Starting phenix.real_space_refine
on Tue Mar  3 21:02:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7trp_26100/03_2026/7trp_26100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trp_26100/03_2026/7trp_26100.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trp_26100/03_2026/7trp_26100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trp_26100/03_2026/7trp_26100.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trp_26100/03_2026/7trp_26100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trp_26100/03_2026/7trp_26100.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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: 5
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     Cl      1      4.86       5
     C    5535      2.51       5
     N    1461      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8681
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2079
          Classifications: {'peptide': 267}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 10, 'TRANS': 256}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2591
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "G"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 423
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 1786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1786
          Classifications: {'peptide': 235}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1768
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 38
    Chain: "R"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 34
          Unusual residues: {'IUE': 1, 'IXO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.60, per 1000 atoms: 0.18
  Number of scatterers: 8681
  At special positions: 0
  Unit cell: (93.79, 119.52, 123.67, 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)
     Cl      1     17.00
     S      64     16.00
     O    1620      8.00
     N    1461      7.00
     C    5535      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 426 " - pdb=" SG  CYS R 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04

  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: 0.64
  Conformation dependent library (CDL) restraints added in 327.3 milliseconds
  

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 13 sheets defined
      38.6% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 60
      removed outlier: 3.624A  pdb=" N   ASN R  60 " --> pdb=" O   SER R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 64
    Processing helix  chain 'R' and resid 66 through 84
      removed outlier: 4.384A  pdb=" N   PHE R  70 " --> pdb=" O   VAL R  66 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU R  71 " --> pdb=" O   ASN R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 84 through 96
    Processing helix  chain 'R' and resid 102 through 136
    Processing helix  chain 'R' and resid 145 through 175
      Proline residue:  R 166  - end of helix
      removed outlier: 5.184A  pdb=" N   GLN R 172 " --> pdb=" O   ILE R 168 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   PHE R 173 " --> pdb=" O   LEU R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 191
      removed outlier: 3.564A  pdb=" N   LEU R 190 " --> pdb=" O   ILE R 187 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 204
    Processing helix  chain 'R' and resid 204 through 223
      removed outlier: 3.906A  pdb=" N   ARG R 223 " --> pdb=" O   SER R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 426
      Proline residue:  R 415  - end of helix
      removed outlier: 3.537A  pdb=" N   THR R 424 " --> pdb=" O   VAL R 420 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   PHE R 425 " --> pdb=" O   LEU R 421 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 431 through 448
      removed outlier: 3.798A  pdb=" N   SER R 446 " --> pdb=" O   CYS R 442 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 448 through 454
    Processing helix  chain 'R' and resid 457 through 463
      removed outlier: 3.625A  pdb=" N   LYS R 461 " --> pdb=" O   ASN R 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.573A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.653A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 4.355A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 4.128A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.556A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.628A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.254A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.792A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.812A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 331 through 351
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.500A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.700A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.994A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.132A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.016A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.611A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.013A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.013A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.626A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.271A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1275 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1398
        1.31 -     1.44: 2469
        1.44 -     1.57: 4903
        1.57 -     1.69: 1
        1.69 -     1.82: 94
  Bond restraints: 8865
  Sorted by residual:
  bond pdb=" C10 IXO R 702 "
       pdb=" N11 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.270  1.475 -0.205 2.00e-02 2.50e+03 1.05e+02
  bond pdb=" C10 IXO R 702 "
       pdb=" C14 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.492  1.331  0.161 2.00e-02 2.50e+03 6.50e+01
  bond pdb=" C13 IXO R 702 "
       pdb=" O12 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.439  1.544 -0.105 2.00e-02 2.50e+03 2.74e+01
  bond pdb=" C05 IXO R 702 "
       pdb=" C06 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.450  1.528 -0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" C07 IXO R 702 "
       pdb=" C08 IXO R 702 "
    ideal  model  delta    sigma   weight residual
    1.454  1.530 -0.076 2.00e-02 2.50e+03 1.45e+01
  ... (remaining 8860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 11627
        2.00 -     4.00: 356
        4.00 -     6.00: 41
        6.00 -     8.00: 14
        8.00 -     9.99: 3
  Bond angle restraints: 12041
  Sorted by residual:
  angle pdb=" N   GLY H 209 "
        pdb=" CA  GLY H 209 "
        pdb=" C   GLY H 209 "
      ideal   model   delta    sigma   weight residual
     113.18  121.40   -8.22 2.37e+00 1.78e-01 1.20e+01
  angle pdb=" C   ARG H 191 "
        pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
      ideal   model   delta    sigma   weight residual
     121.54  127.91   -6.37 1.91e+00 2.74e-01 1.11e+01
  angle pdb=" N   ALA R 165 "
        pdb=" CA  ALA R 165 "
        pdb=" C   ALA R 165 "
      ideal   model   delta    sigma   weight residual
     112.75  117.28   -4.53 1.36e+00 5.41e-01 1.11e+01
  angle pdb=" CA  TRP R 440 "
        pdb=" CB  TRP R 440 "
        pdb=" CG  TRP R 440 "
      ideal   model   delta    sigma   weight residual
     113.60  107.43    6.17 1.90e+00 2.77e-01 1.05e+01
  angle pdb=" N   CYS R 429 "
        pdb=" CA  CYS R 429 "
        pdb=" C   CYS R 429 "
      ideal   model   delta    sigma   weight residual
     111.07  114.38   -3.31 1.07e+00 8.73e-01 9.54e+00
  ... (remaining 12036 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 4906
       16.99 -    33.98: 270
       33.98 -    50.97: 45
       50.97 -    67.96: 9
       67.96 -    84.95: 4
  Dihedral angle restraints: 5234
    sinusoidal: 1974
      harmonic: 3260
  Sorted by residual:
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE A 196 "
           pdb=" C   PHE A 196 "
           pdb=" N   LYS A 197 "
           pdb=" CA  LYS A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.48   18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  HIS H  35 "
           pdb=" C   HIS H  35 "
           pdb=" N   TRP H  36 "
           pdb=" CA  TRP H  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 5231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1099
       0.064 -    0.127: 225
       0.127 -    0.191: 53
       0.191 -    0.255: 5
       0.255 -    0.318: 3
  Chirality restraints: 1385
  Sorted by residual:
  chirality pdb=" CB  VAL R 444 "
            pdb=" CA  VAL R 444 "
            pdb=" CG1 VAL R 444 "
            pdb=" CG2 VAL R 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.53e+00
  chirality pdb=" CB  ILE A 184 "
            pdb=" CA  ILE A 184 "
            pdb=" CG1 ILE A 184 "
            pdb=" CG2 ILE A 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CB  THR R  90 "
            pdb=" CA  THR R  90 "
            pdb=" OG1 THR R  90 "
            pdb=" CG2 THR R  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1382 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   IUE R 701 "    0.035 2.00e-02 2.50e+03   3.45e-02 4.17e+01
        pdb=" C   IUE R 701 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   IUE R 701 "   -0.039 2.00e-02 2.50e+03
        pdb=" C1  IUE R 701 "    0.013 2.00e-02 2.50e+03
        pdb=" C2  IUE R 701 "    0.029 2.00e-02 2.50e+03
        pdb=" C3  IUE R 701 "    0.014 2.00e-02 2.50e+03
        pdb=" C4  IUE R 701 "   -0.012 2.00e-02 2.50e+03
        pdb=" C5  IUE R 701 "    0.036 2.00e-02 2.50e+03
        pdb=" C6  IUE R 701 "    0.004 2.00e-02 2.50e+03
        pdb=" C7  IUE R 701 "   -0.003 2.00e-02 2.50e+03
        pdb=" C9  IUE R 701 "   -0.086 2.00e-02 2.50e+03
        pdb=" N2  IUE R 701 "    0.046 2.00e-02 2.50e+03
        pdb=" S   IUE R 701 "    0.016 2.00e-02 2.50e+03
        pdb="CL   IUE R 701 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 IUE R 701 "   -0.057 2.00e-02 2.50e+03   4.82e-02 2.91e+01
        pdb=" C4  IUE R 701 "   -0.045 2.00e-02 2.50e+03
        pdb=" C9  IUE R 701 "    0.021 2.00e-02 2.50e+03
        pdb=" N1  IUE R 701 "    0.076 2.00e-02 2.50e+03
        pdb=" O1  IUE R 701 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 113 "   -0.019 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   TYR R 113 "    0.065 2.00e-02 2.50e+03
        pdb=" O   TYR R 113 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL R 114 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2315
        2.81 -     3.33: 7729
        3.33 -     3.85: 14628
        3.85 -     4.38: 17643
        4.38 -     4.90: 30339
  Nonbonded interactions: 72654
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 113 "
            pdb=" OH  TYR R 416 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   THR R 433 "
            pdb=" OG  SER R 436 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OH  TYR H 175 "
            pdb=" OE2 GLU A   8 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   ASN R  87 "
            pdb=" OG1 THR R  90 "
     model   vdw
     2.329 3.040
  ... (remaining 72649 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:             1.120
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.740
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
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      :  0.006   0.205   8869  Z= 0.277
  Angle     :  0.818   9.994  12049  Z= 0.464
  Chirality :  0.056   0.318   1385
  Planarity :  0.007   0.085   1511
  Dihedral  : 11.233  84.947   3118
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.64 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.23), residues: 1106
  helix: -0.02 (0.24), residues: 382
  sheet:  0.22 (0.29), residues: 300
  loop : -0.74 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 191 
 TYR   0.029   0.002   TYR R 215 
 PHE   0.035   0.003   PHE R 189 
 TRP   0.036   0.002   TRP R 440 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 ( 8865)
  covalent geometry    : angle       0.81768 (12041)
  SS BOND              : bond        0.00455 (    4)
  SS BOND              : angle       1.13729 (    8)
  hydrogen bonds       : bond        0.13106 (  448)
  hydrogen bonds       : angle       5.89039 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 162
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: R  210 ILE cc_start: 0.8052 (mm) cc_final: 0.7814 (mp)
REVERT: R  223 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7722 (ttm110)
REVERT: B  270 ILE cc_start: 0.9015 (pt) cc_final: 0.8768 (tp)
REVERT: H  186 GLN cc_start: 0.8733 (tt0) cc_final: 0.8461 (tt0)
REVERT: H  220 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7958 (mm-30)
REVERT: A  302 TYR cc_start: 0.8938 (t80) cc_final: 0.8697 (t80)
REVERT: A  306 GLN cc_start: 0.8868 (mm110) cc_final: 0.8296 (mp10)
REVERT: A  308 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8306 (mt-10)
  outliers start: 2
  outliers final: 0
  residues processed: 163
  average time/residue: 0.7736
  time to fit residues: 131.7848
Evaluate side-chains
  123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
R 117 ASN
R 172 GLN
B 268 ASN
H  39 GLN
H 194 ASN
A 188 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.105933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.066871 restraints weight = 14774.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 2.69
r_work: 0.2730 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2603 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8869  Z= 0.156
  Angle     :  0.539   5.933  12049  Z= 0.295
  Chirality :  0.042   0.135   1385
  Planarity :  0.004   0.054   1511
  Dihedral  :  4.748  22.983   1225
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  8.49 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.25), residues: 1106
  helix:  1.70 (0.26), residues: 394
  sheet:  0.73 (0.30), residues: 282
  loop : -0.30 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.015   0.001   TYR H 190 
 PHE   0.014   0.001   PHE R 189 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8865)
  covalent geometry    : angle       0.53915 (12041)
  SS BOND              : bond        0.00370 (    4)
  SS BOND              : angle       0.70935 (    8)
  hydrogen bonds       : bond        0.04108 (  448)
  hydrogen bonds       : angle       4.46241 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.268 
Fit side-chains
REVERT: R  127 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8576 (p)
REVERT: B  172 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8266 (tp30)
REVERT: B  217 MET cc_start: 0.8634 (pmm) cc_final: 0.8336 (pmt)
REVERT: B  254 ASP cc_start: 0.8644 (t70) cc_final: 0.8389 (t70)
REVERT: B  266 HIS cc_start: 0.8804 (t-90) cc_final: 0.8552 (t-170)
REVERT: G   15 LEU cc_start: 0.8257 (tt) cc_final: 0.7965 (tm)
REVERT: H   73 ASP cc_start: 0.8271 (t70) cc_final: 0.8047 (t70)
REVERT: H  186 GLN cc_start: 0.9214 (tt0) cc_final: 0.8894 (tt0)
REVERT: A  302 TYR cc_start: 0.8797 (t80) cc_final: 0.8474 (t80)
REVERT: A  306 GLN cc_start: 0.8926 (mm110) cc_final: 0.8358 (mp10)
REVERT: A  308 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8366 (mt-10)
  outliers start: 18
  outliers final: 4
  residues processed: 137
  average time/residue: 0.7992
  time to fit residues: 114.6478
Evaluate side-chains
  118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 6 optimal weight:    0.3980
   chunk 15 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0470
   chunk 56 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    1.2880

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.105712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.066889 restraints weight = 14518.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.66
r_work: 0.2733 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2607 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8869  Z= 0.142
  Angle     :  0.522   5.583  12049  Z= 0.283
  Chirality :  0.041   0.137   1385
  Planarity :  0.004   0.051   1511
  Dihedral  :  4.588  30.345   1225
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.74 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.25), residues: 1106
  helix:  1.95 (0.26), residues: 395
  sheet:  0.70 (0.30), residues: 287
  loop : -0.06 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  24 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.015   0.001   PHE R  84 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8865)
  covalent geometry    : angle       0.52199 (12041)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       0.74455 (    8)
  hydrogen bonds       : bond        0.03902 (  448)
  hydrogen bonds       : angle       4.38524 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.337 
Fit side-chains
REVERT: R  127 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8642 (p)
REVERT: B  172 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8273 (tp30)
REVERT: B  217 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8380 (pmt)
REVERT: B  254 ASP cc_start: 0.8676 (t70) cc_final: 0.8458 (t70)
REVERT: B  266 HIS cc_start: 0.8897 (t-90) cc_final: 0.8551 (t-170)
REVERT: G   15 LEU cc_start: 0.8369 (tt) cc_final: 0.8068 (tm)
REVERT: H  186 GLN cc_start: 0.9234 (tt0) cc_final: 0.8903 (tt0)
REVERT: A  302 TYR cc_start: 0.8813 (t80) cc_final: 0.8539 (t80)
REVERT: A  306 GLN cc_start: 0.8932 (mm110) cc_final: 0.8350 (mp10)
  outliers start: 19
  outliers final: 8
  residues processed: 127
  average time/residue: 0.7438
  time to fit residues: 99.2360
Evaluate side-chains
  121 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 83 optimal weight:    8.9990
   chunk 106 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0030
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.7796

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.066972 restraints weight = 14823.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.68
r_work: 0.2731 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8869  Z= 0.145
  Angle     :  0.524   5.562  12049  Z= 0.284
  Chirality :  0.041   0.138   1385
  Planarity :  0.004   0.051   1511
  Dihedral  :  4.712  38.063   1225
  Min Nonbonded Distance : 1.684

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.21 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.25), residues: 1106
  helix:  1.96 (0.26), residues: 395
  sheet:  0.70 (0.30), residues: 287
  loop : -0.06 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  24 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.014   0.001   PHE R  84 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8865)
  covalent geometry    : angle       0.52363 (12041)
  SS BOND              : bond        0.00333 (    4)
  SS BOND              : angle       0.75793 (    8)
  hydrogen bonds       : bond        0.03905 (  448)
  hydrogen bonds       : angle       4.38666 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.284 
Fit side-chains
REVERT: R  127 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8640 (p)
REVERT: B  172 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8269 (tp30)
REVERT: B  217 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8380 (pmt)
REVERT: B  254 ASP cc_start: 0.8678 (t70) cc_final: 0.8458 (t70)
REVERT: B  266 HIS cc_start: 0.8891 (t-90) cc_final: 0.8556 (t-170)
REVERT: G   15 LEU cc_start: 0.8361 (tt) cc_final: 0.8061 (tm)
REVERT: H  186 GLN cc_start: 0.9232 (tt0) cc_final: 0.8901 (tt0)
REVERT: A  302 TYR cc_start: 0.8813 (t80) cc_final: 0.8537 (t80)
REVERT: A  306 GLN cc_start: 0.8931 (mm110) cc_final: 0.8349 (mp10)
  outliers start: 9
  outliers final: 7
  residues processed: 115
  average time/residue: 0.7795
  time to fit residues: 94.0123
Evaluate side-chains
  118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 44 optimal weight:    0.3980
   chunk 78 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 63 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 79 optimal weight:    0.2980
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.105261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.066351 restraints weight = 14790.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 2.70
r_work: 0.2719 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2593 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8869  Z= 0.145
  Angle     :  0.533   7.989  12049  Z= 0.288
  Chirality :  0.041   0.140   1385
  Planarity :  0.004   0.055   1511
  Dihedral  :  4.470  20.421   1225
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.14 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.26), residues: 1106
  helix:  2.06 (0.27), residues: 395
  sheet:  0.67 (0.30), residues: 292
  loop :  0.07 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  42 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.021   0.001   PHE R  84 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8865)
  covalent geometry    : angle       0.53255 (12041)
  SS BOND              : bond        0.00314 (    4)
  SS BOND              : angle       0.94047 (    8)
  hydrogen bonds       : bond        0.03829 (  448)
  hydrogen bonds       : angle       4.39921 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.277 
Fit side-chains
REVERT: R  127 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8643 (p)
REVERT: B  172 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8251 (tp30)
REVERT: B  217 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8398 (pmt)
REVERT: B  254 ASP cc_start: 0.8672 (t70) cc_final: 0.8440 (t70)
REVERT: B  266 HIS cc_start: 0.8932 (t-90) cc_final: 0.8629 (t-170)
REVERT: G   15 LEU cc_start: 0.8322 (tt) cc_final: 0.8018 (tm)
REVERT: H   43 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8610 (mmtm)
REVERT: H  186 GLN cc_start: 0.9192 (tt0) cc_final: 0.8798 (tt0)
REVERT: A  205 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8239 (mmm160)
REVERT: A  302 TYR cc_start: 0.8822 (t80) cc_final: 0.8550 (t80)
REVERT: A  306 GLN cc_start: 0.8928 (mm110) cc_final: 0.8346 (mp10)
  outliers start: 17
  outliers final: 9
  residues processed: 126
  average time/residue: 0.7154
  time to fit residues: 94.5792
Evaluate side-chains
  125 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0050
   overall best weight:    1.1196

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.105150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.066352 restraints weight = 14757.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.70
r_work: 0.2718 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2591 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8869  Z= 0.145
  Angle     :  0.533   7.989  12049  Z= 0.288
  Chirality :  0.041   0.140   1385
  Planarity :  0.004   0.055   1511
  Dihedral  :  4.470  20.421   1225
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.21 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.26), residues: 1106
  helix:  2.06 (0.27), residues: 395
  sheet:  0.67 (0.30), residues: 292
  loop :  0.07 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  42 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.021   0.001   PHE R  84 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8865)
  covalent geometry    : angle       0.53255 (12041)
  SS BOND              : bond        0.00314 (    4)
  SS BOND              : angle       0.94047 (    8)
  hydrogen bonds       : bond        0.03829 (  448)
  hydrogen bonds       : angle       4.39921 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.340 
Fit side-chains
REVERT: R  127 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (p)
REVERT: B  172 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8245 (tp30)
REVERT: B  217 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8398 (pmt)
REVERT: B  254 ASP cc_start: 0.8676 (t70) cc_final: 0.8444 (t70)
REVERT: B  266 HIS cc_start: 0.8920 (t-90) cc_final: 0.8617 (t-170)
REVERT: G   15 LEU cc_start: 0.8290 (tt) cc_final: 0.7994 (tm)
REVERT: H   43 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8618 (mmtm)
REVERT: H  186 GLN cc_start: 0.9190 (tt0) cc_final: 0.8797 (tt0)
REVERT: A  302 TYR cc_start: 0.8808 (t80) cc_final: 0.8535 (t80)
REVERT: A  306 GLN cc_start: 0.8927 (mm110) cc_final: 0.8344 (mp10)
  outliers start: 11
  outliers final: 9
  residues processed: 119
  average time/residue: 0.7440
  time to fit residues: 92.9766
Evaluate side-chains
  124 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.105121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.066319 restraints weight = 14903.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 2.71
r_work: 0.2717 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2591 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8869  Z= 0.145
  Angle     :  0.533   7.989  12049  Z= 0.288
  Chirality :  0.041   0.140   1385
  Planarity :  0.004   0.055   1511
  Dihedral  :  4.470  20.421   1225
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.43 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.26), residues: 1106
  helix:  2.06 (0.27), residues: 395
  sheet:  0.67 (0.30), residues: 292
  loop :  0.07 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  42 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.021   0.001   PHE R  84 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8865)
  covalent geometry    : angle       0.53255 (12041)
  SS BOND              : bond        0.00314 (    4)
  SS BOND              : angle       0.94047 (    8)
  hydrogen bonds       : bond        0.03829 (  448)
  hydrogen bonds       : angle       4.39921 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.332 
Fit side-chains
REVERT: R  127 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8631 (p)
REVERT: B  172 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8248 (tp30)
REVERT: B  217 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8399 (pmt)
REVERT: B  254 ASP cc_start: 0.8677 (t70) cc_final: 0.8444 (t70)
REVERT: B  266 HIS cc_start: 0.8920 (t-90) cc_final: 0.8619 (t-170)
REVERT: G   15 LEU cc_start: 0.8288 (tt) cc_final: 0.7992 (tm)
REVERT: H   43 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8619 (mmtm)
REVERT: H  186 GLN cc_start: 0.9193 (tt0) cc_final: 0.8802 (tt0)
REVERT: A  302 TYR cc_start: 0.8808 (t80) cc_final: 0.8535 (t80)
REVERT: A  306 GLN cc_start: 0.8927 (mm110) cc_final: 0.8344 (mp10)
  outliers start: 11
  outliers final: 9
  residues processed: 118
  average time/residue: 0.7455
  time to fit residues: 92.4204
Evaluate side-chains
  124 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  127 SER
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  432 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 29 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
R  68 ASN
R 172 GLN
A 188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.104839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.066128 restraints weight = 14666.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.67
r_work: 0.2712 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2585 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8869  Z= 0.154
  Angle     :  0.553   9.696  12049  Z= 0.296
  Chirality :  0.042   0.137   1385
  Planarity :  0.004   0.056   1511
  Dihedral  :  4.441  20.087   1225
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.78 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.26), residues: 1106
  helix:  2.06 (0.27), residues: 395
  sheet:  0.65 (0.30), residues: 288
  loop :  0.07 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  24 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.040   0.001   PHE R  84 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8865)
  covalent geometry    : angle       0.55239 (12041)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       0.85904 (    8)
  hydrogen bonds       : bond        0.03863 (  448)
  hydrogen bonds       : angle       4.39840 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.317 
Fit side-chains
REVERT: R  148 MET cc_start: 0.6723 (mmp) cc_final: 0.6476 (mmm)
REVERT: B  172 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8257 (tm-30)
REVERT: B  217 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8392 (pmt)
REVERT: B  254 ASP cc_start: 0.8662 (t70) cc_final: 0.8425 (t70)
REVERT: B  266 HIS cc_start: 0.8918 (t-90) cc_final: 0.8623 (t-170)
REVERT: G   15 LEU cc_start: 0.8311 (tt) cc_final: 0.8029 (tm)
REVERT: H  186 GLN cc_start: 0.9186 (tt0) cc_final: 0.8814 (tt0)
REVERT: A  306 GLN cc_start: 0.8937 (mm110) cc_final: 0.8362 (mp10)
  outliers start: 15
  outliers final: 5
  residues processed: 122
  average time/residue: 0.7281
  time to fit residues: 93.1926
Evaluate side-chains
  116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  315 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 104 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0000
   chunk 103 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.106050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.067419 restraints weight = 14500.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 2.66
r_work: 0.2741 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8869  Z= 0.121
  Angle     :  0.566   9.501  12049  Z= 0.300
  Chirality :  0.042   0.169   1385
  Planarity :  0.004   0.058   1511
  Dihedral  :  4.434  20.181   1225
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.96 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.26), residues: 1106
  helix:  2.09 (0.27), residues: 395
  sheet:  0.69 (0.30), residues: 281
  loop :  0.03 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  24 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.014   0.001   PHE R 189 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8865)
  covalent geometry    : angle       0.56505 (12041)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       1.04580 (    8)
  hydrogen bonds       : bond        0.03710 (  448)
  hydrogen bonds       : angle       4.37835 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.344 
Fit side-chains
REVERT: R  148 MET cc_start: 0.6752 (mmp) cc_final: 0.6510 (mmm)
REVERT: B  172 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8270 (tm-30)
REVERT: B  217 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8425 (pmt)
REVERT: B  254 ASP cc_start: 0.8687 (t70) cc_final: 0.8477 (t70)
REVERT: B  266 HIS cc_start: 0.8926 (t-90) cc_final: 0.8658 (t-170)
REVERT: G   15 LEU cc_start: 0.8362 (tt) cc_final: 0.8087 (tm)
REVERT: H  186 GLN cc_start: 0.9219 (tt0) cc_final: 0.8838 (tt0)
REVERT: A  205 ARG cc_start: 0.8175 (mmp-170) cc_final: 0.7963 (mmm160)
REVERT: A  306 GLN cc_start: 0.8916 (mm110) cc_final: 0.8371 (mp10)
  outliers start: 12
  outliers final: 8
  residues processed: 121
  average time/residue: 0.7377
  time to fit residues: 93.7047
Evaluate side-chains
  122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  315 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 94 optimal weight:    0.3980
   chunk 37 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.067357 restraints weight = 14599.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 2.68
r_work: 0.2740 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8869  Z= 0.121
  Angle     :  0.566   9.500  12049  Z= 0.300
  Chirality :  0.042   0.169   1385
  Planarity :  0.004   0.058   1511
  Dihedral  :  4.434  20.181   1225
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 14.39 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.26), residues: 1106
  helix:  2.09 (0.27), residues: 395
  sheet:  0.69 (0.30), residues: 281
  loop :  0.03 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  24 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.014   0.001   PHE R 189 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8865)
  covalent geometry    : angle       0.56505 (12041)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       1.04580 (    8)
  hydrogen bonds       : bond        0.03710 (  448)
  hydrogen bonds       : angle       4.37835 ( 1275)

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

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

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2212 Ramachandran restraints generated.
    1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.283 
Fit side-chains
REVERT: R  148 MET cc_start: 0.6737 (mmp) cc_final: 0.6497 (mmm)
REVERT: B  172 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B  217 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8423 (pmt)
REVERT: B  254 ASP cc_start: 0.8688 (t70) cc_final: 0.8475 (t70)
REVERT: B  266 HIS cc_start: 0.8926 (t-90) cc_final: 0.8660 (t-170)
REVERT: G   15 LEU cc_start: 0.8351 (tt) cc_final: 0.8076 (tm)
REVERT: H  186 GLN cc_start: 0.9221 (tt0) cc_final: 0.8841 (tt0)
REVERT: A  205 ARG cc_start: 0.8181 (mmp-170) cc_final: 0.7970 (mmm160)
REVERT: A  306 GLN cc_start: 0.8915 (mm110) cc_final: 0.8369 (mp10)
  outliers start: 9
  outliers final: 8
  residues processed: 117
  average time/residue: 0.7821
  time to fit residues: 95.9917
Evaluate side-chains
  122 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  315 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 84 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 102 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 79 optimal weight:    0.1980
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.067391 restraints weight = 14466.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 2.66
r_work: 0.2740 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8869  Z= 0.121
  Angle     :  0.566   9.500  12049  Z= 0.300
  Chirality :  0.042   0.169   1385
  Planarity :  0.004   0.058   1511
  Dihedral  :  4.434  20.181   1225
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 14.39 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.26), residues: 1106
  helix:  2.09 (0.27), residues: 395
  sheet:  0.69 (0.30), residues: 281
  loop :  0.03 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  24 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.014   0.001   PHE R 189 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8865)
  covalent geometry    : angle       0.56505 (12041)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       1.04580 (    8)
  hydrogen bonds       : bond        0.03710 (  448)
  hydrogen bonds       : angle       4.37835 ( 1275)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4833.22 seconds
wall clock time: 82 minutes 37.41 seconds (4957.41 seconds total)