Starting phenix.real_space_refine
on Sun Mar 17 07:20:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqo_25389/03_2024/7sqo_25389_trim.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqo_25389/03_2024/7sqo_25389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqo_25389/03_2024/7sqo_25389.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqo_25389/03_2024/7sqo_25389.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqo_25389/03_2024/7sqo_25389_trim.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqo_25389/03_2024/7sqo_25389_trim.pdb"
  }
  resolution = 3.17
  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=   0.009 sd=   0.098
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 78 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    5528      2.51       5
     N    1454      2.21       5
     O    1568      1.98       5
     H    8331      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R PHE  162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 16949
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 4304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 4304
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 8, 'TRANS': 261}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 43
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "A"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 3294
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 7, 'PHE%COO:plan': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 52
    Chain: "B"
      Number of atoms: 5020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5020
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "G"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 803
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 3453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 3453
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 16
    Chain: "R"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 75
          Unusual residues: {'A6F': 1, 'OLA': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'OLA:plan-2': 2}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 7.57, per 1000 atoms: 0.45
  Number of scatterers: 16949
  At special positions: 0
  Unit cell: (94.64, 117.52, 122.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      68     16.00
     O    1568      8.00
     N    1454      7.00
     C    5528      6.00
     H    8331      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 127 " - pdb=" SG  CYS R 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 14.10
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.2% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'R' and resid 55 through 82
      removed outlier: 4.319A  pdb=" N   ALA R  59 " --> pdb=" O   TRP R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 117
      removed outlier: 3.735A  pdb=" N   PHE R  92 " --> pdb=" O   VAL R  88 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU R 108 " --> pdb=" O   THR R 104 " (cutoff:3.500A)
      Proline residue:  R 109  - end of helix
    Processing helix  chain 'R' and resid 123 through 157
      Proline residue:  R 131  - end of helix
    Processing helix  chain 'R' and resid 165 through 184
      removed outlier: 4.062A  pdb=" N   MET R 184 " --> pdb=" O   SER R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 190
      removed outlier: 3.883A  pdb=" N   ILE R 189 " --> pdb=" O   ILE R 185 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 232
    Processing helix  chain 'R' and resid 232 through 253
    Processing helix  chain 'R' and resid 294 through 317
    Processing helix  chain 'R' and resid 317 through 328
    Processing helix  chain 'R' and resid 340 through 365
      removed outlier: 3.789A  pdb=" N   ALA R 344 " --> pdb=" O   GLU R 340 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 368 through 378
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.592A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 213
      removed outlier: 4.119A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.981A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.795A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.774A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.753A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 191 through 192
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186
    Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186
      removed outlier: 6.631A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.780A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105
      removed outlier: 5.746A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.527A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 191
      removed outlier: 4.277A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234
      removed outlier: 6.859A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.687A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60
      removed outlier: 5.159A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 129 through 130
    Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.527A  pdb=" N   GLU E 234 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)

    437 hydrogen bonds defined for protein.
    1227 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: 6.33

  Time building geometry restraints manager: 14.56 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8299
        1.03 -     1.23: 32
        1.23 -     1.42: 3709
        1.42 -     1.62: 4990
        1.62 -     1.81: 98
  Bond restraints: 17128
  Sorted by residual:
  bond pdb=" C10 OLA R 503 "
       pdb=" C9  OLA R 503 "
    ideal  model  delta    sigma   weight residual
    1.332  1.470 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" C10 OLA R 504 "
       pdb=" C9  OLA R 504 "
    ideal  model  delta    sigma   weight residual
    1.332  1.470 -0.138 2.00e-02 2.50e+03 4.74e+01
  bond pdb=" N25 A6F R 505 "
       pdb=" S26 A6F R 505 "
    ideal  model  delta    sigma   weight residual
    1.647  1.696 -0.049 2.00e-02 2.50e+03 6.12e+00
  bond pdb=" C7  A6F R 505 "
       pdb=" N1  A6F R 505 "
    ideal  model  delta    sigma   weight residual
    1.356  1.400 -0.044 2.00e-02 2.50e+03 4.76e+00
  bond pdb=" C1  OLA R 504 "
       pdb=" C2  OLA R 504 "
    ideal  model  delta    sigma   weight residual
    1.542  1.510  0.032 2.00e-02 2.50e+03 2.63e+00
  ... (remaining 17123 not shown)

  Histogram of bond angle deviations from ideal:
       99.86 -   106.69: 227
      106.69 -   113.51: 19867
      113.51 -   120.33: 5598
      120.33 -   127.15: 4966
      127.15 -   133.98: 98
  Bond angle restraints: 30756
  Sorted by residual:
  angle pdb=" N   ALA B 302 "
        pdb=" CA  ALA B 302 "
        pdb=" CB  ALA B 302 "
      ideal   model   delta    sigma   weight residual
     114.17  110.93    3.24 1.14e+00 7.69e-01 8.08e+00
  angle pdb=" C11 OLA R 504 "
        pdb=" C10 OLA R 504 "
        pdb=" C9  OLA R 504 "
      ideal   model   delta    sigma   weight residual
     127.87  119.65    8.22 3.00e+00 1.11e-01 7.50e+00
  angle pdb=" C11 OLA R 503 "
        pdb=" C10 OLA R 503 "
        pdb=" C9  OLA R 503 "
      ideal   model   delta    sigma   weight residual
     127.87  120.07    7.80 3.00e+00 1.11e-01 6.76e+00
  angle pdb=" C10 OLA R 504 "
        pdb=" C9  OLA R 504 "
        pdb=" C8  OLA R 504 "
      ideal   model   delta    sigma   weight residual
     127.72  119.93    7.79 3.00e+00 1.11e-01 6.75e+00
  angle pdb=" C10 OLA R 503 "
        pdb=" C9  OLA R 503 "
        pdb=" C8  OLA R 503 "
      ideal   model   delta    sigma   weight residual
     127.72  119.93    7.79 3.00e+00 1.11e-01 6.74e+00
  ... (remaining 30751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 7446
       17.95 -    35.90: 541
       35.90 -    53.85: 153
       53.85 -    71.80: 20
       71.80 -    89.75: 1
  Dihedral angle restraints: 8161
    sinusoidal: 4296
      harmonic: 3865
  Sorted by residual:
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASP B 290 "
           pdb=" C   ASP B 290 "
           pdb=" N   ASP B 291 "
           pdb=" CA  ASP B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.73   21.27     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.52   17.48     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 8158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1066
       0.045 -    0.089: 238
       0.089 -    0.133: 66
       0.133 -    0.178: 3
       0.178 -    0.222: 1
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" C3  A6F R 505 "
            pdb=" C2  A6F R 505 "
            pdb=" C4  A6F R 505 "
            pdb=" N25 A6F R 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.34    2.56   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" C13 A6F R 505 "
            pdb=" C14 A6F R 505 "
            pdb=" C18 A6F R 505 "
            pdb=" O12 A6F R 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.65   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1371 not shown)

  Planarity restraints: 2558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA R 504 "   -0.162 2.00e-02 2.50e+03   1.27e-01 1.61e+02
        pdb=" C11 OLA R 504 "    0.075 2.00e-02 2.50e+03
        pdb=" C8  OLA R 504 "   -0.076 2.00e-02 2.50e+03
        pdb=" C9  OLA R 504 "    0.163 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA R 503 "    0.148 2.00e-02 2.50e+03   1.16e-01 1.34e+02
        pdb=" C11 OLA R 503 "   -0.070 2.00e-02 2.50e+03
        pdb=" C8  OLA R 503 "    0.069 2.00e-02 2.50e+03
        pdb=" C9  OLA R 503 "   -0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 234 "    0.014 2.00e-02 2.50e+03   7.54e-03 1.71e+00
        pdb=" CG  PHE B 234 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 234 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 234 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 234 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 234 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 234 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 234 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 234 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 234 "    0.003 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 234 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 234 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2555 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 1298
        2.21 -     2.80: 35706
        2.80 -     3.40: 46615
        3.40 -     4.00: 61999
        4.00 -     4.60: 95436
  Nonbonded interactions: 241054
  Sorted by model distance:
  nonbonded pdb=" HG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     1.608 1.850
  nonbonded pdb=" O   VAL R 113 "
            pdb=" HG1 THR R 117 "
     model   vdw
     1.618 1.850
  nonbonded pdb=" O   ALA R 359 "
            pdb=" H   ILE R 363 "
     model   vdw
     1.625 1.850
  nonbonded pdb="HD21 ASN R  72 "
            pdb=" OD2 ASP R 100 "
     model   vdw
     1.626 1.850
  nonbonded pdb=" O   PHE A 259 "
            pdb=" HZ2 LYS A 317 "
     model   vdw
     1.629 1.850
  ... (remaining 241049 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.260
  Extract box with map and model:          3.880
  Check model and map are aligned:         0.250
  Set scattering table:                    0.170
  Process input model:                     55.610
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.138   8797  Z= 0.272
  Angle     :  0.588   8.217  11926  Z= 0.295
  Chirality :  0.040   0.222   1374
  Planarity :  0.005   0.127   1487
  Dihedral  : 13.249  89.751   3115
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.20 (0.27), residues: 1089
  helix:  1.98 (0.28), residues: 375
  sheet: -1.24 (0.31), residues: 290
  loop : -1.19 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  47 
 HIS   0.003   0.001   HIS R 224 
 PHE   0.022   0.001   PHE B 234 
 TYR   0.021   0.001   TYR B  59 
 ARG   0.002   0.000   ARG E  38 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  185 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8428 (m-30) cc_final: 0.8184 (m-30)
REVERT: B  291 ASP cc_start: 0.7593 (m-30) cc_final: 0.7280 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.4983
  time to fit residues: 123.4756
Evaluate side-chains
  161 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.3980
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
R 324 ASN
A 269 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8797  Z= 0.289
  Angle     :  0.529   6.173  11926  Z= 0.286
  Chirality :  0.040   0.142   1374
  Planarity :  0.003   0.031   1487
  Dihedral  :  6.026  56.790   1265
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  8.08 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.36 (0.26), residues: 1089
  helix:  1.76 (0.28), residues: 378
  sheet: -1.23 (0.31), residues: 289
  loop : -1.31 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  47 
 HIS   0.007   0.001   HIS R 224 
 PHE   0.019   0.001   PHE B 234 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A  32 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  165 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 160
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8483 (m-30) cc_final: 0.8221 (m-30)
REVERT: A  304 GLN cc_start: 0.8093 (tt0) cc_final: 0.7707 (mt0)
  outliers start: 5
  outliers final: 5
  residues processed: 164
  average time/residue: 0.5195
  time to fit residues: 115.3399
Evaluate side-chains
  156 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   67 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0670
   chunk 99 optimal weight:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 98 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8797  Z= 0.158
  Angle     :  0.487   5.648  11926  Z= 0.259
  Chirality :  0.039   0.139   1374
  Planarity :  0.003   0.032   1487
  Dihedral  :  5.526  59.078   1265
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.52 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.28 (0.27), residues: 1089
  helix:  1.81 (0.28), residues: 378
  sheet: -1.22 (0.31), residues: 286
  loop : -1.21 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 224 
 PHE   0.016   0.001   PHE B 234 
 TYR   0.007   0.001   TYR E 215 
 ARG   0.004   0.000   ARG R 328 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  173 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 166
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8498 (m-30) cc_final: 0.8235 (m-30)
  outliers start: 7
  outliers final: 6
  residues processed: 170
  average time/residue: 0.5354
  time to fit residues: 121.4436
Evaluate side-chains
  160 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 154
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain E residue   73 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 94 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8797  Z= 0.214
  Angle     :  0.494   5.688  11926  Z= 0.266
  Chirality :  0.039   0.135   1374
  Planarity :  0.003   0.031   1487
  Dihedral  :  5.304  54.938   1265
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.52 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.30 (0.27), residues: 1089
  helix:  1.80 (0.28), residues: 378
  sheet: -1.23 (0.31), residues: 291
  loop : -1.22 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 224 
 PHE   0.016   0.001   PHE B 234 
 TYR   0.007   0.001   TYR E 215 
 ARG   0.004   0.000   ARG E 206 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  164 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8517 (m-30) cc_final: 0.8252 (m-30)
REVERT: B  289 TYR cc_start: 0.8533 (m-80) cc_final: 0.8323 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 160
  average time/residue: 0.4847
  time to fit residues: 105.1012
Evaluate side-chains
  160 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   83 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8797  Z= 0.306
  Angle     :  0.523   5.737  11926  Z= 0.282
  Chirality :  0.040   0.164   1374
  Planarity :  0.003   0.029   1487
  Dihedral  :  5.284  50.614   1265
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.52 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.38 (0.26), residues: 1089
  helix:  1.72 (0.27), residues: 378
  sheet: -1.26 (0.31), residues: 293
  loop : -1.26 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  47 
 HIS   0.003   0.001   HIS R 224 
 PHE   0.024   0.001   PHE B 234 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 328 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  171 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8536 (m-30) cc_final: 0.8271 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 166
  average time/residue: 0.4847
  time to fit residues: 108.2240
Evaluate side-chains
  163 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain R residue  343 TYR
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   83 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 105 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 306 GLN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8797  Z= 0.234
  Angle     :  0.507   5.710  11926  Z= 0.272
  Chirality :  0.040   0.140   1374
  Planarity :  0.003   0.028   1487
  Dihedral  :  5.239  52.202   1265
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.85 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.34 (0.27), residues: 1089
  helix:  1.72 (0.27), residues: 378
  sheet: -1.21 (0.32), residues: 293
  loop : -1.23 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 224 
 PHE   0.020   0.001   PHE B 234 
 TYR   0.009   0.001   TYR A 302 
 ARG   0.002   0.000   ARG R 328 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  170 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8529 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  251 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7973 (mtt90)
REVERT: B  289 TYR cc_start: 0.8566 (m-80) cc_final: 0.8314 (m-80)
  outliers start: 9
  outliers final: 9
  residues processed: 166
  average time/residue: 0.5031
  time to fit residues: 110.8021
Evaluate side-chains
  163 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain R residue  343 TYR
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   83 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8797  Z= 0.241
  Angle     :  0.512   5.710  11926  Z= 0.273
  Chirality :  0.040   0.137   1374
  Planarity :  0.003   0.029   1487
  Dihedral  :  5.189  56.888   1265
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.51 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.32 (0.27), residues: 1089
  helix:  1.73 (0.27), residues: 380
  sheet: -1.20 (0.32), residues: 293
  loop : -1.22 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 224 
 PHE   0.020   0.001   PHE B 234 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 328 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  172 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 162
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8507 (m-30) cc_final: 0.8236 (m-30)
REVERT: B  262 MET cc_start: 0.8127 (ptm) cc_final: 0.7889 (ptm)
  outliers start: 10
  outliers final: 10
  residues processed: 168
  average time/residue: 0.4887
  time to fit residues: 110.6571
Evaluate side-chains
  165 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain R residue  343 TYR
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   83 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0980
   chunk 51 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 91 optimal weight:    0.4980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8797  Z= 0.266
  Angle     :  0.521   5.734  11926  Z= 0.279
  Chirality :  0.040   0.139   1374
  Planarity :  0.003   0.030   1487
  Dihedral  :  5.007  42.502   1265
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.73 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.35 (0.27), residues: 1089
  helix:  1.71 (0.27), residues: 380
  sheet: -1.22 (0.32), residues: 293
  loop : -1.25 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  47 
 HIS   0.003   0.001   HIS R 224 
 PHE   0.020   0.001   PHE B 234 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 328 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  174 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 162
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8509 (m-30) cc_final: 0.8242 (m-30)
REVERT: B  262 MET cc_start: 0.8134 (ptm) cc_final: 0.7900 (ptm)
  outliers start: 12
  outliers final: 12
  residues processed: 169
  average time/residue: 0.5260
  time to fit residues: 117.0570
Evaluate side-chains
  172 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  343 TYR
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  160 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 103 optimal weight:    0.1980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.5980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8797  Z= 0.157
  Angle     :  0.502   9.276  11926  Z= 0.263
  Chirality :  0.040   0.238   1374
  Planarity :  0.003   0.069   1487
  Dihedral  :  4.763  43.520   1265
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 14.06 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.17 (0.27), residues: 1089
  helix:  1.78 (0.27), residues: 381
  sheet: -1.10 (0.32), residues: 294
  loop : -1.08 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 351 
 HIS   0.004   0.001   HIS R 224 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.011   0.001   TYR A 302 
 ARG   0.011   0.000   ARG E 148 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  173 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  192 GLU cc_start: 0.6467 (tm-30) cc_final: 0.5935 (tm-30)
REVERT: A    9 ASP cc_start: 0.8490 (m-30) cc_final: 0.8223 (m-30)
REVERT: B  262 MET cc_start: 0.8143 (ptm) cc_final: 0.7921 (ptm)
REVERT: B  289 TYR cc_start: 0.8539 (m-80) cc_final: 0.8253 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 169
  average time/residue: 0.5021
  time to fit residues: 113.2607
Evaluate side-chains
  170 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 1.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain R residue  343 TYR
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   83 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 71 optimal weight:    0.2980
   chunk 108 optimal weight:    0.4980
   chunk 99 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 92 optimal weight:    0.2980
   chunk 26 optimal weight:    8.9990
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.195   8797  Z= 0.300
  Angle     :  0.837  59.200  11926  Z= 0.500
  Chirality :  0.041   0.395   1374
  Planarity :  0.003   0.066   1487
  Dihedral  :  4.763  43.524   1265
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.95 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.16 (0.27), residues: 1089
  helix:  1.78 (0.27), residues: 381
  sheet: -1.09 (0.32), residues: 294
  loop : -1.08 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 224 
 PHE   0.013   0.001   PHE B 234 
 TYR   0.009   0.001   TYR A 302 
 ARG   0.008   0.000   ARG E 148 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   85 is missing expected H atoms. Skipping.
Residue LYS  128 is missing expected H atoms. Skipping.
Residue LYS  294 is missing expected H atoms. Skipping.
Residue VAL  308 is missing expected H atoms. Skipping.
Residue ILE  362 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue ILE   55 is missing expected H atoms. Skipping.
Residue LEU  232 is missing expected H atoms. Skipping.
Residue VAL  233 is missing expected H atoms. Skipping.
Residue LYS  248 is missing expected H atoms. Skipping.
Residue LYS  271 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  280 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Residue SER  161 is missing expected H atoms. Skipping.
Residue SER  201 is missing expected H atoms. Skipping.
Residue LYS   46 is missing expected H atoms. Skipping.
Residue ALA  121 is missing expected H atoms. Skipping.
Residue ALA  124 is missing expected H atoms. Skipping.
Residue THR  198 is missing expected H atoms. Skipping.
Evaluate side-chains
  169 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  192 GLU cc_start: 0.6453 (tm-30) cc_final: 0.5936 (tm-30)
REVERT: A    9 ASP cc_start: 0.8492 (m-30) cc_final: 0.8223 (m-30)
REVERT: B  262 MET cc_start: 0.8142 (ptm) cc_final: 0.7918 (ptm)
REVERT: B  289 TYR cc_start: 0.8539 (m-80) cc_final: 0.8253 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 165
  average time/residue: 0.5151
  time to fit residues: 113.7385
Evaluate side-chains
  169 residues out of total 956 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 TRP
Chi-restraints excluded: chain R residue  140 VAL
Chi-restraints excluded: chain R residue  343 TYR
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  160 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.138279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.106688 restraints weight = 35802.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.77
r_work: 0.3334 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.195   8797  Z= 0.300
  Angle     :  0.837  59.200  11926  Z= 0.500
  Chirality :  0.041   0.395   1374
  Planarity :  0.003   0.066   1487
  Dihedral  :  4.763  43.524   1265
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.95 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.16 (0.27), residues: 1089
  helix:  1.78 (0.27), residues: 381
  sheet: -1.09 (0.32), residues: 294
  loop : -1.08 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 224 
 PHE   0.013   0.001   PHE B 234 
 TYR   0.009   0.001   TYR A 302 
 ARG   0.008   0.000   ARG E 148 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4610.74 seconds
wall clock time: 81 minutes 51.85 seconds (4911.85 seconds total)