Starting phenix.real_space_refine
on Mon Apr 28 15:46:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pmq_17764/04_2025/8pmq_17764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pmq_17764/04_2025/8pmq_17764.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pmq_17764/04_2025/8pmq_17764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pmq_17764/04_2025/8pmq_17764.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pmq_17764/04_2025/8pmq_17764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pmq_17764/04_2025/8pmq_17764.cif"
  }
  resolution = 3.53
  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=   0.003
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       2      5.49       5
     S      30      5.16       5
     C    5004      2.51       5
     N    1313      2.21       5
     O    1395      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7746
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "2"
      Number of atoms: 2730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 355, 2730
          Classifications: {'peptide': 355}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 11, 'TRANS': 343}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 188
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 14}
          Unresolved non-hydrogen planarities: 106
    Chain: "9"
      Number of atoms: 3249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3249
          Classifications: {'peptide': 412}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 14, 'TRANS': 397}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 206
          Unresolved non-hydrogen dihedrals: 140
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 110
    Chain: "E"
      Number of atoms: 1223
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1223
          Classifications: {'peptide': 164}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 10, 'TRANS': 153}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 159
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 71
    Chain: "U"
      Number of atoms: 542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 542
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 41
    Chain: "2"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "9"
      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   2414  SG  CYS 2 379      39.864 102.744  20.884  1.00 30.00           S
  ATOM   2586  SG  CYS 2 401      36.510 100.570  20.969  1.00 29.77           S
  ATOM   2611  SG  CYS 2 404      37.498 102.692  23.847  1.00 31.98           S
  ATOM   5236  SG  CYS 9 395      46.973  72.158  24.507  1.00 29.24           S
  ATOM   5347  SG  CYS 9 434      50.384  72.607  26.571  1.00 20.06           S
  ATOM   5367  SG  CYS 9 437      50.403  71.416  23.057  1.00 20.18           S

  Time building chain proxies: 5.63, per 1000 atoms: 0.73
  Number of scatterers: 7746
  At special positions: 0
  Unit cell: (98.463, 127.003, 115.587, 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      30     16.00
     P       2     15.00
     O    1395      8.00
     N    1313      7.00
     C    5004      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN 2 501 "
        pdb="ZN    ZN 2 501 " - pdb=" ND1 HIS 2 381 "
        pdb="ZN    ZN 2 501 " - pdb=" SG  CYS 2 379 "
        pdb="ZN    ZN 2 501 " - pdb=" SG  CYS 2 404 "
        pdb="ZN    ZN 2 501 " - pdb=" SG  CYS 2 401 "
      pdb="  ZN 9 601 "
        pdb="ZN    ZN 9 601 " - pdb=" NE2 HIS 2 356 "
        pdb="ZN    ZN 9 601 " - pdb=" SG  CYS 9 437 "
        pdb="ZN    ZN 9 601 " - pdb=" SG  CYS 9 434 "
        pdb="ZN    ZN 9 601 " - pdb=" SG  CYS 9 395 "
      Number of angles added : 6


  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      61.3% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain '2' and resid 2 through 13
      removed outlier: 3.668A  pdb=" N   ALA 2  13 " --> pdb=" O   GLU 2   9 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 26 through 55
    Processing helix  chain '2' and resid 70 through 111
      removed outlier: 3.707A  pdb=" N   ILE 2  77 " --> pdb=" O   LYS 2  73 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER 2  82 " --> pdb=" O   ILE 2  78 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLN 2  85 " --> pdb=" O   LEU 2  81 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ARG 2  86 " --> pdb=" O   SER 2  82 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 112 through 114
      No H-bonds generated for 'chain '2' and resid 112 through 114'
    Processing helix  chain '2' and resid 118 through 123
    Processing helix  chain '2' and resid 128 through 130
      No H-bonds generated for 'chain '2' and resid 128 through 130'
    Processing helix  chain '2' and resid 131 through 146
      removed outlier: 3.547A  pdb=" N   VAL 2 135 " --> pdb=" O   THR 2 131 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU 2 137 " --> pdb=" O   GLU 2 133 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY 2 140 " --> pdb=" O   ASN 2 136 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 158 through 166
    Processing helix  chain '2' and resid 174 through 188
    Processing helix  chain '2' and resid 192 through 204
      removed outlier: 3.794A  pdb=" N   GLU 2 204 " --> pdb=" O   SER 2 200 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 209 through 226
    Processing helix  chain '2' and resid 280 through 300
    Processing helix  chain '2' and resid 306 through 332
      removed outlier: 3.569A  pdb=" N   LEU 2 310 " --> pdb=" O   SER 2 306 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE 2 317 " --> pdb=" O   LEU 2 313 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LYS 2 324 " --> pdb=" O   GLN 2 320 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR 2 327 " --> pdb=" O   ILE 2 323 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 349 through 353
      removed outlier: 3.686A  pdb=" N   THR 2 353 " --> pdb=" O   ASP 2 350 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 385 through 392
    Processing helix  chain '9' and resid 11 through 19
      removed outlier: 3.543A  pdb=" N   ASN 9  19 " --> pdb=" O   HIS 9  15 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 20 through 59
      Proline residue:  9  26  - end of helix
    Processing helix  chain '9' and resid 63 through 116
      removed outlier: 3.819A  pdb=" N   GLN 9  97 " --> pdb=" O   LYS 9  93 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE 9  98 " --> pdb=" O   SER 9  94 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE 9 102 " --> pdb=" O   ILE 9  98 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 129 through 154
      removed outlier: 3.675A  pdb=" N   THR 9 133 " --> pdb=" O   GLU 9 129 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS 9 134 " --> pdb=" O   GLY 9 130 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 168 through 177
    Processing helix  chain '9' and resid 179 through 183
      removed outlier: 3.686A  pdb=" N   ILE 9 183 " --> pdb=" O   ASP 9 180 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 186 through 200
    Processing helix  chain '9' and resid 204 through 214
    Processing helix  chain '9' and resid 214 through 222
      removed outlier: 3.541A  pdb=" N   LEU 9 218 " --> pdb=" O   ASN 9 214 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 225 through 240
      removed outlier: 4.175A  pdb=" N   VAL 9 240 " --> pdb=" O   GLU 9 236 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 242 through 254
    Processing helix  chain '9' and resid 255 through 258
    Processing helix  chain '9' and resid 262 through 271
    Processing helix  chain '9' and resid 347 through 352
    Processing helix  chain '9' and resid 353 through 372
      removed outlier: 4.109A  pdb=" N   SER 9 357 " --> pdb=" O   ASP 9 353 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 377 through 390
      removed outlier: 3.655A  pdb=" N   SER 9 388 " --> pdb=" O   SER 9 384 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU 9 390 " --> pdb=" O   GLY 9 386 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 422 through 429
      removed outlier: 3.763A  pdb=" N   LEU 9 429 " --> pdb=" O   THR 9 425 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 441 through 448
    Processing helix  chain '9' and resid 473 through 486
    Processing helix  chain '9' and resid 508 through 510
      No H-bonds generated for 'chain '9' and resid 508 through 510'
    Processing helix  chain 'E' and resid 5 through 18
      removed outlier: 3.758A  pdb=" N   SER E  18 " --> pdb=" O   LYS E  14 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 91
    Processing helix  chain 'E' and resid 98 through 112
      Proline residue:  E 108  - end of helix
    Processing helix  chain 'E' and resid 121 through 131
    Processing helix  chain 'E' and resid 133 through 147
      removed outlier: 4.185A  pdb=" N   GLU E 137 " --> pdb=" O   LYS E 133 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 156
    Processing helix  chain 'U' and resid 22 through 35
    Processing helix  chain 'U' and resid 37 through 41
    Processing helix  chain 'U' and resid 55 through 59
      removed outlier: 3.539A  pdb=" N   ASP U  58 " --> pdb=" O   THR U  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain '2' and resid 375 through 376
    Processing sheet with id=AA2, first strand: chain '2' and resid 399 through 400
    Processing sheet with id=AA3, first strand: chain '2' and resid 417 through 418
      removed outlier: 6.585A  pdb=" N   ARG 2 417 " --> pdb=" O   VAL 9 470 " (cutoff:3.500A)
      removed outlier: 8.790A  pdb=" N   ASP 9 472 " --> pdb=" O   ARG 2 417 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain '9' and resid 495 through 498
      removed outlier: 4.075A  pdb=" N   LYS 9 503 " --> pdb=" O   ASP 9 498 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 22 through 24
    Processing sheet with id=AA6, first strand: chain 'U' and resid 12 through 16
      removed outlier: 8.988A  pdb=" N   LEU U  67 " --> pdb=" O   GLN U   2 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   PHE U   4 " --> pdb=" O   LEU U  67 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   LEU U  69 " --> pdb=" O   PHE U   4 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LYS U   6 " --> pdb=" O   LEU U  69 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1293 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: 2.17

  Time building geometry restraints manager: 2.58 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: 1578
        1.33 -     1.45: 1753
        1.45 -     1.57: 4527
        1.57 -     1.69: 2
        1.69 -     1.81: 48
  Bond restraints: 7908
  Sorted by residual:
  bond pdb=" O1P SEP E 202 "
       pdb=" P   SEP E 202 "
    ideal  model  delta    sigma   weight residual
    1.610  1.514  0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" O3P SEP E 202 "
       pdb=" P   SEP E 202 "
    ideal  model  delta    sigma   weight residual
    1.610  1.515  0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" O1P SEP E 207 "
       pdb=" P   SEP E 207 "
    ideal  model  delta    sigma   weight residual
    1.610  1.516  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" O2P SEP E 202 "
       pdb=" P   SEP E 202 "
    ideal  model  delta    sigma   weight residual
    1.610  1.516  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" O3P SEP E 207 "
       pdb=" P   SEP E 207 "
    ideal  model  delta    sigma   weight residual
    1.610  1.516  0.094 2.00e-02 2.50e+03 2.21e+01
  ... (remaining 7903 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 10440
        2.10 -     4.20: 261
        4.20 -     6.30: 37
        6.30 -     8.40: 4
        8.40 -    10.50: 2
  Bond angle restraints: 10744
  Sorted by residual:
  angle pdb=" N   LEU E 120 "
        pdb=" CA  LEU E 120 "
        pdb=" C   LEU E 120 "
      ideal   model   delta    sigma   weight residual
     113.50  107.54    5.96 1.23e+00 6.61e-01 2.35e+01
  angle pdb=" N   ILE 2 148 "
        pdb=" CA  ILE 2 148 "
        pdb=" C   ILE 2 148 "
      ideal   model   delta    sigma   weight residual
     113.53  109.15    4.38 9.80e-01 1.04e+00 1.99e+01
  angle pdb=" CA  ASN 2  48 "
        pdb=" C   ASN 2  48 "
        pdb=" O   ASN 2  48 "
      ideal   model   delta    sigma   weight residual
     120.70  116.37    4.33 1.03e+00 9.43e-01 1.77e+01
  angle pdb=" N   ASP E 200 "
        pdb=" CA  ASP E 200 "
        pdb=" C   ASP E 200 "
      ideal   model   delta    sigma   weight residual
     112.47  107.35    5.12 1.24e+00 6.50e-01 1.70e+01
  angle pdb=" CA  ASP E 205 "
        pdb=" C   ASP E 205 "
        pdb=" O   ASP E 205 "
      ideal   model   delta    sigma   weight residual
     121.87  117.65    4.22 1.10e+00 8.26e-01 1.47e+01
  ... (remaining 10739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 4232
       16.94 -    33.88: 409
       33.88 -    50.82: 89
       50.82 -    67.76: 19
       67.76 -    84.70: 5
  Dihedral angle restraints: 4754
    sinusoidal: 1762
      harmonic: 2992
  Sorted by residual:
  dihedral pdb=" CA  HIS 2 380 "
           pdb=" C   HIS 2 380 "
           pdb=" N   HIS 2 381 "
           pdb=" CA  HIS 2 381 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.67   26.33     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  PHE 9 459 "
           pdb=" C   PHE 9 459 "
           pdb=" N   GLU 9 460 "
           pdb=" CA  GLU 9 460 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.26  -21.74     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  TRP E 105 "
           pdb=" C   TRP E 105 "
           pdb=" N   MET E 106 "
           pdb=" CA  MET E 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.40  -15.60     0      5.00e+00 4.00e-02 9.74e+00
  ... (remaining 4751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1034
       0.056 -    0.113: 196
       0.113 -    0.169: 25
       0.169 -    0.226: 8
       0.226 -    0.282: 2
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" CA  SEP E 202 "
            pdb=" N   SEP E 202 "
            pdb=" C   SEP E 202 "
            pdb=" CB  SEP E 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.79   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  ILE E 204 "
            pdb=" N   ILE E 204 "
            pdb=" C   ILE E 204 "
            pdb=" CB  ILE E 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  ILE 2  51 "
            pdb=" N   ILE 2  51 "
            pdb=" C   ILE 2  51 "
            pdb=" CB  ILE 2  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1262 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 138 "   -0.017 2.00e-02 2.50e+03   3.40e-02 1.16e+01
        pdb=" C   LYS E 138 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LYS E 138 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ILE E 139 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU E 141 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   GLU E 141 "    0.043 2.00e-02 2.50e+03
        pdb=" O   GLU E 141 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR E 142 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU E 199 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.10e+00
        pdb=" C   GLU E 199 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLU E 199 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASP E 200 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1827
        2.79 -     3.32: 7480
        3.32 -     3.85: 12074
        3.85 -     4.37: 13437
        4.37 -     4.90: 23899
  Nonbonded interactions: 58717
  Sorted by model distance:
  nonbonded pdb=" O   PRO 2 362 "
            pdb=" NZ  LYS 2 365 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   GLU 9 162 "
            pdb=" OG1 THR 9 163 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" NZ  LYS 9 215 "
            pdb=" OE2 GLU 9 226 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OE2 GLU 2 341 "
            pdb=" ND1 HIS 9 452 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" O   SER 9 117 "
            pdb=" OG  SER 9 117 "
     model   vdw
     2.376 3.040
  ... (remaining 58712 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
========== 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  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:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.470
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
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      :  0.005   0.096   7917  Z= 0.313
  Angle     :  0.748  10.504  10750  Z= 0.449
  Chirality :  0.048   0.282   1265
  Planarity :  0.005   0.092   1346
  Dihedral  : 14.379  84.696   2794
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  1.01 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.28), residues: 981
  helix:  1.77 (0.23), residues: 561
  sheet:  0.23 (0.86), residues: 41
  loop : -1.68 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 105 
 HIS   0.003   0.001   HIS 2 356 
 PHE   0.013   0.001   PHE 9  87 
 TYR   0.018   0.002   TYR 9  95 
 ARG   0.006   0.001   ARG E   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13545 (  445)
  hydrogen bonds       : angle       5.12558 ( 1293)
  metal coordination   : bond        0.02435 (    8)
  metal coordination   : angle       5.66101 (    6)
  covalent geometry    : bond        0.00534 ( 7908)
  covalent geometry    : angle       0.73593 (10744)
  Misc. bond           : bond        0.06842 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.859 
Fit side-chains
REVERT: 2   49 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7999 (ttmm)
REVERT: 2  329 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7502 (tpp-160)
  outliers start: 4
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2203
  time to fit residues: 40.1561
Evaluate side-chains
  108 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   49 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 75 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
2  52 GLN
U  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.108887 restraints weight = 11373.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.110648 restraints weight = 7084.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111921 restraints weight = 5198.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7917  Z= 0.179
  Angle     :  0.594  10.684  10750  Z= 0.299
  Chirality :  0.041   0.160   1265
  Planarity :  0.004   0.047   1346
  Dihedral  :  4.957  55.591   1070
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  8.94 %
    Favored  : 89.29 %
  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 (0.28), residues: 981
  helix:  2.24 (0.22), residues: 565
  sheet:  0.30 (0.87), residues: 39
  loop : -1.65 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 105 
 HIS   0.003   0.001   HIS 9  51 
 PHE   0.014   0.001   PHE 9   7 
 TYR   0.021   0.002   TYR 9  95 
 ARG   0.004   0.001   ARG E   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05741 (  445)
  hydrogen bonds       : angle       4.11950 ( 1293)
  metal coordination   : bond        0.00973 (    8)
  metal coordination   : angle       4.38280 (    6)
  covalent geometry    : bond        0.00434 ( 7908)
  covalent geometry    : angle       0.58522 (10744)
  Misc. bond           : bond        0.00043 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.973 
Fit side-chains
REVERT: 2   49 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7793 (tmtt)
REVERT: 2  226 MET cc_start: 0.4086 (ttm) cc_final: 0.3756 (ttm)
REVERT: 9  234 TYR cc_start: 0.8070 (t80) cc_final: 0.7493 (t80)
REVERT: E  135 TYR cc_start: 0.6663 (t80) cc_final: 0.6454 (t80)
REVERT: U   33 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8211 (ttmt)
  outliers start: 14
  outliers final: 11
  residues processed: 122
  average time/residue: 0.2037
  time to fit residues: 33.6994
Evaluate side-chains
  117 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   49 LYS
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  216 LEU
Chi-restraints excluded: chain 2 residue  328 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 9 residue   84 ILE
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain E residue   37 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
2 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.127672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.109059 restraints weight = 11710.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.111018 restraints weight = 7333.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.112220 restraints weight = 5348.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7917  Z= 0.175
  Angle     :  0.580  10.276  10750  Z= 0.293
  Chirality :  0.041   0.150   1265
  Planarity :  0.004   0.044   1346
  Dihedral  :  4.783  57.348   1070
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 11.46 %
    Favored  : 85.89 %
  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 (0.28), residues: 981
  helix:  2.35 (0.22), residues: 566
  sheet:  0.19 (0.86), residues: 39
  loop : -1.64 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  93 
 HIS   0.003   0.001   HIS E  33 
 PHE   0.014   0.001   PHE 9   7 
 TYR   0.021   0.002   TYR 9  95 
 ARG   0.004   0.000   ARG 9 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05649 (  445)
  hydrogen bonds       : angle       4.03314 ( 1293)
  metal coordination   : bond        0.01183 (    8)
  metal coordination   : angle       4.43389 (    6)
  covalent geometry    : bond        0.00427 ( 7908)
  covalent geometry    : angle       0.57103 (10744)
  Misc. bond           : bond        0.00045 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 1.008 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8554 (m-80) cc_final: 0.8116 (t80)
REVERT: 2  226 MET cc_start: 0.4351 (ttm) cc_final: 0.3852 (ttm)
REVERT: 2  324 LYS cc_start: 0.8444 (tttt) cc_final: 0.8172 (tttp)
REVERT: 9  234 TYR cc_start: 0.8126 (t80) cc_final: 0.7341 (t80)
REVERT: 9  238 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6544 (tp)
REVERT: 9  497 MET cc_start: 0.7884 (ttp) cc_final: 0.7403 (ttt)
REVERT: E  135 TYR cc_start: 0.6886 (t80) cc_final: 0.6666 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 123
  average time/residue: 0.2014
  time to fit residues: 33.9979
Evaluate side-chains
  118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  328 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 9 residue   84 ILE
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain 9 residue  238 LEU
Chi-restraints excluded: chain 9 residue  351 LEU
Chi-restraints excluded: chain 9 residue  459 PHE
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain U residue    4 PHE
Chi-restraints excluded: chain U residue   44 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0670
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
2 320 GLN
U  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.126374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.107667 restraints weight = 11632.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.109659 restraints weight = 7183.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110828 restraints weight = 5197.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7917  Z= 0.178
  Angle     :  0.585  10.005  10750  Z= 0.295
  Chirality :  0.041   0.156   1265
  Planarity :  0.004   0.043   1346
  Dihedral  :  4.390  31.299   1066
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.35 %
    Favored  : 84.13 %
  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 (0.28), residues: 981
  helix:  2.36 (0.22), residues: 567
  sheet: -0.12 (0.85), residues: 40
  loop : -1.63 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 105 
 HIS   0.003   0.001   HIS 2  50 
 PHE   0.014   0.001   PHE 9   7 
 TYR   0.021   0.002   TYR 9  95 
 ARG   0.003   0.000   ARG 9 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05614 (  445)
  hydrogen bonds       : angle       4.02222 ( 1293)
  metal coordination   : bond        0.01325 (    8)
  metal coordination   : angle       4.81358 (    6)
  covalent geometry    : bond        0.00436 ( 7908)
  covalent geometry    : angle       0.57390 (10744)
  Misc. bond           : bond        0.00059 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.898 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8634 (m-80) cc_final: 0.8226 (t80)
REVERT: 2  324 LYS cc_start: 0.8409 (tttt) cc_final: 0.8143 (tttp)
REVERT: 9  224 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8521 (pp)
REVERT: 9  234 TYR cc_start: 0.8133 (t80) cc_final: 0.7335 (t80)
REVERT: 9  238 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6777 (tp)
REVERT: 9  497 MET cc_start: 0.8042 (ttp) cc_final: 0.7454 (ttt)
REVERT: E  135 TYR cc_start: 0.6890 (t80) cc_final: 0.6674 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1905
  time to fit residues: 30.8375
Evaluate side-chains
  120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   81 LEU
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  328 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 2 residue  363 VAL
Chi-restraints excluded: chain 9 residue   84 ILE
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain 9 residue  224 ILE
Chi-restraints excluded: chain 9 residue  238 LEU
Chi-restraints excluded: chain 9 residue  351 LEU
Chi-restraints excluded: chain 9 residue  459 PHE
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain U residue    4 PHE
Chi-restraints excluded: chain U residue   44 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 44 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 84 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0000
   chunk 58 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.130072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.111376 restraints weight = 11521.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113439 restraints weight = 7131.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.114603 restraints weight = 5154.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7917  Z= 0.125
  Angle     :  0.537   9.922  10750  Z= 0.271
  Chirality :  0.039   0.150   1265
  Planarity :  0.004   0.044   1346
  Dihedral  :  4.147  30.507   1066
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.74 %
    Favored  : 82.49 %
  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:  1.42 (0.28), residues: 981
  helix:  2.56 (0.22), residues: 563
  sheet:  0.12 (0.86), residues: 39
  loop : -1.60 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 105 
 HIS   0.003   0.001   HIS E  33 
 PHE   0.012   0.001   PHE 9   7 
 TYR   0.016   0.001   TYR 9  95 
 ARG   0.002   0.000   ARG E   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04776 (  445)
  hydrogen bonds       : angle       3.77757 ( 1293)
  metal coordination   : bond        0.00841 (    8)
  metal coordination   : angle       3.55082 (    6)
  covalent geometry    : bond        0.00288 ( 7908)
  covalent geometry    : angle       0.53025 (10744)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 1.012 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8526 (m-80) cc_final: 0.8169 (t80)
REVERT: 2  324 LYS cc_start: 0.8299 (tttt) cc_final: 0.8066 (tttp)
REVERT: 9  224 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8539 (pp)
REVERT: 9  234 TYR cc_start: 0.7979 (t80) cc_final: 0.7209 (t80)
REVERT: 9  238 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6670 (tp)
REVERT: 9  497 MET cc_start: 0.8044 (ttp) cc_final: 0.7448 (ttt)
REVERT: E  135 TYR cc_start: 0.6889 (t80) cc_final: 0.6682 (t80)
REVERT: U   31 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8422 (tm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 123
  average time/residue: 0.1964
  time to fit residues: 33.4473
Evaluate side-chains
  124 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   81 LEU
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  317 ILE
Chi-restraints excluded: chain 2 residue  328 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 2 residue  363 VAL
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain 9 residue  224 ILE
Chi-restraints excluded: chain 9 residue  238 LEU
Chi-restraints excluded: chain 9 residue  351 LEU
Chi-restraints excluded: chain 9 residue  459 PHE
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain U residue    4 PHE
Chi-restraints excluded: chain U residue   44 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 31 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0970
   chunk 36 optimal weight:    0.0870
   chunk 64 optimal weight:    0.1980
   chunk 37 optimal weight:    0.2980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.2156

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

Flipped N/Q/H residues before XYZ refinement:
2 320 GLN
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.135274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116552 restraints weight = 11562.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.118459 restraints weight = 7110.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.119783 restraints weight = 5196.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7917  Z= 0.103
  Angle     :  0.502   9.908  10750  Z= 0.254
  Chirality :  0.038   0.134   1265
  Planarity :  0.004   0.045   1346
  Dihedral  :  3.884  27.951   1066
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.87 %
    Favored  : 81.99 %
  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:  1.56 (0.28), residues: 981
  helix:  2.62 (0.22), residues: 567
  sheet:  0.45 (0.86), residues: 38
  loop : -1.52 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 105 
 HIS   0.002   0.000   HIS E  33 
 PHE   0.010   0.001   PHE 9   7 
 TYR   0.016   0.001   TYR 2 296 
 ARG   0.002   0.000   ARG E   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  445)
  hydrogen bonds       : angle       3.59212 ( 1293)
  metal coordination   : bond        0.00672 (    8)
  metal coordination   : angle       3.02293 (    6)
  covalent geometry    : bond        0.00222 ( 7908)
  covalent geometry    : angle       0.49752 (10744)
  Misc. bond           : bond        0.00016 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.981 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8435 (m-80) cc_final: 0.8196 (t80)
REVERT: 9  234 TYR cc_start: 0.7938 (t80) cc_final: 0.7192 (t80)
REVERT: 9  347 TYR cc_start: 0.7999 (m-80) cc_final: 0.7693 (m-80)
REVERT: 9  497 MET cc_start: 0.7984 (ttp) cc_final: 0.7379 (ttt)
REVERT: U   31 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8401 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 129
  average time/residue: 0.2010
  time to fit residues: 35.9194
Evaluate side-chains
  121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   81 LEU
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  317 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 2 residue  363 VAL
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain 9 residue  208 ILE
Chi-restraints excluded: chain 9 residue  395 CYS
Chi-restraints excluded: chain 9 residue  459 PHE
Chi-restraints excluded: chain E residue   37 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0970
   chunk 23 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
9 154 ASN
U  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.129015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.110337 restraints weight = 11619.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112161 restraints weight = 7203.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.113590 restraints weight = 5286.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7917  Z= 0.153
  Angle     :  0.565  10.043  10750  Z= 0.284
  Chirality :  0.040   0.155   1265
  Planarity :  0.004   0.043   1346
  Dihedral  :  4.051  28.409   1066
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.37 %
    Favored  : 80.60 %
  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:  1.47 (0.28), residues: 981
  helix:  2.52 (0.22), residues: 571
  sheet: -0.06 (0.83), residues: 41
  loop : -1.50 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 105 
 HIS   0.003   0.001   HIS E  33 
 PHE   0.014   0.001   PHE 9   7 
 TYR   0.022   0.002   TYR 9  95 
 ARG   0.002   0.000   ARG 9 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05045 (  445)
  hydrogen bonds       : angle       3.75434 ( 1293)
  metal coordination   : bond        0.01257 (    8)
  metal coordination   : angle       4.09880 (    6)
  covalent geometry    : bond        0.00373 ( 7908)
  covalent geometry    : angle       0.55664 (10744)
  Misc. bond           : bond        0.00039 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.833 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8529 (m-80) cc_final: 0.8136 (t80)
REVERT: 9  234 TYR cc_start: 0.8128 (t80) cc_final: 0.7387 (t80)
REVERT: 9  265 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8458 (tt)
REVERT: 9  497 MET cc_start: 0.8062 (ttp) cc_final: 0.7477 (ttt)
REVERT: U   31 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8424 (tm-30)
  outliers start: 24
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1985
  time to fit residues: 32.9920
Evaluate side-chains
  125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   81 LEU
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  317 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 2 residue  363 VAL
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain 9 residue  208 ILE
Chi-restraints excluded: chain 9 residue  265 LEU
Chi-restraints excluded: chain 9 residue  351 LEU
Chi-restraints excluded: chain 9 residue  395 CYS
Chi-restraints excluded: chain 9 residue  459 PHE
Chi-restraints excluded: chain U residue    4 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 46 optimal weight:    0.0570
   chunk 76 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 80 optimal weight:    0.3980
   chunk 85 optimal weight:    0.2980
   chunk 42 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
9 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.113081 restraints weight = 11652.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.114976 restraints weight = 7175.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116428 restraints weight = 5224.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7917  Z= 0.122
  Angle     :  0.534  10.840  10750  Z= 0.269
  Chirality :  0.039   0.147   1265
  Planarity :  0.004   0.043   1346
  Dihedral  :  3.940  28.734   1066
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.25 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.28), residues: 981
  helix:  2.59 (0.22), residues: 570
  sheet: -0.10 (0.83), residues: 41
  loop : -1.49 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 105 
 HIS   0.002   0.001   HIS E  33 
 PHE   0.011   0.001   PHE 9   7 
 TYR   0.016   0.001   TYR 9  95 
 ARG   0.001   0.000   ARG E   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04520 (  445)
  hydrogen bonds       : angle       3.63497 ( 1293)
  metal coordination   : bond        0.00876 (    8)
  metal coordination   : angle       3.43824 (    6)
  covalent geometry    : bond        0.00282 ( 7908)
  covalent geometry    : angle       0.52770 (10744)
  Misc. bond           : bond        0.00026 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.975 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8452 (m-80) cc_final: 0.8122 (t80)
REVERT: 9  234 TYR cc_start: 0.8085 (t80) cc_final: 0.7325 (t80)
REVERT: 9  238 LEU cc_start: 0.7548 (tp) cc_final: 0.7153 (mt)
REVERT: 9  265 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8337 (tt)
REVERT: 9  347 TYR cc_start: 0.7956 (m-80) cc_final: 0.7705 (m-80)
REVERT: 9  497 MET cc_start: 0.8026 (ttp) cc_final: 0.7417 (ttt)
REVERT: U   31 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8433 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1965
  time to fit residues: 33.2977
Evaluate side-chains
  120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   81 LEU
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  317 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 2 residue  363 VAL
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain 9 residue  208 ILE
Chi-restraints excluded: chain 9 residue  265 LEU
Chi-restraints excluded: chain 9 residue  351 LEU
Chi-restraints excluded: chain 9 residue  395 CYS
Chi-restraints excluded: chain 9 residue  459 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 94 optimal weight:    0.4980
   chunk 69 optimal weight:    0.7980
   chunk 59 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
9 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.127705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.108921 restraints weight = 11836.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110769 restraints weight = 7304.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112140 restraints weight = 5303.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7917  Z= 0.173
  Angle     :  0.583   9.603  10750  Z= 0.297
  Chirality :  0.041   0.173   1265
  Planarity :  0.004   0.043   1346
  Dihedral  :  4.176  28.716   1066
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.88 %
    Favored  : 80.60 %
  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:  1.44 (0.28), residues: 981
  helix:  2.48 (0.22), residues: 571
  sheet:  0.05 (0.85), residues: 39
  loop : -1.51 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 105 
 HIS   0.003   0.001   HIS E  33 
 PHE   0.022   0.002   PHE 9 262 
 TYR   0.022   0.002   TYR 9  95 
 ARG   0.003   0.000   ARG 9 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05370 (  445)
  hydrogen bonds       : angle       3.83951 ( 1293)
  metal coordination   : bond        0.01515 (    8)
  metal coordination   : angle       4.39979 (    6)
  covalent geometry    : bond        0.00425 ( 7908)
  covalent geometry    : angle       0.57363 (10744)
  Misc. bond           : bond        0.00044 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.233 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8561 (m-80) cc_final: 0.8133 (t80)
REVERT: 9  265 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8398 (tt)
REVERT: 9  497 MET cc_start: 0.8090 (ttp) cc_final: 0.7498 (ttt)
REVERT: U   31 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8452 (tm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 117
  average time/residue: 0.2252
  time to fit residues: 36.6795
Evaluate side-chains
  121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   81 LEU
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  317 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 2 residue  363 VAL
Chi-restraints excluded: chain 9 residue   48 LEU
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  145 ILE
Chi-restraints excluded: chain 9 residue  208 ILE
Chi-restraints excluded: chain 9 residue  265 LEU
Chi-restraints excluded: chain 9 residue  351 LEU
Chi-restraints excluded: chain 9 residue  395 CYS
Chi-restraints excluded: chain 9 residue  459 PHE
Chi-restraints excluded: chain U residue    4 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0170
   chunk 11 optimal weight:    0.0470
   chunk 33 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0870
   chunk 28 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0870
   chunk 10 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.1672

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

Flipped N/Q/H residues before XYZ refinement:
9 154 ASN
** U  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.135246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.116760 restraints weight = 11671.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118897 restraints weight = 7073.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.120183 restraints weight = 5039.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7917  Z= 0.106
  Angle     :  0.529  11.457  10750  Z= 0.269
  Chirality :  0.038   0.169   1265
  Planarity :  0.004   0.044   1346
  Dihedral  :  3.832  28.423   1066
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.88 %
    Favored  : 80.23 %
  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:  1.64 (0.28), residues: 981
  helix:  2.65 (0.22), residues: 570
  sheet:  0.34 (0.86), residues: 38
  loop : -1.45 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 105 
 HIS   0.002   0.000   HIS E  33 
 PHE   0.008   0.001   PHE 9   7 
 TYR   0.016   0.001   TYR 9 234 
 ARG   0.002   0.000   ARG E   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  445)
  hydrogen bonds       : angle       3.53436 ( 1293)
  metal coordination   : bond        0.00639 (    8)
  metal coordination   : angle       2.95777 (    6)
  covalent geometry    : bond        0.00223 ( 7908)
  covalent geometry    : angle       0.52414 (10744)
  Misc. bond           : bond        0.00015 (    1)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 1.630 
Fit side-chains
REVERT: 2    8 PHE cc_start: 0.8388 (m-80) cc_final: 0.8144 (t80)
REVERT: 2  187 LEU cc_start: 0.8097 (tp) cc_final: 0.7890 (tt)
REVERT: 2  352 LEU cc_start: 0.8584 (mt) cc_final: 0.8345 (mt)
REVERT: 2  372 ASN cc_start: 0.7956 (t0) cc_final: 0.7406 (t0)
REVERT: 9  265 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8404 (tt)
REVERT: 9  497 MET cc_start: 0.7965 (ttp) cc_final: 0.7353 (ttt)
REVERT: U   31 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8405 (tm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 119
  average time/residue: 0.2305
  time to fit residues: 38.3912
Evaluate side-chains
  123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   39 GLN
Chi-restraints excluded: chain 2 residue   81 LEU
Chi-restraints excluded: chain 2 residue   92 VAL
Chi-restraints excluded: chain 2 residue  203 MET
Chi-restraints excluded: chain 2 residue  211 THR
Chi-restraints excluded: chain 2 residue  317 ILE
Chi-restraints excluded: chain 2 residue  346 VAL
Chi-restraints excluded: chain 2 residue  363 VAL
Chi-restraints excluded: chain 9 residue   96 CYS
Chi-restraints excluded: chain 9 residue  154 ASN
Chi-restraints excluded: chain 9 residue  265 LEU
Chi-restraints excluded: chain 9 residue  395 CYS
Chi-restraints excluded: chain 9 residue  459 PHE
Chi-restraints excluded: chain U residue    4 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 61 optimal weight:    0.0770
   chunk 79 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 84 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
9 154 ASN
U  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.131519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112888 restraints weight = 11602.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.114876 restraints weight = 7218.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.116105 restraints weight = 5252.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7917  Z= 0.145
  Angle     :  0.564  10.938  10750  Z= 0.287
  Chirality :  0.040   0.182   1265
  Planarity :  0.004   0.044   1346
  Dihedral  :  3.983  26.953   1066
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.88 %
    Favored  : 79.85 %
  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:  1.57 (0.28), residues: 981
  helix:  2.59 (0.22), residues: 571
  sheet: -0.14 (0.83), residues: 41
  loop : -1.46 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 105 
 HIS   0.003   0.001   HIS E  33 
 PHE   0.021   0.001   PHE 9 262 
 TYR   0.021   0.002   TYR 9  95 
 ARG   0.002   0.000   ARG 9 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04797 (  445)
  hydrogen bonds       : angle       3.67456 ( 1293)
  metal coordination   : bond        0.01239 (    8)
  metal coordination   : angle       4.04479 (    6)
  covalent geometry    : bond        0.00348 ( 7908)
  covalent geometry    : angle       0.55648 (10744)
  Misc. bond           : bond        0.00027 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2701.53 seconds
wall clock time: 48 minutes 9.74 seconds (2889.74 seconds total)