Starting phenix.real_space_refine
on Tue Sep 24 23:05:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/09_2024/8e3x_27872.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/09_2024/8e3x_27872.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/09_2024/8e3x_27872.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/09_2024/8e3x_27872.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/09_2024/8e3x_27872.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3x_27872/09_2024/8e3x_27872.cif"
  }
  resolution = 2.3
  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=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5692      2.51       5
     N    1558      2.21       5
     O    1668      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8979
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1921
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "P"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 221
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "R"
      Number of atoms: 2841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2841
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 13, 'TRANS': 348}
          Chain breaks: 2
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 137
          Unresolved non-hydrogen angles: 176
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 79
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 5.28, per 1000 atoms: 0.59
  Number of scatterers: 8979
  At special positions: 0
  Unit cell: (92.96, 94.62, 159.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1668      8.00
     N    1558      7.00
     C    5692      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  34 " - pdb=" SG  CYS R  63 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  54 " - pdb=" SG  CYS R 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  77 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.06
  Conformation dependent library (CDL) restraints added in 957.4 milliseconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      41.4% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 4.009A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.514A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.708A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.542A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 27
    Processing helix  chain 'R' and resid 25 through 45
      removed outlier: 3.620A  pdb=" N   GLN R  31 " --> pdb=" O   PHE R  27 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   MET R  33 " --> pdb=" O   LYS R  29 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   CYS R  34 " --> pdb=" O   GLU R  30 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU R  35 " --> pdb=" O   GLN R  31 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU R  36 " --> pdb=" O   ALA R  32 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   GLN R  39 " --> pdb=" O   LEU R  35 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET R  45 " --> pdb=" O   ALA R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 177
    Processing helix  chain 'R' and resid 183 through 211
    Processing helix  chain 'R' and resid 211 through 218
      removed outlier: 3.614A  pdb=" N   SER R 216 " --> pdb=" O   ALA R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 257
      removed outlier: 3.658A  pdb=" N   LYS R 227 " --> pdb=" O   THR R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 291
      Proline residue:  R 277  - end of helix
    Processing helix  chain 'R' and resid 302 through 336
      removed outlier: 3.779A  pdb=" N   ILE R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 346 through 363
      removed outlier: 3.556A  pdb=" N   ARG R 350 " --> pdb=" O   SER R 346 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU R 357 " --> pdb=" O   ARG R 353 " (cutoff:3.500A)
      Proline residue:  R 360  - end of helix
    Processing helix  chain 'R' and resid 366 through 371
      removed outlier: 4.506A  pdb=" N   PHE R 371 " --> pdb=" O   THR R 367 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 377 through 386
    Processing helix  chain 'R' and resid 388 through 390
      No H-bonds generated for 'chain 'R' and resid 388 through 390'
    Processing helix  chain 'R' and resid 391 through 401
    Processing helix  chain 'R' and resid 404 through 417
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 7.259A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.291A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.172A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.859A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.582A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.509A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.086A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.694A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.708A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 5.431A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1317 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: 2.36

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1541
        1.32 -     1.45: 2519
        1.45 -     1.57: 5015
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 9159
  Sorted by residual:
  bond pdb=" CA  SER R 316 "
       pdb=" CB  SER R 316 "
    ideal  model  delta    sigma   weight residual
    1.528  1.480  0.048 1.59e-02 3.96e+03 9.20e+00
  bond pdb=" C   LEU R 251 "
       pdb=" O   LEU R 251 "
    ideal  model  delta    sigma   weight residual
    1.237  1.201  0.036 1.19e-02 7.06e+03 9.04e+00
  bond pdb=" N   LEU R 361 "
       pdb=" CA  LEU R 361 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.036 1.31e-02 5.83e+03 7.72e+00
  bond pdb=" C   LEU R 249 "
       pdb=" O   LEU R 249 "
    ideal  model  delta    sigma   weight residual
    1.237  1.207  0.029 1.17e-02 7.31e+03 6.30e+00
  bond pdb=" N   TYR R 400 "
       pdb=" CA  TYR R 400 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.32e-02 5.74e+03 5.53e+00
  ... (remaining 9154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 12168
        1.85 -     3.70: 195
        3.70 -     5.55: 26
        5.55 -     7.40: 9
        7.40 -     9.25: 2
  Bond angle restraints: 12400
  Sorted by residual:
  angle pdb=" N   ASN R 320 "
        pdb=" CA  ASN R 320 "
        pdb=" C   ASN R 320 "
      ideal   model   delta    sigma   weight residual
     112.23  105.58    6.65 1.26e+00 6.30e-01 2.79e+01
  angle pdb=" N   SER R 316 "
        pdb=" CA  SER R 316 "
        pdb=" C   SER R 316 "
      ideal   model   delta    sigma   weight residual
     111.36  105.78    5.58 1.09e+00 8.42e-01 2.62e+01
  angle pdb=" N   ILE R 188 "
        pdb=" CA  ILE R 188 "
        pdb=" C   ILE R 188 "
      ideal   model   delta    sigma   weight residual
     110.62  105.82    4.80 1.02e+00 9.61e-01 2.21e+01
  angle pdb=" N   PHE R 362 "
        pdb=" CA  PHE R 362 "
        pdb=" C   PHE R 362 "
      ideal   model   delta    sigma   weight residual
     114.12  107.73    6.39 1.39e+00 5.18e-01 2.11e+01
  angle pdb=" N   LEU R 244 "
        pdb=" CA  LEU R 244 "
        pdb=" C   LEU R 244 "
      ideal   model   delta    sigma   weight residual
     111.36  106.63    4.73 1.09e+00 8.42e-01 1.89e+01
  ... (remaining 12395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4879
       16.07 -    32.13: 428
       32.13 -    48.20: 92
       48.20 -    64.26: 16
       64.26 -    80.33: 8
  Dihedral angle restraints: 5423
    sinusoidal: 2113
      harmonic: 3310
  Sorted by residual:
  dihedral pdb=" CB  CYS R  77 "
           pdb=" SG  CYS R  77 "
           pdb=" SG  CYS R 134 "
           pdb=" CB  CYS R 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.58  -57.58     1      1.00e+01 1.00e-02 4.45e+01
  dihedral pdb=" CB  CYS R  34 "
           pdb=" SG  CYS R  34 "
           pdb=" SG  CYS R  63 "
           pdb=" CB  CYS R  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.56   41.56     1      1.00e+01 1.00e-02 2.42e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.59   36.59     1      1.00e+01 1.00e-02 1.89e+01
  ... (remaining 5420 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1116
       0.050 -    0.101: 204
       0.101 -    0.151: 46
       0.151 -    0.202: 4
       0.202 -    0.252: 3
  Chirality restraints: 1373
  Sorted by residual:
  chirality pdb=" CA  ASN R 186 "
            pdb=" N   ASN R 186 "
            pdb=" C   ASN R 186 "
            pdb=" CB  ASN R 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  PHE R 242 "
            pdb=" N   PHE R 242 "
            pdb=" C   PHE R 242 "
            pdb=" CB  PHE R 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ASN R 191 "
            pdb=" N   ASN R 191 "
            pdb=" C   ASN R 191 "
            pdb=" CB  ASN R 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1370 not shown)

  Planarity restraints: 1585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 315 "    0.013 2.00e-02 2.50e+03   2.75e-02 7.56e+00
        pdb=" C   GLY R 315 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLY R 315 "    0.018 2.00e-02 2.50e+03
        pdb=" N   SER R 316 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 319 "    0.009 2.00e-02 2.50e+03   1.91e-02 3.64e+00
        pdb=" C   VAL R 319 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   VAL R 319 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN R 320 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO B 236 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1582 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1681
        2.77 -     3.30: 8600
        3.30 -     3.84: 15318
        3.84 -     4.37: 17983
        4.37 -     4.90: 31029
  Nonbonded interactions: 74611
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE2 GLU B  12 "
            pdb=" ND2 ASN B  16 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.344 3.040
  ... (remaining 74606 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     21.400
  Find NCS groups from input model:        0.100
  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:11.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
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      :  0.003   0.048   9159  Z= 0.197
  Angle     :  0.582   9.249  12400  Z= 0.389
  Chirality :  0.042   0.252   1373
  Planarity :  0.003   0.045   1585
  Dihedral  : 13.023  80.331   3267
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  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:  1.49 (0.25), residues: 1120
  helix:  2.27 (0.25), residues: 434
  sheet:  0.92 (0.32), residues: 222
  loop : -0.19 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.016   0.001   PHE R 252 
 TYR   0.025   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A 389 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7556 (ptp-170)
REVERT: B  340 ASN cc_start: 0.7767 (t0) cc_final: 0.7566 (t0)
REVERT: R   33 MET cc_start: 0.7147 (pmm) cc_final: 0.6896 (pmm)
REVERT: R   82 ARG cc_start: 0.7318 (tpt-90) cc_final: 0.6857 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 1.5536
  time to fit residues: 240.8201
Evaluate side-chains
  109 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A  54 ASN
A 292 ASN
B 268 ASN
N  13 GLN
N  77 ASN
R 189 HIS
R 336 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9159  Z= 0.181
  Angle     :  0.498   7.414  12400  Z= 0.268
  Chirality :  0.040   0.139   1373
  Planarity :  0.004   0.053   1585
  Dihedral  :  3.607  15.418   1241
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  8.12 %
    Favored  : 91.03 %
  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:  1.75 (0.25), residues: 1120
  helix:  2.62 (0.25), residues: 435
  sheet:  1.13 (0.33), residues: 219
  loop : -0.23 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 243 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.031   0.001   TYR R 157 
 ARG   0.007   0.000   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8274 (pm20) cc_final: 0.7987 (pm20)
REVERT: B  340 ASN cc_start: 0.7956 (t0) cc_final: 0.7701 (t0)
REVERT: R   82 ARG cc_start: 0.7440 (tpt-90) cc_final: 0.6967 (mtp85)
REVERT: R  174 ILE cc_start: 0.7980 (tt) cc_final: 0.7656 (tp)
REVERT: R  412 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7720 (mmtt)
  outliers start: 8
  outliers final: 0
  residues processed: 116
  average time/residue: 1.3945
  time to fit residues: 171.5175
Evaluate side-chains
  104 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 83 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
B 268 ASN
N  13 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9159  Z= 0.168
  Angle     :  0.477   7.122  12400  Z= 0.258
  Chirality :  0.040   0.191   1373
  Planarity :  0.003   0.046   1585
  Dihedral  :  3.652  15.860   1241
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.07 %
    Favored  : 89.98 %
  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:  1.80 (0.25), residues: 1120
  helix:  2.69 (0.25), residues: 434
  sheet:  1.17 (0.33), residues: 220
  loop : -0.23 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.028   0.001   TYR R 157 
 ARG   0.009   0.000   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8257 (pm20) cc_final: 0.7950 (pm20)
REVERT: B  134 ARG cc_start: 0.7786 (ptp-110) cc_final: 0.7501 (ptp-110)
REVERT: B  340 ASN cc_start: 0.8010 (t0) cc_final: 0.7755 (t0)
REVERT: R   82 ARG cc_start: 0.7484 (tpt-90) cc_final: 0.7000 (mtp85)
REVERT: R  174 ILE cc_start: 0.7969 (tt) cc_final: 0.7656 (tp)
REVERT: R  412 LYS cc_start: 0.8207 (ptpt) cc_final: 0.7701 (mmtt)
  outliers start: 9
  outliers final: 0
  residues processed: 112
  average time/residue: 1.4865
  time to fit residues: 175.9742
Evaluate side-chains
  103 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 60 optimal weight:    0.1980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 268 ASN
N  13 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9159  Z= 0.259
  Angle     :  0.522   8.019  12400  Z= 0.284
  Chirality :  0.041   0.158   1373
  Planarity :  0.004   0.051   1585
  Dihedral  :  4.077  19.418   1241
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.23 %
    Favored  : 88.50 %
  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 (0.25), residues: 1120
  helix:  2.52 (0.25), residues: 435
  sheet:  0.98 (0.32), residues: 231
  loop : -0.25 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.017   0.001   PHE G  61 
 TYR   0.029   0.001   TYR R 157 
 ARG   0.010   0.000   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7499 (mtm-85)
REVERT: A  314 GLU cc_start: 0.8280 (pm20) cc_final: 0.7927 (pm20)
REVERT: B  134 ARG cc_start: 0.7697 (ptp-110) cc_final: 0.7386 (ptp-110)
REVERT: B  334 SER cc_start: 0.8027 (m) cc_final: 0.7217 (t)
REVERT: B  340 ASN cc_start: 0.8297 (t0) cc_final: 0.8084 (t0)
REVERT: P   20 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7286 (mmpt)
REVERT: R  174 ILE cc_start: 0.8040 (tt) cc_final: 0.7748 (tp)
REVERT: R  412 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7678 (mmtt)
  outliers start: 12
  outliers final: 3
  residues processed: 115
  average time/residue: 1.4415
  time to fit residues: 175.4384
Evaluate side-chains
  104 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
N  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9159  Z= 0.326
  Angle     :  0.555   9.454  12400  Z= 0.302
  Chirality :  0.042   0.153   1373
  Planarity :  0.004   0.053   1585
  Dihedral  :  4.275  21.161   1241
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 11.81 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1120
  helix:  2.26 (0.24), residues: 442
  sheet:  0.92 (0.32), residues: 231
  loop : -0.37 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.019   0.002   PHE G  61 
 TYR   0.031   0.002   TYR R 157 
 ARG   0.012   0.001   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8297 (pm20) cc_final: 0.7946 (pm20)
REVERT: B  134 ARG cc_start: 0.7657 (ptp-110) cc_final: 0.7337 (ptp-110)
REVERT: P   21 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8369 (tmtt)
REVERT: R  412 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7767 (mmtt)
  outliers start: 8
  outliers final: 4
  residues processed: 113
  average time/residue: 1.4855
  time to fit residues: 177.5357
Evaluate side-chains
  107 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0020
   chunk 103 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
N  13 GLN
** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9159  Z= 0.167
  Angle     :  0.483   8.987  12400  Z= 0.263
  Chirality :  0.039   0.138   1373
  Planarity :  0.003   0.048   1585
  Dihedral  :  3.903  18.208   1241
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 12.66 %
    Favored  : 86.71 %
  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:  1.59 (0.25), residues: 1120
  helix:  2.50 (0.24), residues: 441
  sheet:  0.92 (0.32), residues: 229
  loop : -0.34 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.024   0.001   TYR R 157 
 ARG   0.010   0.000   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8271 (pm20) cc_final: 0.7906 (pm20)
REVERT: B  134 ARG cc_start: 0.7706 (ptp-110) cc_final: 0.7374 (ptp-110)
REVERT: B  334 SER cc_start: 0.7770 (m) cc_final: 0.7073 (t)
REVERT: R  412 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7799 (mmtt)
  outliers start: 6
  outliers final: 2
  residues processed: 110
  average time/residue: 1.5195
  time to fit residues: 177.1831
Evaluate side-chains
  103 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
N  13 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9159  Z= 0.332
  Angle     :  0.571  10.993  12400  Z= 0.307
  Chirality :  0.042   0.154   1373
  Planarity :  0.004   0.053   1585
  Dihedral  :  4.269  21.309   1241
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 14.03 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1120
  helix:  2.29 (0.24), residues: 442
  sheet:  0.77 (0.33), residues: 233
  loop : -0.31 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.018   0.001   PHE G  61 
 TYR   0.028   0.001   TYR R 157 
 ARG   0.013   0.001   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8308 (pm20) cc_final: 0.7946 (pm20)
REVERT: B  134 ARG cc_start: 0.7673 (ptp-110) cc_final: 0.7337 (ptp-110)
REVERT: B  217 MET cc_start: 0.8522 (pmm) cc_final: 0.8254 (pmt)
REVERT: R  412 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7807 (mmtt)
  outliers start: 6
  outliers final: 4
  residues processed: 105
  average time/residue: 1.5532
  time to fit residues: 172.3753
Evaluate side-chains
  103 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0770
   overall best weight:    1.7544

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
N  13 GLN
** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9159  Z= 0.275
  Angle     :  0.544  11.697  12400  Z= 0.292
  Chirality :  0.041   0.150   1373
  Planarity :  0.004   0.056   1585
  Dihedral  :  4.213  20.655   1241
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 14.14 %
    Favored  : 85.44 %
  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:  1.43 (0.25), residues: 1120
  helix:  2.32 (0.24), residues: 442
  sheet:  0.81 (0.33), residues: 231
  loop : -0.35 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE G  61 
 TYR   0.027   0.001   TYR R 157 
 ARG   0.012   0.000   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8319 (pm20) cc_final: 0.7959 (pm20)
REVERT: B  134 ARG cc_start: 0.7670 (ptp-110) cc_final: 0.7338 (ptp-110)
REVERT: B  217 MET cc_start: 0.8529 (pmm) cc_final: 0.8249 (pmt)
REVERT: G   22 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6821 (mt-10)
REVERT: R  412 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7749 (mmtt)
  outliers start: 4
  outliers final: 3
  residues processed: 106
  average time/residue: 1.5509
  time to fit residues: 173.4565
Evaluate side-chains
  102 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0040
   chunk 30 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 105 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
N  13 GLN
** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9159  Z= 0.172
  Angle     :  0.515  11.038  12400  Z= 0.275
  Chirality :  0.039   0.138   1373
  Planarity :  0.004   0.060   1585
  Dihedral  :  3.887  18.016   1241
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 14.56 %
    Favored  : 85.02 %
  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 (0.25), residues: 1120
  helix:  2.53 (0.25), residues: 442
  sheet:  0.84 (0.33), residues: 229
  loop : -0.37 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.023   0.001   TYR R 157 
 ARG   0.014   0.000   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8295 (pm20) cc_final: 0.7934 (pm20)
REVERT: B  134 ARG cc_start: 0.7684 (ptp-110) cc_final: 0.7382 (ptp-110)
REVERT: B  217 MET cc_start: 0.8551 (pmm) cc_final: 0.8284 (pmt)
REVERT: B  334 SER cc_start: 0.7808 (m) cc_final: 0.7120 (t)
REVERT: N   89 GLU cc_start: 0.8508 (pm20) cc_final: 0.8225 (pm20)
  outliers start: 4
  outliers final: 3
  residues processed: 105
  average time/residue: 1.4821
  time to fit residues: 164.6420
Evaluate side-chains
  100 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 101 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
N  13 GLN
** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9159  Z= 0.201
  Angle     :  0.522  11.954  12400  Z= 0.279
  Chirality :  0.039   0.141   1373
  Planarity :  0.004   0.062   1585
  Dihedral  :  3.939  18.569   1241
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.77 %
    Favored  : 84.92 %
  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 (0.25), residues: 1120
  helix:  2.52 (0.24), residues: 442
  sheet:  0.78 (0.33), residues: 231
  loop : -0.33 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.024   0.001   TYR R 157 
 ARG   0.015   0.000   ARG N 105 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 GLU cc_start: 0.8303 (pm20) cc_final: 0.7932 (pm20)
REVERT: B  134 ARG cc_start: 0.7690 (ptp-110) cc_final: 0.7380 (ptp-110)
REVERT: B  217 MET cc_start: 0.8542 (pmm) cc_final: 0.8263 (pmt)
REVERT: B  334 SER cc_start: 0.7871 (m) cc_final: 0.7232 (t)
REVERT: N   89 GLU cc_start: 0.8482 (pm20) cc_final: 0.8166 (pm20)
  outliers start: 3
  outliers final: 3
  residues processed: 101
  average time/residue: 1.4918
  time to fit residues: 159.4035
Evaluate side-chains
  100 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:   20.0000
   chunk 77 optimal weight:   40.0000
   chunk 5 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
N  13 GLN
** R 234 HIS ** 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 = 0.3640 r_free = 0.3640 target = 0.111616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.069200 restraints weight = 14435.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.55
r_work: 0.2760 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9159  Z= 0.254
  Angle     :  0.549  12.108  12400  Z= 0.294
  Chirality :  0.041   0.148   1373
  Planarity :  0.004   0.063   1585
  Dihedral  :  4.110  20.087   1241
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 14.66 %
    Favored  : 85.02 %
  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:  1.50 (0.25), residues: 1120
  helix:  2.42 (0.24), residues: 442
  sheet:  0.76 (0.33), residues: 231
  loop : -0.32 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.013   0.001   PHE G  61 
 TYR   0.026   0.001   TYR R 157 
 ARG   0.014   0.000   ARG N 105 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3880.21 seconds
wall clock time: 68 minutes 21.61 seconds (4101.61 seconds total)