Starting phenix.real_space_refine
on Thu Mar 13 07:19:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7trp_26100/03_2025/7trp_26100.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trp_26100/03_2025/7trp_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_2025/7trp_26100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trp_26100/03_2025/7trp_26100.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trp_26100/03_2025/7trp_26100.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trp_26100/03_2025/7trp_26100.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLN:plan1': 1, 'ARG:plan': 2}
          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: {'GLU:plan': 1, 'ARG: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: 5.40, per 1000 atoms: 0.62
  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: 2.51
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.95
  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: 2.68

  Time building geometry restraints manager: 2.84 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:             0.720
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.560
  Find NCS groups from input model:        0.110
  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:             0.000
  Load rotamer database and sin/cos tables:13.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.200
-------------------------------------------------------------------------------
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   8865  Z= 0.371
  Angle     :  0.818   9.994  12041  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 (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: -0.43 (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
 TRP   0.036   0.002   TRP R 440 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.035   0.003   PHE R 189 
 TYR   0.029   0.002   TYR R 215 
 ARG   0.006   0.000   ARG H 191 

*********************** 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  : 0.964 
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: 0.8352 (mt-10)
  outliers start: 2
  outliers final: 0
  residues processed: 163
  average time/residue: 1.6853
  time to fit residues: 287.6472
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  : 1.076 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.105720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.066718 restraints weight = 14553.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.66
r_work: 0.2725 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8865  Z= 0.239
  Angle     :  0.548   5.943  12041  Z= 0.300
  Chirality :  0.042   0.136   1385
  Planarity :  0.004   0.055   1511
  Dihedral  :  4.815  29.534   1225
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  8.27 %
    Favored  : 89.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.96 (0.25), residues: 1106
  helix:  1.65 (0.26), residues: 393
  sheet:  0.71 (0.30), residues: 282
  loop : -0.29 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 440 
 HIS   0.009   0.001   HIS A 188 
 PHE   0.015   0.001   PHE R 189 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.005   0.001   ARG B  19 

*********************** 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
  146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.928 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6456 (mtt) cc_final: 0.6253 (mtp)
REVERT: R  127 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8579 (p)
REVERT: B  172 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8264 (tp30)
REVERT: B  217 MET cc_start: 0.8585 (pmm) cc_final: 0.8311 (pmt)
REVERT: B  254 ASP cc_start: 0.8627 (t70) cc_final: 0.8415 (t70)
REVERT: B  266 HIS cc_start: 0.8791 (t-90) cc_final: 0.8544 (t-170)
REVERT: G   15 LEU cc_start: 0.8272 (tt) cc_final: 0.7983 (tm)
REVERT: H  186 GLN cc_start: 0.9219 (tt0) cc_final: 0.8886 (tt0)
REVERT: A  302 TYR cc_start: 0.8808 (t80) cc_final: 0.8494 (t80)
REVERT: A  306 GLN cc_start: 0.8951 (mm110) cc_final: 0.8361 (mp10)
REVERT: A  308 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8539 (mt-10)
  outliers start: 18
  outliers final: 4
  residues processed: 136
  average time/residue: 1.5770
  time to fit residues: 225.2450
Evaluate side-chains
  116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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 9 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0030
   chunk 49 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0040
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.6006

-------------------------------------------------------------------------------
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 = 0.105462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.066478 restraints weight = 14777.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 2.69
r_work: 0.2721 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8865  Z= 0.244
  Angle     :  0.548   5.684  12041  Z= 0.297
  Chirality :  0.042   0.132   1385
  Planarity :  0.004   0.048   1511
  Dihedral  :  4.715  25.112   1225
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.63 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.25), residues: 1106
  helix:  1.89 (0.26), residues: 394
  sheet:  0.72 (0.30), residues: 287
  loop : -0.14 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.013   0.002   HIS A 195 
 PHE   0.014   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.004   0.000   ARG A  24 

*********************** 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
  130 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.119 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6534 (mtt) cc_final: 0.6327 (mtp)
REVERT: R  127 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8576 (p)
REVERT: R  136 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7980 (mttm)
REVERT: B  172 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8268 (tp30)
REVERT: B  217 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8315 (pmt)
REVERT: B  254 ASP cc_start: 0.8658 (t70) cc_final: 0.8446 (t70)
REVERT: B  266 HIS cc_start: 0.8855 (t-90) cc_final: 0.8546 (t-170)
REVERT: G   15 LEU cc_start: 0.8265 (tt) cc_final: 0.7976 (tm)
REVERT: H  186 GLN cc_start: 0.9219 (tt0) cc_final: 0.8905 (tt0)
REVERT: A  302 TYR cc_start: 0.8798 (t80) cc_final: 0.8462 (t80)
REVERT: A  306 GLN cc_start: 0.8925 (mm110) cc_final: 0.8351 (mp10)
  outliers start: 17
  outliers final: 6
  residues processed: 121
  average time/residue: 2.0691
  time to fit residues: 263.1233
Evaluate side-chains
  119 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
A  47 ASN
A 188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.106145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.067632 restraints weight = 14690.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 2.66
r_work: 0.2739 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2612 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8865  Z= 0.167
  Angle     :  0.515   6.055  12041  Z= 0.279
  Chirality :  0.041   0.142   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.541  23.385   1225
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.60 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.26), residues: 1106
  helix:  2.03 (0.27), residues: 395
  sheet:  0.69 (0.30), residues: 287
  loop : -0.03 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 188 
 PHE   0.022   0.001   PHE R  84 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.006   0.000   ARG B  42 

*********************** 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
  133 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.078 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6592 (mtt) cc_final: 0.6362 (mtp)
REVERT: R  111 LEU cc_start: 0.7735 (tp) cc_final: 0.7524 (tm)
REVERT: R  127 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8603 (p)
REVERT: R  136 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7943 (mttm)
REVERT: R  419 MET cc_start: 0.7092 (mtm) cc_final: 0.6864 (mtp)
REVERT: B  172 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8262 (tp30)
REVERT: B  217 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8364 (pmt)
REVERT: B  254 ASP cc_start: 0.8656 (t70) cc_final: 0.8431 (t70)
REVERT: B  266 HIS cc_start: 0.8887 (t-90) cc_final: 0.8596 (t-170)
REVERT: G   15 LEU cc_start: 0.8283 (tt) cc_final: 0.7990 (tm)
REVERT: G   52 THR cc_start: 0.7830 (p) cc_final: 0.7591 (t)
REVERT: H  186 GLN cc_start: 0.9216 (tt0) cc_final: 0.8804 (tt0)
REVERT: A  205 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7647 (mmp-170)
REVERT: A  302 TYR cc_start: 0.8793 (t80) cc_final: 0.8516 (t80)
REVERT: A  306 GLN cc_start: 0.8921 (mm110) cc_final: 0.8335 (mp10)
  outliers start: 16
  outliers final: 8
  residues processed: 123
  average time/residue: 1.5107
  time to fit residues: 195.7983
Evaluate side-chains
  120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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  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 95 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.9384

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.104244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.065422 restraints weight = 14728.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.68
r_work: 0.2697 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8865  Z= 0.265
  Angle     :  0.541   6.843  12041  Z= 0.292
  Chirality :  0.042   0.140   1385
  Planarity :  0.004   0.050   1511
  Dihedral  :  4.517  21.373   1225
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.24 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.26), residues: 1106
  helix:  2.02 (0.27), residues: 395
  sheet:  0.64 (0.30), residues: 281
  loop : -0.00 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 188 
 PHE   0.028   0.002   PHE R  84 
 TYR   0.016   0.001   TYR B 105 
 ARG   0.008   0.001   ARG B  42 

*********************** 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
  133 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: R  127 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8628 (p)
REVERT: R  184 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7138 (mm-40)
REVERT: B  172 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: B  217 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8377 (pmt)
REVERT: B  254 ASP cc_start: 0.8686 (t70) cc_final: 0.8465 (t70)
REVERT: B  266 HIS cc_start: 0.8873 (t-90) cc_final: 0.8650 (t-170)
REVERT: G   15 LEU cc_start: 0.8305 (tt) cc_final: 0.8016 (tm)
REVERT: H   43 LYS cc_start: 0.8924 (mmtm) cc_final: 0.8713 (mmmm)
REVERT: H  186 GLN cc_start: 0.9208 (tt0) cc_final: 0.8812 (tt0)
REVERT: A  306 GLN cc_start: 0.8937 (mm110) cc_final: 0.8398 (mp10)
  outliers start: 17
  outliers final: 7
  residues processed: 126
  average time/residue: 1.5484
  time to fit residues: 205.3632
Evaluate side-chains
  127 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  184 GLN
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   52 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 61 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0970
   chunk 81 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.8184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.104886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.065946 restraints weight = 14638.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.69
r_work: 0.2709 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2582 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8865  Z= 0.177
  Angle     :  0.546   8.919  12041  Z= 0.293
  Chirality :  0.041   0.133   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.753  54.144   1225
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.96 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1106
  helix:  2.02 (0.27), residues: 395
  sheet:  0.63 (0.30), residues: 286
  loop :  0.06 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.014   0.001   PHE R 189 
 TYR   0.013   0.001   TYR H 190 
 ARG   0.012   0.001   ARG A  24 

*********************** 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
  136 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 1.179 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6656 (mtt) cc_final: 0.6444 (mtp)
REVERT: R  127 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8636 (p)
REVERT: R  136 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7935 (mttm)
REVERT: B  172 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: B  217 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8372 (pmt)
REVERT: B  254 ASP cc_start: 0.8690 (t70) cc_final: 0.8459 (t70)
REVERT: B  266 HIS cc_start: 0.8876 (t-90) cc_final: 0.8653 (t-170)
REVERT: G   15 LEU cc_start: 0.8292 (tt) cc_final: 0.8008 (tm)
REVERT: H   43 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8697 (mmmm)
REVERT: H  186 GLN cc_start: 0.9194 (tt0) cc_final: 0.8772 (tt0)
REVERT: H  246 GLU cc_start: 0.7762 (pm20) cc_final: 0.7551 (pm20)
REVERT: A  306 GLN cc_start: 0.8907 (mm110) cc_final: 0.8354 (mp10)
REVERT: A  308 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8479 (mt-10)
  outliers start: 17
  outliers final: 7
  residues processed: 128
  average time/residue: 2.0446
  time to fit residues: 274.9931
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  : 1.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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 92 optimal weight:    0.0470
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
** B  44 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 = 0.3569 r_free = 0.3569 target = 0.104869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.065967 restraints weight = 14821.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.70
r_work: 0.2708 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2581 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8865  Z= 0.177
  Angle     :  0.546   8.919  12041  Z= 0.293
  Chirality :  0.041   0.133   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.753  54.144   1225
  Min Nonbonded Distance : 1.678

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 15.25 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1106
  helix:  2.02 (0.27), residues: 395
  sheet:  0.63 (0.30), residues: 286
  loop :  0.06 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.014   0.001   PHE R 189 
 TYR   0.013   0.001   TYR H 190 
 ARG   0.012   0.001   ARG A  24 

*********************** 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
  118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.944 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6654 (mtt) cc_final: 0.6441 (mtp)
REVERT: R  127 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8634 (p)
REVERT: R  136 LYS cc_start: 0.8166 (mmtm) cc_final: 0.7937 (mttm)
REVERT: B  172 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8240 (tm-30)
REVERT: B  217 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8378 (pmt)
REVERT: B  254 ASP cc_start: 0.8689 (t70) cc_final: 0.8455 (t70)
REVERT: B  266 HIS cc_start: 0.8879 (t-90) cc_final: 0.8658 (t-170)
REVERT: G   15 LEU cc_start: 0.8281 (tt) cc_final: 0.7998 (tm)
REVERT: H   43 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8697 (mmmm)
REVERT: H  186 GLN cc_start: 0.9191 (tt0) cc_final: 0.8769 (tt0)
REVERT: H  246 GLU cc_start: 0.7765 (pm20) cc_final: 0.7555 (pm20)
REVERT: A  306 GLN cc_start: 0.8906 (mm110) cc_final: 0.8350 (mp10)
  outliers start: 9
  outliers final: 7
  residues processed: 113
  average time/residue: 1.6606
  time to fit residues: 197.2150
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  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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 39 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.1980
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
R 172 GLN
** B  44 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 = 0.3569 r_free = 0.3569 target = 0.104858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.065927 restraints weight = 15011.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.71
r_work: 0.2708 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8865  Z= 0.177
  Angle     :  0.546   8.919  12041  Z= 0.293
  Chirality :  0.041   0.133   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.753  54.144   1225
  Min Nonbonded Distance : 1.678

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 15.25 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1106
  helix:  2.02 (0.27), residues: 395
  sheet:  0.63 (0.30), residues: 286
  loop :  0.06 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 195 
 PHE   0.014   0.001   PHE R 189 
 TYR   0.013   0.001   TYR H 190 
 ARG   0.012   0.001   ARG A  24 

*********************** 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
  118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.975 
Fit side-chains
REVERT: R   86 MET cc_start: 0.6652 (mtt) cc_final: 0.6438 (mtp)
REVERT: R  127 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8635 (p)
REVERT: R  136 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7935 (mttm)
REVERT: B  172 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: B  217 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8377 (pmt)
REVERT: B  254 ASP cc_start: 0.8690 (t70) cc_final: 0.8455 (t70)
REVERT: B  266 HIS cc_start: 0.8879 (t-90) cc_final: 0.8658 (t-170)
REVERT: G   15 LEU cc_start: 0.8279 (tt) cc_final: 0.7995 (tm)
REVERT: H   43 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8696 (mmmm)
REVERT: H  186 GLN cc_start: 0.9193 (tt0) cc_final: 0.8771 (tt0)
REVERT: H  246 GLU cc_start: 0.7766 (pm20) cc_final: 0.7555 (pm20)
REVERT: A  306 GLN cc_start: 0.8906 (mm110) cc_final: 0.8351 (mp10)
  outliers start: 9
  outliers final: 7
  residues processed: 113
  average time/residue: 1.6999
  time to fit residues: 201.8205
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  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.105486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.066725 restraints weight = 14618.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.67
r_work: 0.2725 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8865  Z= 0.202
  Angle     :  0.561  10.294  12041  Z= 0.300
  Chirality :  0.042   0.201   1385
  Planarity :  0.004   0.049   1511
  Dihedral  :  4.386  18.739   1225
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.50 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1106
  helix:  2.08 (0.27), residues: 393
  sheet:  0.67 (0.30), residues: 286
  loop :  0.10 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.015   0.001   PHE R 189 
 TYR   0.013   0.001   TYR H 190 
 ARG   0.011   0.001   ARG B  42 

*********************** 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
  135 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
REVERT: B  172 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8341 (tp30)
REVERT: B  217 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8414 (pmt)
REVERT: B  254 ASP cc_start: 0.8675 (t70) cc_final: 0.8443 (t70)
REVERT: G   15 LEU cc_start: 0.8346 (tt) cc_final: 0.8073 (tm)
REVERT: H   43 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8736 (mmmm)
REVERT: H  186 GLN cc_start: 0.9191 (tt0) cc_final: 0.8897 (tt0)
REVERT: A   33 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8311 (tp30)
REVERT: A  205 ARG cc_start: 0.8068 (mmp-170) cc_final: 0.7664 (mmp-170)
REVERT: A  306 GLN cc_start: 0.8924 (mm110) cc_final: 0.8378 (mp10)
REVERT: A  308 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8482 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 128
  average time/residue: 2.2283
  time to fit residues: 298.4969
Evaluate side-chains
  128 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue  104 VAL
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 H residue    3 GLN
Chi-restraints excluded: chain A residue   33 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 92 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.105780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.067062 restraints weight = 14645.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 2.67
r_work: 0.2735 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8865  Z= 0.182
  Angle     :  0.592  12.827  12041  Z= 0.315
  Chirality :  0.041   0.197   1385
  Planarity :  0.005   0.066   1511
  Dihedral  :  4.377  18.747   1225
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 15.36 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1106
  helix:  1.99 (0.27), residues: 396
  sheet:  0.69 (0.30), residues: 286
  loop :  0.08 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 195 
 PHE   0.015   0.001   PHE R 189 
 TYR   0.014   0.001   TYR H 190 
 ARG   0.012   0.001   ARG B  19 

********************** 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
  130 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.988 
Fit side-chains
REVERT: B  172 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8378 (tp30)
REVERT: B  217 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8428 (pmt)
REVERT: B  254 ASP cc_start: 0.8652 (t70) cc_final: 0.8427 (t70)
REVERT: G   15 LEU cc_start: 0.8344 (tt) cc_final: 0.8074 (tm)
REVERT: G   58 GLU cc_start: 0.8956 (pt0) cc_final: 0.8749 (mp0)
REVERT: H   43 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8729 (mmmm)
REVERT: H  180 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8598 (mtt180)
REVERT: H  186 GLN cc_start: 0.9188 (tt0) cc_final: 0.8936 (tt0)
REVERT: H  222 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7796 (tm-30)
REVERT: A   33 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8303 (tp30)
REVERT: A  205 ARG cc_start: 0.8113 (mmp-170) cc_final: 0.7713 (mmp-170)
REVERT: A  306 GLN cc_start: 0.8929 (mm110) cc_final: 0.8365 (mp10)
REVERT: A  308 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8315 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 126
  average time/residue: 1.6726
  time to fit residues: 221.1610
Evaluate side-chains
  127 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue  104 VAL
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 H residue    3 GLN
Chi-restraints excluded: chain A residue   33 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 83 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.1980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.106036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.067643 restraints weight = 14539.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 2.64
r_work: 0.2745 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8865  Z= 0.163
  Angle     :  0.590  12.550  12041  Z= 0.313
  Chirality :  0.041   0.186   1385
  Planarity :  0.004   0.058   1511
  Dihedral  :  4.359  19.344   1225
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 15.90 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1106
  helix:  2.01 (0.27), residues: 396
  sheet:  0.72 (0.31), residues: 279
  loop :  0.07 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.014   0.001   PHE R 189 
 TYR   0.015   0.001   TYR H 190 
 ARG   0.012   0.001   ARG A  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10282.26 seconds
wall clock time: 179 minutes 35.41 seconds (10775.41 seconds total)