Starting phenix.real_space_refine
on Tue Sep 24 14:55:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpi_27636/09_2024/8dpi_27636_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpi_27636/09_2024/8dpi_27636.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpi_27636/09_2024/8dpi_27636.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpi_27636/09_2024/8dpi_27636.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpi_27636/09_2024/8dpi_27636_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpi_27636/09_2024/8dpi_27636_trim.cif"
  }
  resolution = 3.4
  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=   0.002 sd=   0.027
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      56      5.16       5
     Cl      1      4.86       5
     C    5230      2.51       5
     N    1364      2.21       5
     O    1499      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-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8150
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1935
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 9, 'TRANS': 254}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 205
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 80
    Chain: "B"
      Number of atoms: 1677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1677
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 6, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 128
          Unresolved non-hydrogen angles: 152
          Unresolved non-hydrogen dihedrals: 106
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 93
    Chain: "C"
      Number of atoms: 2479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2479
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 84
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 87
    Chain: "D"
      Number of atoms: 284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 284
          Classifications: {'peptide': 42}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 39}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "E"
      Number of atoms: 1734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1734
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'CLR': 1, 'T4U': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.97, per 1000 atoms: 0.61
  Number of scatterers: 8150
  At special positions: 0
  Unit cell: (89.18, 119.21, 133.77, 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      56     16.00
     O    1499      8.00
     N    1364      7.00
     C    5230      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 127 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2048

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      39.1% alpha, 26.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 80
      removed outlier: 3.501A  pdb=" N   ILE A  65 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   SER A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 106
      removed outlier: 5.007A  pdb=" N   PHE A  91 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LEU A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A  93 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
      removed outlier: 3.626A  pdb=" N   LEU A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 157
      removed outlier: 4.233A  pdb=" N   SER A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 166
      removed outlier: 4.220A  pdb=" N   HIS A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 185
      removed outlier: 3.773A  pdb=" N   ALA A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLY A 184 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 196
      removed outlier: 3.936A  pdb=" N   VAL A 191 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A 195 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 200
    Processing helix  chain 'A' and resid 211 through 223
      removed outlier: 4.419A  pdb=" N   ILE A 217 " --> pdb=" O   ASN A 213 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   SER A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   PHE A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 245
      removed outlier: 3.639A  pdb=" N   ALA A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 337
      removed outlier: 4.218A  pdb=" N   GLU A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LYS A 308 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   SER A 310 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
      Proline residue:  A 326  - end of helix
      removed outlier: 3.505A  pdb=" N   ILE A 329 " --> pdb=" O   CYS A 325 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 360
      removed outlier: 3.804A  pdb=" N   VAL A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   TRP A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ILE A 356 " --> pdb=" O   VAL A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 368
    Processing helix  chain 'A' and resid 372 through 383
    Processing helix  chain 'B' and resid 6 through 31
      removed outlier: 4.015A  pdb=" N   GLU B  28 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
    Processing helix  chain 'B' and resid 95 through 101
      removed outlier: 3.510A  pdb=" N   CYS B  99 " --> pdb=" O   TRP B  96 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 116
      No H-bonds generated for 'chain 'B' and resid 114 through 116'
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 3.968A  pdb=" N   ARG B 135 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 156
      removed outlier: 3.643A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 164 through 170
    Processing helix  chain 'B' and resid 185 through 202
      removed outlier: 3.932A  pdb=" N   ALA B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 3.631A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 24
    Processing helix  chain 'C' and resid 29 through 34
      removed outlier: 3.510A  pdb=" N   ILE C  33 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 37
      No H-bonds generated for 'chain 'C' and resid 35 through 37'
    Processing helix  chain 'D' and resid 17 through 24
      removed outlier: 3.620A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.583A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.602A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76
      removed outlier: 4.732A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
      removed outlier: 9.941A  pdb=" N   ALA B 105 " --> pdb=" O   THR B  33 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   ARG B  35 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 9.258A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.842A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ALA C 328 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   LEU C 318 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   GLY C 330 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.920A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.967A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.814A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.617A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA C 203 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.601A  pdb=" N   ALA C 231 " --> pdb=" O   GLY C 244 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG C 251 " --> pdb=" O   THR C 243 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 4.041A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.929A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.224A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.224A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129
      removed outlier: 3.517A  pdb=" N   VAL E 143 " --> pdb=" O   ILE E 204 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.856A  pdb=" N   GLY E 213 " --> pdb=" O   LEU E 233 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.856A  pdb=" N   GLY E 213 " --> pdb=" O   LEU E 233 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLN E 219 " --> pdb=" O   THR E 226 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    1098 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: 2.53

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2562
        1.34 -     1.46: 1345
        1.46 -     1.57: 4327
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 8318
  Sorted by residual:
  bond pdb=" N   VAL A 156 "
       pdb=" CA  VAL A 156 "
    ideal  model  delta    sigma   weight residual
    1.460  1.514 -0.054 1.09e-02 8.42e+03 2.47e+01
  bond pdb=" N   VAL A 160 "
       pdb=" CA  VAL A 160 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.21e-02 6.83e+03 7.41e+00
  bond pdb=" CA  SER A 158 "
       pdb=" CB  SER A 158 "
    ideal  model  delta    sigma   weight residual
    1.530  1.489  0.041 1.58e-02 4.01e+03 6.78e+00
  bond pdb=" N   PRO A 159 "
       pdb=" CA  PRO A 159 "
    ideal  model  delta    sigma   weight residual
    1.469  1.438  0.031 1.28e-02 6.10e+03 5.75e+00
  bond pdb=" N   SER A 158 "
       pdb=" CA  SER A 158 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.41e-02 5.03e+03 4.04e+00
  ... (remaining 8313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 11217
        1.97 -     3.93: 99
        3.93 -     5.90: 19
        5.90 -     7.87: 3
        7.87 -     9.83: 1
  Bond angle restraints: 11339
  Sorted by residual:
  angle pdb=" CA  GLU A 161 "
        pdb=" C   GLU A 161 "
        pdb=" O   GLU A 161 "
      ideal   model   delta    sigma   weight residual
     120.70  116.56    4.14 1.03e+00 9.43e-01 1.62e+01
  angle pdb=" C   GLU A 161 "
        pdb=" CA  GLU A 161 "
        pdb=" CB  GLU A 161 "
      ideal   model   delta    sigma   weight residual
     110.90  116.67   -5.77 1.58e+00 4.01e-01 1.33e+01
  angle pdb=" O   ALA A 155 "
        pdb=" C   ALA A 155 "
        pdb=" N   VAL A 156 "
      ideal   model   delta    sigma   weight residual
     122.43  117.84    4.59 1.34e+00 5.57e-01 1.17e+01
  angle pdb=" N   VAL A 160 "
        pdb=" CA  VAL A 160 "
        pdb=" C   VAL A 160 "
      ideal   model   delta    sigma   weight residual
     110.72  107.36    3.36 1.01e+00 9.80e-01 1.11e+01
  angle pdb=" N   VAL A 352 "
        pdb=" CA  VAL A 352 "
        pdb=" C   VAL A 352 "
      ideal   model   delta    sigma   weight residual
     113.53  110.36    3.17 9.80e-01 1.04e+00 1.05e+01
  ... (remaining 11334 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.49: 4860
       31.49 -    62.98: 40
       62.98 -    94.47: 7
       94.47 -   125.96: 3
      125.96 -   157.44: 1
  Dihedral angle restraints: 4911
    sinusoidal: 1747
      harmonic: 3164
  Sorted by residual:
  dihedral pdb=" C09 T4U A 501 "
           pdb=" C04 T4U A 501 "
           pdb=" C05 T4U A 501 "
           pdb=" N13 T4U A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -79.13   78.31 -157.44     1      3.00e+01 1.11e-03 2.05e+01
  dihedral pdb=" C04 T4U A 501 "
           pdb=" C05 T4U A 501 "
           pdb=" N13 T4U A 501 "
           pdb=" C07 T4U A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.43  -48.79  117.22     1      3.00e+01 1.11e-03 1.55e+01
  dihedral pdb=" C2  CLR A 502 "
           pdb=" C3  CLR A 502 "
           pdb=" C4  CLR A 502 "
           pdb=" C5  CLR A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.03   58.78 -113.81     1      3.00e+01 1.11e-03 1.50e+01
  ... (remaining 4908 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.279: 1345
       0.279 -    0.557: 0
       0.557 -    0.836: 0
       0.836 -    1.115: 0
       1.115 -    1.393: 1
  Chirality restraints: 1346
  Sorted by residual:
  chirality pdb=" C08 T4U A 501 "
            pdb=" C01 T4U A 501 "
            pdb=" C07 T4U A 501 "
            pdb=" C11 T4U A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -1.10   -1.39 2.00e-01 2.50e+01 4.85e+01
  chirality pdb=" CA  VAL A 160 "
            pdb=" N   VAL A 160 "
            pdb=" C   VAL A 160 "
            pdb=" CB  VAL A 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  GLU A 161 "
            pdb=" N   GLU A 161 "
            pdb=" C   GLU A 161 "
            pdb=" CB  GLU A 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1343 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 161 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   GLU A 161 "    0.030 2.00e-02 2.50e+03
        pdb=" O   GLU A 161 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   HIS A 162 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E 168 "   -0.018 5.00e-02 4.00e+02   2.75e-02 1.21e+00
        pdb=" N   PRO E 169 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO E 169 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO E 169 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 364 "   -0.018 5.00e-02 4.00e+02   2.70e-02 1.17e+00
        pdb=" N   PRO A 365 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 365 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 365 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 741
        2.75 -     3.29: 7554
        3.29 -     3.82: 12729
        3.82 -     4.36: 14541
        4.36 -     4.90: 26432
  Nonbonded interactions: 61997
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 245 "
            pdb=" OD1 ASP C 247 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER C 161 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NH1 ARG B  93 "
            pdb=" OD1 ASP B 124 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OG  SER C  74 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.290 3.040
  ... (remaining 61992 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:             1.010
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.690
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8318  Z= 0.173
  Angle     :  0.522   9.834  11339  Z= 0.293
  Chirality :  0.057   1.393   1346
  Planarity :  0.003   0.028   1422
  Dihedral  : 11.004 157.444   2857
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.31 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  1.83 %
    Favored  : 97.19 %
  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:  1.79 (0.26), residues: 1065
  helix:  2.12 (0.30), residues: 325
  sheet:  1.49 (0.30), residues: 286
  loop :  0.38 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 130 
 HIS   0.004   0.001   HIS E 220 
 PHE   0.009   0.001   PHE C 199 
 TYR   0.011   0.001   TYR A 153 
 ARG   0.002   0.000   ARG B 132 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 193
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ILE cc_start: 0.7217 (pt) cc_final: 0.6993 (mt)
REVERT: A  143 MET cc_start: 0.6776 (mmt) cc_final: 0.6550 (mmt)
REVERT: A  208 VAL cc_start: 0.7824 (p) cc_final: 0.7553 (t)
REVERT: A  238 ILE cc_start: 0.6819 (mm) cc_final: 0.6112 (mm)
REVERT: A  300 MET cc_start: 0.7616 (ttp) cc_final: 0.6659 (tpp)
REVERT: B  119 GLN cc_start: 0.7944 (tp40) cc_final: 0.7655 (mm-40)
REVERT: B  122 LEU cc_start: 0.8231 (mt) cc_final: 0.7994 (mp)
REVERT: B  186 VAL cc_start: 0.7001 (t) cc_final: 0.6798 (p)
REVERT: B  195 LYS cc_start: 0.7361 (tttt) cc_final: 0.6743 (tttt)
REVERT: C   52 ARG cc_start: 0.6935 (mtt-85) cc_final: 0.6675 (mtt-85)
REVERT: C  188 MET cc_start: 0.6641 (mmm) cc_final: 0.6284 (mmp)
REVERT: C  227 SER cc_start: 0.7461 (t) cc_final: 0.7186 (m)
REVERT: C  232 ILE cc_start: 0.7591 (mt) cc_final: 0.7313 (tt)
REVERT: C  277 SER cc_start: 0.7519 (t) cc_final: 0.6819 (m)
REVERT: E   98 ARG cc_start: 0.7053 (ttp-170) cc_final: 0.6516 (ptt180)
REVERT: E  128 MET cc_start: 0.7663 (mmm) cc_final: 0.7343 (mmm)
  outliers start: 8
  outliers final: 2
  residues processed: 199
  average time/residue: 0.2151
  time to fit residues: 56.3836
Evaluate side-chains
  162 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain C residue  196 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
B  98 GLN
B 229 ASN
C  88 ASN
C 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8318  Z= 0.300
  Angle     :  0.651  11.424  11339  Z= 0.345
  Chirality :  0.047   0.159   1346
  Planarity :  0.005   0.045   1422
  Dihedral  :  8.436 152.112   1240
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  :  8.91 %
    Favored  : 88.03 %
  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:  1.45 (0.26), residues: 1065
  helix:  1.82 (0.29), residues: 341
  sheet:  1.19 (0.30), residues: 288
  loop :  0.20 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 130 
 HIS   0.008   0.002   HIS B 209 
 PHE   0.020   0.002   PHE C 199 
 TYR   0.032   0.003   TYR E  59 
 ARG   0.003   0.001   ARG C  49 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 VAL cc_start: 0.7894 (p) cc_final: 0.7539 (m)
REVERT: A  300 MET cc_start: 0.7609 (ttp) cc_final: 0.6761 (tpp)
REVERT: B   23 LEU cc_start: 0.6838 (mp) cc_final: 0.6563 (mt)
REVERT: B   99 CYS cc_start: 0.7260 (p) cc_final: 0.7021 (m)
REVERT: B  119 GLN cc_start: 0.8071 (tp40) cc_final: 0.7737 (mm-40)
REVERT: B  122 LEU cc_start: 0.8291 (mt) cc_final: 0.8064 (mp)
REVERT: B  149 LEU cc_start: 0.7413 (tp) cc_final: 0.7055 (tp)
REVERT: B  195 LYS cc_start: 0.7516 (tttt) cc_final: 0.7203 (tttt)
REVERT: C   52 ARG cc_start: 0.6891 (mtt-85) cc_final: 0.6628 (mtt-85)
REVERT: C   61 MET cc_start: 0.7230 (tmm) cc_final: 0.6917 (tmm)
REVERT: C  188 MET cc_start: 0.6936 (mmm) cc_final: 0.6667 (mmp)
REVERT: C  227 SER cc_start: 0.7653 (t) cc_final: 0.7307 (m)
REVERT: C  277 SER cc_start: 0.7610 (t) cc_final: 0.6882 (m)
  outliers start: 25
  outliers final: 15
  residues processed: 190
  average time/residue: 0.2153
  time to fit residues: 53.4699
Evaluate side-chains
  176 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  196 THR
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  183 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0020
   chunk 87 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 33 optimal weight:    0.1980
   chunk 78 optimal weight:    7.9990
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
E  35 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8318  Z= 0.157
  Angle     :  0.524  10.001  11339  Z= 0.279
  Chirality :  0.043   0.137   1346
  Planarity :  0.004   0.039   1422
  Dihedral  :  7.800 151.769   1236
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 10.87 %
    Favored  : 86.08 %
  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:  1.72 (0.27), residues: 1065
  helix:  2.24 (0.29), residues: 343
  sheet:  1.24 (0.30), residues: 295
  loop :  0.23 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 130 
 HIS   0.003   0.001   HIS E 220 
 PHE   0.018   0.001   PHE B 167 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.003   0.000   ARG C  49 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 MET cc_start: 0.7628 (ttp) cc_final: 0.6773 (tpp)
REVERT: A  372 ASN cc_start: 0.6273 (t0) cc_final: 0.5784 (t0)
REVERT: B   23 LEU cc_start: 0.6866 (mp) cc_final: 0.6646 (mt)
REVERT: B   95 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7794 (mmtp)
REVERT: B   99 CYS cc_start: 0.7257 (p) cc_final: 0.7001 (m)
REVERT: B  117 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7287 (mtp180)
REVERT: B  119 GLN cc_start: 0.7954 (tp40) cc_final: 0.7683 (mm-40)
REVERT: B  186 VAL cc_start: 0.7399 (p) cc_final: 0.7119 (p)
REVERT: B  195 LYS cc_start: 0.7287 (tttt) cc_final: 0.6929 (tttt)
REVERT: B  225 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7396 (mmm160)
REVERT: C   52 ARG cc_start: 0.6858 (mtt-85) cc_final: 0.6633 (mtt-85)
REVERT: C   61 MET cc_start: 0.7328 (tmm) cc_final: 0.7101 (tmm)
REVERT: C  117 LEU cc_start: 0.8102 (mt) cc_final: 0.7792 (mt)
REVERT: C  196 THR cc_start: 0.7442 (p) cc_final: 0.6953 (t)
REVERT: C  227 SER cc_start: 0.7552 (t) cc_final: 0.7272 (m)
REVERT: C  277 SER cc_start: 0.7574 (t) cc_final: 0.6829 (m)
  outliers start: 25
  outliers final: 18
  residues processed: 176
  average time/residue: 0.2348
  time to fit residues: 54.0525
Evaluate side-chains
  177 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 50 optimal weight:    0.2980
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
C 132 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8318  Z= 0.194
  Angle     :  0.546  10.727  11339  Z= 0.288
  Chirality :  0.043   0.139   1346
  Planarity :  0.004   0.045   1422
  Dihedral  :  7.848 151.429   1235
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 11.84 %
    Favored  : 84.00 %
  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:  1.64 (0.27), residues: 1065
  helix:  2.18 (0.29), residues: 346
  sheet:  1.16 (0.30), residues: 293
  loop :  0.19 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 130 
 HIS   0.004   0.001   HIS E 220 
 PHE   0.015   0.002   PHE C 199 
 TYR   0.020   0.002   TYR E  59 
 ARG   0.002   0.000   ARG C 314 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 155
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 MET cc_start: 0.7485 (ttp) cc_final: 0.6808 (tpp)
REVERT: A  372 ASN cc_start: 0.6378 (t0) cc_final: 0.5786 (t0)
REVERT: B   23 LEU cc_start: 0.6865 (mp) cc_final: 0.6585 (mt)
REVERT: B   83 MET cc_start: 0.7956 (ttp) cc_final: 0.7729 (mtp)
REVERT: B   99 CYS cc_start: 0.7192 (p) cc_final: 0.6986 (m)
REVERT: B  119 GLN cc_start: 0.7982 (tp40) cc_final: 0.7719 (mm-40)
REVERT: B  195 LYS cc_start: 0.7187 (tttt) cc_final: 0.6933 (tttt)
REVERT: B  225 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7439 (mmm160)
REVERT: C   52 ARG cc_start: 0.6840 (mtt-85) cc_final: 0.6636 (mtt-85)
REVERT: C  117 LEU cc_start: 0.8112 (mt) cc_final: 0.7779 (mt)
REVERT: C  196 THR cc_start: 0.7419 (p) cc_final: 0.6928 (t)
REVERT: C  227 SER cc_start: 0.7605 (t) cc_final: 0.7291 (m)
REVERT: C  234 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6136 (m-80)
REVERT: C  277 SER cc_start: 0.7500 (t) cc_final: 0.6793 (m)
  outliers start: 34
  outliers final: 25
  residues processed: 170
  average time/residue: 0.2403
  time to fit residues: 52.6654
Evaluate side-chains
  175 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0870
   chunk 1 optimal weight:    8.9990
   chunk 77 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.1962

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
D  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8318  Z= 0.290
  Angle     :  0.613  10.474  11339  Z= 0.324
  Chirality :  0.045   0.144   1346
  Planarity :  0.004   0.058   1422
  Dihedral  :  8.079 152.675   1235
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 12.82 %
    Favored  : 82.54 %
  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:  1.26 (0.26), residues: 1065
  helix:  1.86 (0.29), residues: 352
  sheet:  1.02 (0.30), residues: 292
  loop : -0.12 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 130 
 HIS   0.006   0.002   HIS B 209 
 PHE   0.026   0.002   PHE C 234 
 TYR   0.028   0.002   TYR E  59 
 ARG   0.002   0.000   ARG E  67 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 158
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.5609 (mtt) cc_final: 0.5367 (mtt)
REVERT: A  300 MET cc_start: 0.7563 (ttp) cc_final: 0.6878 (tpp)
REVERT: B  119 GLN cc_start: 0.7956 (tp40) cc_final: 0.7696 (mm-40)
REVERT: B  149 LEU cc_start: 0.7617 (tp) cc_final: 0.7294 (tp)
REVERT: C   52 ARG cc_start: 0.6862 (mtt-85) cc_final: 0.6638 (mtt-85)
REVERT: C  117 LEU cc_start: 0.8009 (mt) cc_final: 0.7638 (mt)
REVERT: C  150 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7779 (mmt-90)
REVERT: C  188 MET cc_start: 0.7098 (mmp) cc_final: 0.6721 (mmm)
REVERT: C  196 THR cc_start: 0.7346 (p) cc_final: 0.6869 (t)
REVERT: C  227 SER cc_start: 0.7705 (t) cc_final: 0.7347 (m)
REVERT: C  277 SER cc_start: 0.7491 (t) cc_final: 0.6679 (m)
REVERT: E  233 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7767 (mp)
  outliers start: 38
  outliers final: 30
  residues processed: 179
  average time/residue: 0.2385
  time to fit residues: 55.8007
Evaluate side-chains
  185 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  233 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN
C  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8318  Z= 0.337
  Angle     :  0.643  10.821  11339  Z= 0.339
  Chirality :  0.046   0.150   1346
  Planarity :  0.005   0.063   1422
  Dihedral  :  8.207 152.460   1235
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 13.68 %
    Favored  : 81.56 %
  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:  0.86 (0.26), residues: 1065
  helix:  1.55 (0.28), residues: 356
  sheet:  0.87 (0.31), residues: 287
  loop : -0.44 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 130 
 HIS   0.007   0.002   HIS B 209 
 PHE   0.025   0.003   PHE C 234 
 TYR   0.029   0.003   TYR E  59 
 ARG   0.004   0.000   ARG C  68 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.5613 (mtt) cc_final: 0.5375 (mtt)
REVERT: A  148 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7367 (tt)
REVERT: A  300 MET cc_start: 0.7619 (ttp) cc_final: 0.6900 (tpp)
REVERT: B  119 GLN cc_start: 0.7990 (tp40) cc_final: 0.7749 (mm-40)
REVERT: B  149 LEU cc_start: 0.7754 (tp) cc_final: 0.7429 (tp)
REVERT: B  225 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7557 (mmm160)
REVERT: C   52 ARG cc_start: 0.6881 (mtt-85) cc_final: 0.6654 (mtt-85)
REVERT: C  117 LEU cc_start: 0.7971 (mt) cc_final: 0.7588 (mt)
REVERT: C  150 ARG cc_start: 0.7999 (mmt-90) cc_final: 0.7782 (mmt-90)
REVERT: C  196 THR cc_start: 0.7312 (p) cc_final: 0.6841 (t)
REVERT: C  227 SER cc_start: 0.7719 (t) cc_final: 0.7373 (m)
REVERT: C  277 SER cc_start: 0.7518 (t) cc_final: 0.6714 (m)
REVERT: E   98 ARG cc_start: 0.7123 (ttp-170) cc_final: 0.6812 (ttp-170)
REVERT: E  106 SER cc_start: 0.8721 (t) cc_final: 0.8495 (p)
REVERT: E  128 MET cc_start: 0.8027 (mmm) cc_final: 0.7796 (mmm)
REVERT: E  233 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7538 (mp)
  outliers start: 39
  outliers final: 33
  residues processed: 180
  average time/residue: 0.2343
  time to fit residues: 54.4664
Evaluate side-chains
  191 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  207 CYS
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  223 ASN
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  233 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0570
   chunk 104 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6748
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8318  Z= 0.201
  Angle     :  0.568  10.945  11339  Z= 0.297
  Chirality :  0.043   0.158   1346
  Planarity :  0.004   0.056   1422
  Dihedral  :  7.980 151.640   1235
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 14.53 %
    Favored  : 80.95 %
  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:  1.08 (0.27), residues: 1065
  helix:  1.97 (0.29), residues: 355
  sheet:  0.76 (0.30), residues: 291
  loop : -0.36 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 130 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.020   0.002   PHE E 227 
 TYR   0.017   0.002   TYR B 212 
 ARG   0.002   0.000   ARG C  49 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 158
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.5362 (mtt)
REVERT: A  300 MET cc_start: 0.7557 (ttp) cc_final: 0.6860 (tpp)
REVERT: B  119 GLN cc_start: 0.7967 (tp40) cc_final: 0.7725 (mm-40)
REVERT: B  149 LEU cc_start: 0.7799 (tp) cc_final: 0.7454 (tp)
REVERT: B  225 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7521 (mmm160)
REVERT: C   52 ARG cc_start: 0.6862 (mtt-85) cc_final: 0.6636 (mtt-85)
REVERT: C  117 LEU cc_start: 0.7909 (mt) cc_final: 0.7543 (mt)
REVERT: C  150 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7751 (mmt-90)
REVERT: C  196 THR cc_start: 0.7294 (p) cc_final: 0.6815 (t)
REVERT: C  219 ARG cc_start: 0.7355 (mtp180) cc_final: 0.7077 (ttp-170)
REVERT: C  227 SER cc_start: 0.7560 (t) cc_final: 0.7300 (m)
REVERT: C  277 SER cc_start: 0.7451 (t) cc_final: 0.6726 (m)
REVERT: E   67 ARG cc_start: 0.6661 (mtp180) cc_final: 0.6452 (mtp180)
REVERT: E   98 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6820 (ttp-170)
REVERT: E  106 SER cc_start: 0.8671 (t) cc_final: 0.8444 (p)
REVERT: E  227 PHE cc_start: 0.7751 (m-80) cc_final: 0.7370 (m-10)
REVERT: E  233 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7502 (mp)
  outliers start: 37
  outliers final: 30
  residues processed: 176
  average time/residue: 0.2387
  time to fit residues: 54.4773
Evaluate side-chains
  188 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  223 ASN
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  155 ASN
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  325 MET
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  233 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 62 optimal weight:    0.3980
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 81 optimal weight:    0.2980
   chunk 94 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8318  Z= 0.162
  Angle     :  0.536  10.826  11339  Z= 0.279
  Chirality :  0.042   0.135   1346
  Planarity :  0.004   0.049   1422
  Dihedral  :  7.816 150.517   1235
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 14.29 %
    Favored  : 81.32 %
  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:  1.25 (0.27), residues: 1065
  helix:  2.17 (0.29), residues: 354
  sheet:  0.73 (0.30), residues: 294
  loop : -0.22 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 130 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.014   0.001   PHE C 199 
 TYR   0.016   0.001   TYR B 212 
 ARG   0.002   0.000   ARG C  68 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 153
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.5385 (mtt)
REVERT: A  300 MET cc_start: 0.7494 (ttp) cc_final: 0.6863 (tpp)
REVERT: B  119 GLN cc_start: 0.7959 (tp40) cc_final: 0.7743 (mm-40)
REVERT: B  149 LEU cc_start: 0.7754 (tp) cc_final: 0.7415 (tp)
REVERT: C   49 ARG cc_start: 0.7520 (mpt180) cc_final: 0.7278 (mtt90)
REVERT: C   52 ARG cc_start: 0.6857 (mtt-85) cc_final: 0.6628 (mtt-85)
REVERT: C  117 LEU cc_start: 0.7911 (mt) cc_final: 0.7548 (mt)
REVERT: C  150 ARG cc_start: 0.7951 (mmt-90) cc_final: 0.7749 (mmt-90)
REVERT: C  188 MET cc_start: 0.6995 (mmp) cc_final: 0.6659 (mmt)
REVERT: C  196 THR cc_start: 0.7258 (p) cc_final: 0.6780 (t)
REVERT: C  219 ARG cc_start: 0.7319 (mtp180) cc_final: 0.7045 (ttp-170)
REVERT: C  258 ASP cc_start: 0.5757 (t0) cc_final: 0.5297 (t0)
REVERT: C  277 SER cc_start: 0.7434 (t) cc_final: 0.6737 (m)
REVERT: E   98 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6834 (ttp-170)
REVERT: E  106 SER cc_start: 0.8648 (t) cc_final: 0.8417 (p)
  outliers start: 36
  outliers final: 29
  residues processed: 173
  average time/residue: 0.2384
  time to fit residues: 53.6091
Evaluate side-chains
  180 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  207 CYS
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain B residue  223 ASN
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  325 MET
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.3980
   chunk 97 optimal weight:    0.4980
   chunk 99 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0980
   chunk 29 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8318  Z= 0.170
  Angle     :  0.546   9.804  11339  Z= 0.283
  Chirality :  0.043   0.135   1346
  Planarity :  0.004   0.052   1422
  Dihedral  :  7.788 149.839   1235
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 14.65 %
    Favored  : 81.07 %
  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 (0.27), residues: 1065
  helix:  2.23 (0.29), residues: 355
  sheet:  0.75 (0.30), residues: 296
  loop : -0.19 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 130 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.017   0.001   PHE E 227 
 TYR   0.015   0.001   TYR B 212 
 ARG   0.003   0.000   ARG E  67 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.5652 (mtt) cc_final: 0.5445 (mtt)
REVERT: A  300 MET cc_start: 0.7461 (ttp) cc_final: 0.6882 (tpp)
REVERT: B  119 GLN cc_start: 0.7962 (tp40) cc_final: 0.7752 (mm-40)
REVERT: C   49 ARG cc_start: 0.7519 (mpt180) cc_final: 0.7263 (mtt90)
REVERT: C   52 ARG cc_start: 0.6859 (mtt-85) cc_final: 0.6634 (mtt-85)
REVERT: C  117 LEU cc_start: 0.7911 (mt) cc_final: 0.7533 (mt)
REVERT: C  188 MET cc_start: 0.6993 (mmp) cc_final: 0.6626 (mmm)
REVERT: C  196 THR cc_start: 0.7262 (p) cc_final: 0.6780 (t)
REVERT: C  258 ASP cc_start: 0.5761 (t0) cc_final: 0.5305 (t0)
REVERT: C  277 SER cc_start: 0.7495 (t) cc_final: 0.6751 (m)
REVERT: E   98 ARG cc_start: 0.7154 (ttp-170) cc_final: 0.6867 (mtp180)
REVERT: E  106 SER cc_start: 0.8640 (t) cc_final: 0.8391 (p)
  outliers start: 35
  outliers final: 28
  residues processed: 169
  average time/residue: 0.2342
  time to fit residues: 51.7613
Evaluate side-chains
  176 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  207 CYS
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 71 optimal weight:    0.5980
   chunk 107 optimal weight:    0.8980
   chunk 99 optimal weight:    0.3980
   chunk 85 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8318  Z= 0.209
  Angle     :  0.569   9.928  11339  Z= 0.296
  Chirality :  0.043   0.140   1346
  Planarity :  0.004   0.054   1422
  Dihedral  :  7.849 149.797   1235
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 14.65 %
    Favored  : 81.44 %
  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:  1.24 (0.27), residues: 1065
  helix:  2.16 (0.29), residues: 356
  sheet:  0.72 (0.30), residues: 296
  loop : -0.22 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 130 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.022   0.002   PHE E 227 
 TYR   0.017   0.002   TYR E  59 
 ARG   0.004   0.000   ARG E  67 

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 MET cc_start: 0.7476 (ttp) cc_final: 0.6918 (tpp)
REVERT: B  119 GLN cc_start: 0.7964 (tp40) cc_final: 0.7739 (mm-40)
REVERT: C   52 ARG cc_start: 0.6859 (mtt-85) cc_final: 0.6640 (mtt-85)
REVERT: C  117 LEU cc_start: 0.7901 (mt) cc_final: 0.7518 (mt)
REVERT: C  188 MET cc_start: 0.6981 (mmp) cc_final: 0.6625 (mmm)
REVERT: C  196 THR cc_start: 0.7261 (p) cc_final: 0.6796 (t)
REVERT: C  219 ARG cc_start: 0.7322 (mtp180) cc_final: 0.7051 (ttp-170)
REVERT: C  258 ASP cc_start: 0.5785 (t0) cc_final: 0.5330 (t0)
REVERT: C  277 SER cc_start: 0.7455 (t) cc_final: 0.6679 (m)
REVERT: E   98 ARG cc_start: 0.7183 (ttp-170) cc_final: 0.6795 (mtp180)
REVERT: E  106 SER cc_start: 0.8661 (t) cc_final: 0.8418 (p)
  outliers start: 32
  outliers final: 28
  residues processed: 169
  average time/residue: 0.2467
  time to fit residues: 53.9970
Evaluate side-chains
  178 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  207 CYS
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   21 LYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  211 CYS
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  281 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
B  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.145036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.125636 restraints weight = 12347.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.26
r_work: 0.3554 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8318  Z= 0.197
  Angle     :  0.568  10.076  11339  Z= 0.295
  Chirality :  0.043   0.137   1346
  Planarity :  0.004   0.053   1422
  Dihedral  :  7.842 149.756   1235
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.02 %
    Favored  : 81.44 %
  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:  1.24 (0.27), residues: 1065
  helix:  2.16 (0.29), residues: 358
  sheet:  0.75 (0.31), residues: 287
  loop : -0.24 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 130 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.023   0.002   PHE E 227 
 TYR   0.015   0.001   TYR B 212 
 ARG   0.002   0.000   ARG B 226 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2202.94 seconds
wall clock time: 39 minutes 41.36 seconds (2381.36 seconds total)