Starting phenix.real_space_refine
on Sat Apr  6 03:54:36 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713_updated.pdb"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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       7      5.49       5
     S      51      5.16       5
     C    4382      2.51       5
     N    1231      2.21       5
     O    1244      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 6917
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "b"
      Number of atoms: 2134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2134
          Classifications: {'peptide': 296}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 11, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 213
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 127
    Chain: "2"
      Number of atoms: 1212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1212
          Classifications: {'peptide': 156}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 11, 'TRANS': 144}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 43
    Chain: "i"
      Number of atoms: 3017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3017
          Classifications: {'peptide': 395}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 17, 'TRANS': 377}
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 112
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 15, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 114
    Chain: "u"
      Number of atoms: 552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 552
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 36
    Chain: "b"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "i"
      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   1865  SG  CYS b 354      34.319  76.743  20.414  1.00 38.66           S
  ATOM   2005  SG  CYS b 374      34.034  73.285  21.978  1.00 43.27           S
  ATOM   2030  SG  CYS b 377      32.056  76.493  23.338  1.00 44.14           S
  ATOM   5669  SG  CYS i 302      63.822  66.968  20.941  1.00 25.69           S
  ATOM   5746  SG  CYS i 314      65.272  68.705  24.005  1.00 25.97           S
  ATOM   5766  SG  CYS i 317      66.348  69.591  20.248  1.00 26.45           S

  Time building chain proxies: 4.33, per 1000 atoms: 0.63
  Number of scatterers: 6917
  At special positions: 0
  Unit cell: (123.395, 110.63, 105.524, 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      51     16.00
     P       7     15.00
     O    1244      8.00
     N    1231      7.00
     C    4382      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  - 3.50
        Amino acid           : False - 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: 2.63
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN b 501 "
        pdb="ZN    ZN b 501 " - pdb=" ND1 HIS b 356 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 354 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 374 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 377 "
      pdb="  ZN i 401 "
        pdb="ZN    ZN i 401 " - pdb=" NE2 HIS b 331 "
        pdb="ZN    ZN i 401 " - pdb=" SG  CYS i 302 "
        pdb="ZN    ZN i 401 " - pdb=" SG  CYS i 317 "
        pdb="ZN    ZN i 401 " - pdb=" SG  CYS i 314 "
      Number of angles added : 6


  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1752

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      55.3% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'b' and resid 2 through 45
      removed outlier: 3.613A  pdb=" N   GLU b  10 " --> pdb=" O   THR b   6 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE b  43 " --> pdb=" O   LEU b  39 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU b  44 " --> pdb=" O   LYS b  40 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN b  45 " --> pdb=" O   HIS b  41 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 55 through 96
      removed outlier: 4.273A  pdb=" N   LEU b  59 " --> pdb=" O   GLY b  55 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   VAL b  60 " --> pdb=" O   THR b  56 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   HIS b  79 " --> pdb=" O   LEU b  75 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS b  80 " --> pdb=" O   ALA b  76 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ILE b  82 " --> pdb=" O   ASP b  78 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   HIS b  83 " --> pdb=" O   HIS b  79 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   SER b  84 " --> pdb=" O   LYS b  80 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   SER b  85 " --> pdb=" O   ASP b  81 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL b  86 " --> pdb=" O   ILE b  82 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER b  87 " --> pdb=" O   HIS b  83 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 113 through 128
      removed outlier: 4.259A  pdb=" N   LEU b 117 " --> pdb=" O   ASP b 113 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 132 through 142
      removed outlier: 3.506A  pdb=" N   GLU b 141 " --> pdb=" O   GLU b 137 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 148 through 164
      Proline residue:  b 153  - end of helix
      removed outlier: 3.726A  pdb=" N   GLU b 156 " --> pdb=" O   GLU b 152 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU b 157 " --> pdb=" O   PRO b 153 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 263 through 274
    Processing helix  chain 'b' and resid 281 through 305
      Proline residue:  b 294  - end of helix
      removed outlier: 5.124A  pdb=" N   ASN b 298 " --> pdb=" O   PRO b 294 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 326 through 328
      No H-bonds generated for 'chain 'b' and resid 326 through 328'
    Processing helix  chain 'b' and resid 360 through 366
    Processing helix  chain '2' and resid 8 through 20
    Processing helix  chain '2' and resid 89 through 92
      No H-bonds generated for 'chain '2' and resid 89 through 92'
    Processing helix  chain '2' and resid 101 through 107
    Processing helix  chain '2' and resid 109 through 114
    Processing helix  chain '2' and resid 124 through 132
      removed outlier: 3.679A  pdb=" N   HIS 2 132 " --> pdb=" O   ALA 2 128 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 134 through 147
    Processing helix  chain 'i' and resid 7 through 17
    Processing helix  chain 'i' and resid 20 through 60
      Proline residue:  i  25  - end of helix
      removed outlier: 3.660A  pdb=" N   VAL i  50 " --> pdb=" O   HIS i  46 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   SER i  59 " --> pdb=" O   GLU i  55 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLY i  60 " --> pdb=" O   LYS i  56 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 64 through 110
      removed outlier: 4.369A  pdb=" N   VAL i  68 " --> pdb=" O   ASP i  65 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   SER i  69 " --> pdb=" O   SER i  66 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU i  87 " --> pdb=" O   LYS i  84 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS i 109 " --> pdb=" O   LEU i 106 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   SER i 110 " --> pdb=" O   LYS i 107 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 117 through 136
    Processing helix  chain 'i' and resid 139 through 149
    Processing helix  chain 'i' and resid 158 through 172
    Processing helix  chain 'i' and resid 177 through 184
    Processing helix  chain 'i' and resid 186 through 191
    Processing helix  chain 'i' and resid 196 through 210
    Processing helix  chain 'i' and resid 214 through 227
      removed outlier: 4.236A  pdb=" N   SER i 226 " --> pdb=" O   ARG i 222 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN i 227 " --> pdb=" O   LYS i 223 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 230 through 244
      removed outlier: 3.885A  pdb=" N   ALA i 244 " --> pdb=" O   GLY i 241 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 252 through 258
      removed outlier: 4.928A  pdb=" N   LEU i 257 " --> pdb=" O   PRO i 253 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 262 through 277
    Processing helix  chain 'i' and resid 285 through 297
    Processing helix  chain 'i' and resid 300 through 303
    Processing helix  chain 'i' and resid 315 through 317
      No H-bonds generated for 'chain 'i' and resid 315 through 317'
    Processing helix  chain 'i' and resid 319 through 324
    Processing helix  chain 'i' and resid 364 through 370
    Processing helix  chain 'i' and resid 387 through 389
      No H-bonds generated for 'chain 'i' and resid 387 through 389'
    Processing helix  chain 'u' and resid 23 through 33
    Processing helix  chain 'u' and resid 38 through 40
      No H-bonds generated for 'chain 'u' and resid 38 through 40'
    Processing helix  chain 'u' and resid 56 through 59
      No H-bonds generated for 'chain 'u' and resid 56 through 59'
    Processing sheet with id=  A, first strand: chain 'b' and resid 349 through 351
    Processing sheet with id=  B, first strand: chain '2' and resid 25 through 27
    Processing sheet with id=  C, first strand: chain 'i' and resid 353 through 355
    Processing sheet with id=  D, first strand: chain 'u' and resid 12 through 16
      removed outlier: 6.040A  pdb=" N   SER u  65 " --> pdb=" O   PHE u   4 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LYS u   6 " --> pdb=" O   SER u  65 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LEU u  67 " --> pdb=" O   LYS u   6 " (cutoff:3.500A)

    352 hydrogen bonds defined for protein.
    900 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1253
        1.33 -     1.45: 1623
        1.45 -     1.57: 4086
        1.57 -     1.69: 7
        1.69 -     1.81: 75
  Bond restraints: 7044
  Sorted by residual:
  bond pdb=" O2P SEP 2 171 "
       pdb=" P   SEP 2 171 "
    ideal  model  delta    sigma   weight residual
    1.610  1.508  0.102 2.00e-02 2.50e+03 2.59e+01
  bond pdb=" O2P SEP 2 168 "
       pdb=" P   SEP 2 168 "
    ideal  model  delta    sigma   weight residual
    1.610  1.509  0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" O1P SEP 2 168 "
       pdb=" P   SEP 2 168 "
    ideal  model  delta    sigma   weight residual
    1.610  1.511  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" O3P SEP 2 168 "
       pdb=" P   SEP 2 168 "
    ideal  model  delta    sigma   weight residual
    1.610  1.512  0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" O1P SEP 2 169 "
       pdb=" P   SEP 2 169 "
    ideal  model  delta    sigma   weight residual
    1.610  1.513  0.097 2.00e-02 2.50e+03 2.35e+01
  ... (remaining 7039 not shown)

  Histogram of bond angle deviations from ideal:
      100.01 -   106.88: 236
      106.88 -   113.74: 4014
      113.74 -   120.60: 2932
      120.60 -   127.46: 2319
      127.46 -   134.32: 65
  Bond angle restraints: 9566
  Sorted by residual:
  angle pdb=" N   CYS i 178 "
        pdb=" CA  CYS i 178 "
        pdb=" C   CYS i 178 "
      ideal   model   delta    sigma   weight residual
     111.28  106.48    4.80 1.09e+00 8.42e-01 1.94e+01
  angle pdb=" C   TYR b  35 "
        pdb=" N   THR b  36 "
        pdb=" CA  THR b  36 "
      ideal   model   delta    sigma   weight residual
     120.28  114.56    5.72 1.44e+00 4.82e-01 1.58e+01
  angle pdb=" N   ASN b 368 "
        pdb=" CA  ASN b 368 "
        pdb=" C   ASN b 368 "
      ideal   model   delta    sigma   weight residual
     112.72  108.52    4.20 1.14e+00 7.69e-01 1.36e+01
  angle pdb=" CA  GLU b  31 "
        pdb=" C   GLU b  31 "
        pdb=" O   GLU b  31 "
      ideal   model   delta    sigma   weight residual
     121.00  117.41    3.59 1.05e+00 9.07e-01 1.17e+01
  angle pdb=" N   ILE 2 145 "
        pdb=" CA  ILE 2 145 "
        pdb=" C   ILE 2 145 "
      ideal   model   delta    sigma   weight residual
     110.72  107.32    3.40 1.01e+00 9.80e-01 1.13e+01
  ... (remaining 9561 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3872
       17.47 -    34.93: 338
       34.93 -    52.40: 60
       52.40 -    69.86: 18
       69.86 -    87.33: 5
  Dihedral angle restraints: 4293
    sinusoidal: 1598
      harmonic: 2695
  Sorted by residual:
  dihedral pdb=" CA  PRO b 294 "
           pdb=" C   PRO b 294 "
           pdb=" N   ALA b 295 "
           pdb=" CA  ALA b 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ASP i 216 "
           pdb=" CB  ASP i 216 "
           pdb=" CG  ASP i 216 "
           pdb=" OD1 ASP i 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.97   59.97     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CA  GLN i  17 "
           pdb=" C   GLN i  17 "
           pdb=" N   GLU i  18 "
           pdb=" CA  GLU i  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 4290 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 782
       0.039 -    0.078: 218
       0.078 -    0.117: 90
       0.117 -    0.156: 17
       0.156 -    0.195: 7
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CA  PHE b 367 "
            pdb=" N   PHE b 367 "
            pdb=" C   PHE b 367 "
            pdb=" CB  PHE b 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.49e-01
  chirality pdb=" CA  ILE 2 145 "
            pdb=" N   ILE 2 145 "
            pdb=" C   ILE 2 145 "
            pdb=" CB  ILE 2 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" CA  MET b 366 "
            pdb=" N   MET b 366 "
            pdb=" C   MET b 366 "
            pdb=" CB  MET b 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.43e-01
  ... (remaining 1111 not shown)

  Planarity restraints: 1216
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG b 340 "    0.248 9.50e-02 1.11e+02   1.11e-01 7.61e+00
        pdb=" NE  ARG b 340 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG b 340 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG b 340 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG b 340 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR b  71 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR b  71 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR b  71 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL b  72 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS b  69 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   LYS b  69 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LYS b  69 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASP b  70 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1213 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 1
        2.19 -     2.87: 2445
        2.87 -     3.54: 9549
        3.54 -     4.22: 14103
        4.22 -     4.90: 26137
  Nonbonded interactions: 52235
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS 2  87 "
            pdb=" C   GLY u  76 "
     model   vdw
     1.512 3.350
  nonbonded pdb=" OG  SER i 194 "
            pdb=" OD2 ASP i 273 "
     model   vdw
     2.251 2.440
  nonbonded pdb=" OD2 ASP i 126 "
            pdb=" OG  SER i 149 "
     model   vdw
     2.255 2.440
  nonbonded pdb=" O2P SEP 2 171 "
            pdb=" OG  SER i 187 "
     model   vdw
     2.363 2.440
  nonbonded pdb=" O   PHE b 334 "
            pdb=" OG  SER i 336 "
     model   vdw
     2.373 2.440
  ... (remaining 52230 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:          4.380
  Check model and map are aligned:         0.100
  Set scattering table:                    0.070
  Process input model:                     23.190
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
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      :  0.007   0.102   7044  Z= 0.466
  Angle     :  0.734   8.666   9566  Z= 0.432
  Chirality :  0.045   0.195   1114
  Planarity :  0.006   0.111   1216
  Dihedral  : 14.181  87.330   2541
  Min Nonbonded Distance : 1.512

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 901
  helix:  2.01 (0.24), residues: 494
  sheet:  0.82 (0.74), residues: 51
  loop : -1.31 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP i 181 
 HIS   0.007   0.001   HIS i 183 
 PHE   0.012   0.001   PHE 2  63 
 TYR   0.011   0.001   TYR 2 130 
 ARG   0.002   0.000   ARG i 210 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.847 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1795
  time to fit residues: 27.3387
Evaluate side-chains
  94 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0570
   chunk 37 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0470
   chunk 70 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN
i 268 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.0722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7044  Z= 0.145
  Angle     :  0.474   6.384   9566  Z= 0.245
  Chirality :  0.038   0.153   1114
  Planarity :  0.004   0.040   1216
  Dihedral  :  3.885  28.686   1010
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  4.78 %
    Favored  : 93.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.29), residues: 901
  helix:  2.01 (0.23), residues: 502
  sheet:  0.86 (0.75), residues: 53
  loop : -1.22 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.010   0.001   PHE 2  63 
 TYR   0.010   0.001   TYR 2  61 
 ARG   0.003   0.000   ARG i 210 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.823 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1639
  time to fit residues: 23.4365
Evaluate side-chains
  103 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  209 ILE
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0970
   chunk 81 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN
i  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7044  Z= 0.164
  Angle     :  0.462   6.372   9566  Z= 0.236
  Chirality :  0.038   0.156   1114
  Planarity :  0.004   0.043   1216
  Dihedral  :  3.903  30.417   1010
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.14 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.29), residues: 901
  helix:  2.10 (0.24), residues: 499
  sheet:  0.82 (0.74), residues: 53
  loop : -1.14 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.009   0.001   PHE 2  63 
 TYR   0.008   0.001   TYR b  21 
 ARG   0.006   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.764 
Fit side-chains
REVERT: i  240 MET cc_start: 0.8581 (mmt) cc_final: 0.8203 (mmt)
  outliers start: 12
  outliers final: 10
  residues processed: 109
  average time/residue: 0.1802
  time to fit residues: 26.8780
Evaluate side-chains
  108 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 82 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0970
   chunk 72 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
b  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7044  Z= 0.186
  Angle     :  0.469   6.568   9566  Z= 0.239
  Chirality :  0.038   0.157   1114
  Planarity :  0.004   0.047   1216
  Dihedral  :  3.990  32.346   1010
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.17 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.29), residues: 901
  helix:  2.10 (0.24), residues: 500
  sheet:  0.72 (0.72), residues: 53
  loop : -1.15 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.010   0.001   PHE 2  63 
 TYR   0.008   0.001   TYR b  21 
 ARG   0.007   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.816 
Fit side-chains
REVERT: i  153 ASP cc_start: 0.8895 (t0) cc_final: 0.8350 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1570
  time to fit residues: 23.6054
Evaluate side-chains
  108 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 0 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0980
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7044  Z= 0.162
  Angle     :  0.454   6.918   9566  Z= 0.232
  Chirality :  0.038   0.151   1114
  Planarity :  0.004   0.045   1216
  Dihedral  :  3.946  32.372   1010
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.46 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.29), residues: 901
  helix:  2.14 (0.24), residues: 498
  sheet:  0.80 (0.73), residues: 53
  loop : -1.15 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.008   0.001   PHE 2  63 
 TYR   0.007   0.001   TYR i 275 
 ARG   0.005   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.683 
Fit side-chains
REVERT: i  153 ASP cc_start: 0.8913 (t0) cc_final: 0.8313 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 105
  average time/residue: 0.1633
  time to fit residues: 24.3927
Evaluate side-chains
  111 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  131 MET
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** b  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
i 268 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7044  Z= 0.191
  Angle     :  0.468   7.210   9566  Z= 0.239
  Chirality :  0.038   0.153   1114
  Planarity :  0.004   0.044   1216
  Dihedral  :  4.031  33.185   1010
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.62 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.29), residues: 901
  helix:  2.13 (0.24), residues: 499
  sheet:  0.82 (0.74), residues: 53
  loop : -1.19 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.009   0.001   PHE i 225 
 TYR   0.008   0.001   TYR i 275 
 ARG   0.003   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.815 
Fit side-chains
REVERT: b   31 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8172 (tm-30)
REVERT: i  153 ASP cc_start: 0.8906 (t0) cc_final: 0.8278 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1595
  time to fit residues: 23.3265
Evaluate side-chains
  110 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  131 MET
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0030
   chunk 53 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0670
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.4128

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

Flipped N/Q/H residues before XYZ refinement:
b  73 GLN
b 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7044  Z= 0.134
  Angle     :  0.439   7.374   9566  Z= 0.223
  Chirality :  0.037   0.146   1114
  Planarity :  0.004   0.045   1216
  Dihedral  :  3.860  32.186   1010
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.91 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.29), residues: 901
  helix:  2.17 (0.24), residues: 501
  sheet:  1.00 (0.74), residues: 53
  loop : -1.16 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.008   0.001   PHE i 225 
 TYR   0.006   0.001   TYR b  35 
 ARG   0.003   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.746 
Fit side-chains
REVERT: b  317 GLU cc_start: 0.8448 (tt0) cc_final: 0.8228 (tt0)
REVERT: i  153 ASP cc_start: 0.8871 (t0) cc_final: 0.8244 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 111
  average time/residue: 0.1538
  time to fit residues: 24.3199
Evaluate side-chains
  109 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  131 MET
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain 2 residue   79 ILE
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  156 ASN
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7044  Z= 0.231
  Angle     :  0.500   7.286   9566  Z= 0.257
  Chirality :  0.039   0.155   1114
  Planarity :  0.004   0.044   1216
  Dihedral  :  4.096  35.961   1010
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.06 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.29), residues: 901
  helix:  2.10 (0.24), residues: 500
  sheet:  0.78 (0.74), residues: 53
  loop : -1.19 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP b 312 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.010   0.001   PHE 2  63 
 TYR   0.009   0.001   TYR i 275 
 ARG   0.003   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.826 
Fit side-chains
REVERT: i  153 ASP cc_start: 0.8919 (t0) cc_final: 0.8234 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 101
  average time/residue: 0.1470
  time to fit residues: 21.2729
Evaluate side-chains
  106 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  131 MET
Chi-restraints excluded: chain b residue  132 LEU
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  156 ASN
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0770
   chunk 35 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 73 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7044  Z= 0.144
  Angle     :  0.461   7.692   9566  Z= 0.237
  Chirality :  0.038   0.155   1114
  Planarity :  0.004   0.045   1216
  Dihedral  :  3.915  35.261   1010
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.49 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.29), residues: 901
  helix:  2.18 (0.24), residues: 499
  sheet:  0.88 (0.74), residues: 53
  loop : -1.10 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.009   0.001   PHE i 225 
 TYR   0.007   0.001   TYR b  35 
 ARG   0.003   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.781 
Fit side-chains
REVERT: b  317 GLU cc_start: 0.8455 (tt0) cc_final: 0.8240 (tt0)
REVERT: i  153 ASP cc_start: 0.8900 (t0) cc_final: 0.8231 (t0)
  outliers start: 13
  outliers final: 12
  residues processed: 104
  average time/residue: 0.1571
  time to fit residues: 23.3197
Evaluate side-chains
  108 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  131 MET
Chi-restraints excluded: chain b residue  132 LEU
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain 2 residue   79 ILE
Chi-restraints excluded: chain i residue  156 ASN
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain i residue  355 MET
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 89 optimal weight:    0.1980
   chunk 82 optimal weight:    5.9990
   chunk 71 optimal weight:    0.3980
   chunk 7 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 43 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7044  Z= 0.138
  Angle     :  0.460   7.740   9566  Z= 0.236
  Chirality :  0.038   0.146   1114
  Planarity :  0.004   0.044   1216
  Dihedral  :  3.819  34.396   1010
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.22 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.29), residues: 901
  helix:  2.25 (0.24), residues: 499
  sheet:  0.93 (0.77), residues: 47
  loop : -1.08 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.009   0.001   PHE i 225 
 TYR   0.009   0.001   TYR b  35 
 ARG   0.003   0.000   ARG i 173 

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.837 
Fit side-chains
REVERT: i  153 ASP cc_start: 0.8880 (t0) cc_final: 0.8216 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1556
  time to fit residues: 22.2601
Evaluate side-chains
  104 residues out of total 815 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue  132 LEU
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain 2 residue   79 ILE
Chi-restraints excluded: chain i residue  156 ASN
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   67 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 19 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.121598 restraints weight = 9587.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.88
r_work: 0.3241 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7044  Z= 0.176
  Angle     :  0.476   7.515   9566  Z= 0.244
  Chirality :  0.038   0.150   1114
  Planarity :  0.004   0.044   1216
  Dihedral  :  3.908  36.004   1010
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.65 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.29), residues: 901
  helix:  2.25 (0.24), residues: 500
  sheet:  0.89 (0.77), residues: 47
  loop : -1.08 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP i 120 
 HIS   0.002   0.000   HIS i 220 
 PHE   0.009   0.001   PHE i 225 
 TYR   0.013   0.001   TYR b  35 
 ARG   0.003   0.000   ARG i 173 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1722.65 seconds
wall clock time: 31 minutes 58.73 seconds (1918.73 seconds total)