYR D  37 
 ARG   0.017   0.001   ARG L 205 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 211
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.7478 (tt0) cc_final: 0.7267 (mt-10)
REVERT: B   93 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7777 (mp10)
REVERT: C   73 ASN cc_start: 0.8553 (t0) cc_final: 0.8207 (t0)
REVERT: C  110 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8161 (p0)
REVERT: D   83 ARG cc_start: 0.8368 (mmt90) cc_final: 0.8167 (mpt180)
REVERT: E   56 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8909 (ttmp)
REVERT: F   85 ASP cc_start: 0.7796 (m-30) cc_final: 0.7474 (m-30)
REVERT: G   73 ASN cc_start: 0.8625 (t0) cc_final: 0.8116 (t0)
REVERT: H   75 SER cc_start: 0.8810 (t) cc_final: 0.8552 (t)
REVERT: H   76 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7266 (mtp85)
REVERT: L   49 PHE cc_start: 0.6961 (m-80) cc_final: 0.6647 (t80)
REVERT: L  109 PHE cc_start: 0.6032 (t80) cc_final: 0.5657 (t80)
REVERT: L  205 ARG cc_start: 0.7539 (mmm160) cc_final: 0.7243 (tpp-160)
REVERT: L  277 ASP cc_start: 0.8052 (p0) cc_final: 0.7659 (p0)
  outliers start: 24
  outliers final: 20
  residues processed: 219
  average time/residue: 1.6500
  time to fit residues: 387.9289
Evaluate side-chains
  232 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 208
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  213 LEU
Chi-restraints excluded: chain L residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   chunk 114 optimal weight:    0.0870
   chunk 99 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0980
   overall best weight:    1.8364

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

Flipped N/Q/H residues before XYZ refinement:
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14921  Z= 0.258
  Angle     :  0.666  13.905  21379  Z= 0.377
  Chirality :  0.038   0.146   2429
  Planarity :  0.005   0.069   1708
  Dihedral  : 29.213 173.143   4320
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.22 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.27), residues: 1009
  helix:  2.19 (0.21), residues: 626
  sheet: -2.23 (0.69), residues: 48
  loop : -1.13 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP L  42 
 HIS   0.004   0.001   HIS L  95 
 PHE   0.013   0.001   PHE L  49 
 TYR   0.024   0.002   TYR H  80 
 ARG   0.016   0.001   ARG L 205 

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 204
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.7504 (tt0) cc_final: 0.7293 (mt-10)
REVERT: B   93 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7754 (mp10)
REVERT: C   73 ASN cc_start: 0.8589 (t0) cc_final: 0.8233 (t0)
REVERT: C  110 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8156 (p0)
REVERT: D   83 ARG cc_start: 0.8436 (mmt90) cc_final: 0.8226 (mpt180)
REVERT: E   56 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8923 (ttmp)
REVERT: F   85 ASP cc_start: 0.7841 (m-30) cc_final: 0.7536 (m-30)
REVERT: G   73 ASN cc_start: 0.8639 (t0) cc_final: 0.8145 (t0)
REVERT: H   75 SER cc_start: 0.8828 (t) cc_final: 0.8549 (t)
REVERT: H   76 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7327 (mtp85)
REVERT: L  109 PHE cc_start: 0.6084 (t80) cc_final: 0.5719 (t80)
REVERT: L  205 ARG cc_start: 0.7545 (mmm160) cc_final: 0.7227 (tpp-160)
  outliers start: 26
  outliers final: 19
  residues processed: 212
  average time/residue: 1.6371
  time to fit residues: 373.5192
Evaluate side-chains
  224 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   76 ARG
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain L residue   92 THR
Chi-restraints excluded: chain L residue  127 ASP
Chi-restraints excluded: chain L residue  149 VAL
Chi-restraints excluded: chain L residue  213 LEU
Chi-restraints excluded: chain L residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 41 optimal weight:    0.2980
   chunk 101 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.138826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.113037 restraints weight = 28769.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.33
r_work: 0.3404 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14921  Z= 0.197
  Angle     :  0.647  14.625  21379  Z= 0.365
  Chirality :  0.036   0.133   2429
  Planarity :  0.005   0.065   1708
  Dihedral  : 29.120 173.505   4320
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 24.50 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.27), residues: 1009
  helix:  2.34 (0.21), residues: 627
  sheet: -1.62 (0.80), residues: 41
  loop : -1.07 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP L  42 
 HIS   0.007   0.001   HIS L  95 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.024   0.002   TYR D  37 
 ARG   0.015   0.001   ARG L 205 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6038.75 seconds
wall clock time: 108 minutes 18.98 seconds (6498.98 seconds total)